From 7dc093e2a81745e078dd0aecf3a1bdc272fb58e0 Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Fri, 4 Sep 2020 11:25:02 -0400 Subject: [PATCH 01/65] Add Segment class --- src/Segment.h | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 src/Segment.h diff --git a/src/Segment.h b/src/Segment.h new file mode 100644 index 0000000000..74ad9fb237 --- /dev/null +++ b/src/Segment.h @@ -0,0 +1,27 @@ +#ifndef INC_SEGMENT_H +#define INC_SEGMENT_H +namespace Cpptraj { +/// Define a contiguous segment of atoms +class Segment { + public: + /// CONSTRUCTOR + Segment() : begin_(-1), end_(-1) {} + + int Begin() const { return begin_; } + int End() const { return end_; } + int Size() const { return (end_ - begin_); } + + /// Sort by beginning atom, then ending atom. + bool operator<(const Segment& rhs) const { + if (begin_ == rhs.begin_) { + return (end_ < rhs.end_); + } else { + return (begin_ < rhs.begin_); + } + } + private: + int begin_; + int end_; +}; +} +#endif From d5bc3296c6167a0941b0b407a8aff1cdcd10d3a2 Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Fri, 4 Sep 2020 11:25:15 -0400 Subject: [PATCH 02/65] Add Unit class --- src/Unit.h | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 src/Unit.h diff --git a/src/Unit.h b/src/Unit.h new file mode 100644 index 0000000000..431f4109c0 --- /dev/null +++ b/src/Unit.h @@ -0,0 +1,20 @@ +#ifndef INC_UNIT_H +#define INC_UNIT_H +#include "Segment.h" +#include +namespace Cpptraj { +/// Hold 1 or more contiguous segments of atoms +class Unit { + public: + Unit() {} + + typedef std::vector::const_iterator const_iterator; + const_iterator segBegin() const { return segArray_.begin(); } + const_iterator segEnd() const { return segArray_.end(); } + unsigned int nSegments() const { + private: + typedef std::vector SegArrayType; + SegArrayType segArray_; ///< Array of segments that make up the Unit +}; +} +#endif From 5abead044c73f7ae3b539bc82ecd72c7493f40de Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Fri, 4 Sep 2020 19:28:31 -0400 Subject: [PATCH 03/65] Finish up Segment and Unit --- src/Segment.h | 5 +++++ src/Unit.h | 19 +++++++++++++++++-- 2 files changed, 22 insertions(+), 2 deletions(-) diff --git a/src/Segment.h b/src/Segment.h index 74ad9fb237..db3ae945a9 100644 --- a/src/Segment.h +++ b/src/Segment.h @@ -6,6 +6,8 @@ class Segment { public: /// CONSTRUCTOR Segment() : begin_(-1), end_(-1) {} + /// CONSTRUCTOR - Segment size of 1 + Segment(int idx) : begin_(idx), end_(idx+1) {} int Begin() const { return begin_; } int End() const { return end_; } @@ -19,6 +21,9 @@ class Segment { return (begin_ < rhs.begin_); } } + + /// Update the end of the segment + void UpdateEnd(int idx) { end_ = idx + 1; } private: int begin_; int end_; diff --git a/src/Unit.h b/src/Unit.h index 431f4109c0..071afd73c9 100644 --- a/src/Unit.h +++ b/src/Unit.h @@ -6,15 +6,30 @@ namespace Cpptraj { /// Hold 1 or more contiguous segments of atoms class Unit { public: - Unit() {} + /// CONSTRUCTOR - Set last index to large negative so first AddIndex() call creates a Segment + Unit() : lastIdx_(-9999) {} typedef std::vector::const_iterator const_iterator; const_iterator segBegin() const { return segArray_.begin(); } const_iterator segEnd() const { return segArray_.end(); } - unsigned int nSegments() const { + unsigned int nSegments() const { return segArray_.size(); } + + /// Add index to the unit + int AddIndex(int idx) { + int delta = idx - lastIdx_; + if (delta < 1) + return 1; + else if (delta == 1) + segArray_.back().UpdateEnd( idx ); + else + segArray_.push_back( Segment(idx) ); + lastIdx_ = idx; + return 0; + } private: typedef std::vector SegArrayType; SegArrayType segArray_; ///< Array of segments that make up the Unit + int lastIdx_; ///< The last index added to the Unit }; } #endif From 98b3888d12a5abb419f26851b16978c04a267653 Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Fri, 4 Sep 2020 20:54:52 -0400 Subject: [PATCH 04/65] Determine molecule segments --- src/Molecule.h | 4 + src/Segment.h | 4 +- src/Topology.cpp | 15 ++ src/Unit.h | 4 +- src/cpptrajdepend | 624 +++++++++++++++++++++++----------------------- 5 files changed, 335 insertions(+), 316 deletions(-) diff --git a/src/Molecule.h b/src/Molecule.h index b5ed694eee..fb67139262 100644 --- a/src/Molecule.h +++ b/src/Molecule.h @@ -1,5 +1,6 @@ #ifndef INC_MOLECULE_H #define INC_MOLECULE_H +#include "Unit.h" // Class: Molecule /// Hold information for a molecule class Molecule { @@ -15,15 +16,18 @@ class Molecule { void SetLast(int last) { endAtom_ = last; } void SetSolvent() { isSolvent_ = true; } void SetNoSolvent() { isSolvent_ = false; } + Unit& ModifyUnit() { return unit_; } inline int BeginAtom() const { return beginAtom_; } inline int EndAtom() const { return endAtom_; } inline bool IsSolvent() const { return isSolvent_; } inline int NumAtoms() const { return (endAtom_ - beginAtom_); } + Unit const& MolUnit() const { return unit_; } private: int beginAtom_; int endAtom_; bool isSolvent_; + Unit unit_; ///< Hold all molecule segments. }; #endif diff --git a/src/Segment.h b/src/Segment.h index db3ae945a9..85b094544b 100644 --- a/src/Segment.h +++ b/src/Segment.h @@ -1,6 +1,6 @@ #ifndef INC_SEGMENT_H #define INC_SEGMENT_H -namespace Cpptraj { +//namespace Cpptraj { /// Define a contiguous segment of atoms class Segment { public: @@ -28,5 +28,5 @@ class Segment { int begin_; int end_; }; -} +//} #endif diff --git a/src/Topology.cpp b/src/Topology.cpp index 74143108b1..99f4e8f995 100644 --- a/src/Topology.cpp +++ b/src/Topology.cpp @@ -1021,6 +1021,21 @@ int Topology::DetermineMolecules() { // Update molecule information molecules_.resize( numberOfMolecules ); + for (int atomIdx = 0; atomIdx < (int)atoms_.size(); atomIdx++) + { + Atom const& atom = atoms_[atomIdx]; + molecules_[atom.MolNum()].ModifyUnit().AddIndex( atomIdx ); + } + mprintf("Molecule information:\n"); + for (std::vector::const_iterator mol = molecules_.begin(); mol != molecules_.end(); ++mol) + { + mprintf("\t%8li %8u segments:", mol - molecules_.begin(), mol->MolUnit().nSegments()); + for (Unit::const_iterator seg = mol->MolUnit().segBegin(); + seg != mol->MolUnit().segEnd(); ++seg) + mprintf(" %i-%i (%i) ", seg->Begin(), seg->End(), seg->Size()); + mprintf("\n"); + } + if (numberOfMolecules == 0) return 0; std::vector::iterator molecule = molecules_.begin(); molecule->SetFirst(0); diff --git a/src/Unit.h b/src/Unit.h index 071afd73c9..711f146bf2 100644 --- a/src/Unit.h +++ b/src/Unit.h @@ -2,7 +2,7 @@ #define INC_UNIT_H #include "Segment.h" #include -namespace Cpptraj { +//namespace Cpptraj { /// Hold 1 or more contiguous segments of atoms class Unit { public: @@ -31,5 +31,5 @@ class Unit { SegArrayType segArray_; ///< Array of segments that make up the Unit int lastIdx_; ///< The last index added to the Unit }; -} +//} #endif diff --git a/src/cpptrajdepend b/src/cpptrajdepend index e661447540..9e77f0d1d7 100644 --- a/src/cpptrajdepend +++ b/src/cpptrajdepend @@ -1,224 +1,224 @@ -Action.o : Action.cpp Action.h ActionState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h +Action.o : Action.cpp Action.h ActionState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h ActionFrameCounter.o : ActionFrameCounter.cpp ActionFrameCounter.h ArgList.h CpptrajStdio.h -ActionList.o : ActionList.cpp Action.h ActionList.h ActionState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -ActionTopWriter.o : ActionTopWriter.cpp ActionTopWriter.h ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h TypeNameHolder.h Vec3.h -Action_Align.o : Action_Align.cpp Action.h ActionState.h Action_Align.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_Angle.o : Action_Angle.cpp Action.h ActionState.h Action_Angle.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Vec3.h -Action_AreaPerMol.o : Action_AreaPerMol.cpp Action.h ActionState.h Action_AreaPerMol.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_AtomMap.o : Action_AtomMap.cpp Action.h ActionState.h Action_AtomMap.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h StructureMapper.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_AtomicCorr.o : Action_AtomicCorr.cpp Action.h ActionState.h Action_AtomicCorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_AtomicFluct.o : Action_AtomicFluct.cpp Action.h ActionFrameCounter.h ActionState.h Action_AtomicFluct.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_AutoImage.o : Action_AutoImage.cpp Action.h ActionState.h Action_AutoImage.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageRoutines.h ImageTypes.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_Average.o : Action_Average.cpp Action.h ActionFrameCounter.h ActionState.h Action_Average.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Vec3.h -Action_Bounds.o : Action_Bounds.cpp Action.h ActionState.h Action_Bounds.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_Box.o : Action_Box.cpp Action.h ActionState.h Action_Box.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_Center.o : Action_Center.cpp Action.h ActionState.h Action_Center.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_Channel.o : Action_Channel.cpp Action.h ActionState.h Action_Channel.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_CheckChirality.o : Action_CheckChirality.cpp Action.h ActionState.h Action_CheckChirality.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Vec3.h -Action_CheckStructure.o : Action_CheckStructure.cpp Action.h ActionState.h Action_CheckStructure.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_integer.h DataSet_string.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_Closest.o : Action_Closest.cpp Action.h ActionState.h ActionTopWriter.h Action_Closest.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageRoutines.h ImageTypes.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_ClusterDihedral.o : Action_ClusterDihedral.cpp Action.h ActionState.h Action_ClusterDihedral.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Vec3.h -Action_Contacts.o : Action_Contacts.cpp Action.h ActionState.h Action_Contacts.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_CreateCrd.o : Action_CreateCrd.cpp Action.h ActionState.h Action_CreateCrd.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_CreateReservoir.o : Action_CreateReservoir.cpp Action.h ActionState.h Action_CreateReservoir.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h NetcdfFile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_DNAionTracker.o : Action_DNAionTracker.cpp Action.h ActionState.h Action_DNAionTracker.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_DSSP.o : Action_DSSP.cpp Action.h ActionState.h Action_DSSP.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_Density.o : Action_Density.cpp Action.h ActionState.h Action_Density.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_Diffusion.o : Action_Diffusion.cpp Action.h ActionState.h Action_Diffusion.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_Dihedral.o : Action_Dihedral.cpp Action.h ActionState.h Action_Dihedral.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Vec3.h -Action_DihedralRMS.o : Action_DihedralRMS.cpp Action.h ActionState.h Action_DihedralRMS.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Vec3.h -Action_Dipole.o : Action_Dipole.cpp Action.h ActionState.h Action_Dipole.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridAction.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_DistRmsd.o : Action_DistRmsd.cpp Action.h ActionState.h Action_DistRmsd.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_Distance.o : Action_Distance.cpp Action.h ActionState.h Action_Distance.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_Energy.o : Action_Energy.cpp Action.h ActionState.h Action_Energy.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h Energy.h Ewald.h Ewald_ParticleMesh.h Ewald_Regular.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h helpme_standalone.h -Action_Esander.o : Action_Esander.cpp Action.h ActionState.h Action_Esander.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h Energy_Sander.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_FilterByData.o : Action_FilterByData.cpp Action.h ActionState.h Action_FilterByData.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_FixAtomOrder.o : Action_FixAtomOrder.cpp Action.h ActionState.h ActionTopWriter.h Action_FixAtomOrder.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomTopType.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_FixImagedBonds.o : Action_FixImagedBonds.cpp Action.h ActionState.h Action_FixImagedBonds.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_GIST.o : Action_GIST.cpp Action.h ActionState.h Action_GIST.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridDbl.h DataSet_GridFlt.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h ImagedAction.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h cuda_kernels/GistCudaSetup.cuh -Action_Grid.o : Action_Grid.cpp Action.h ActionState.h Action_Grid.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridAction.h GridBin.h MaskArray.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_GridFreeEnergy.o : Action_GridFreeEnergy.cpp Action.h ActionState.h Action_GridFreeEnergy.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridAction.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_HydrogenBond.o : Action_HydrogenBond.cpp Action.h ActionState.h Action_HydrogenBond.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Vec3.h -Action_Image.o : Action_Image.cpp Action.h ActionState.h Action_Image.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h ImageRoutines.h ImageTypes.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_InfraredSpectrum.o : Action_InfraredSpectrum.cpp Action.h ActionState.h Action_InfraredSpectrum.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_Jcoupling.o : Action_Jcoupling.cpp Action.h ActionState.h Action_Jcoupling.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Vec3.h -Action_LESsplit.o : Action_LESsplit.cpp Action.h ActionFrameCounter.h ActionState.h Action_LESsplit.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Vec3.h -Action_LIE.o : Action_LIE.cpp Action.h ActionState.h Action_LIE.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_LipidOrder.o : Action_LipidOrder.cpp Action.h ActionState.h Action_LipidOrder.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_MakeStructure.o : Action_MakeStructure.cpp Action.h ActionState.h Action_MakeStructure.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Vec3.h -Action_Mask.o : Action_Mask.cpp Action.h ActionFrameCounter.h ActionState.h Action_Mask.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Vec3.h -Action_Matrix.o : Action_Matrix.cpp Action.h ActionFrameCounter.h ActionState.h Action_Matrix.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Vector.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_MinImage.o : Action_MinImage.cpp Action.h ActionState.h Action_MinImage.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_Molsurf.o : Action_Molsurf.cpp Action.h ActionState.h Action_Molsurf.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h molsurf.h -Action_MultiDihedral.o : Action_MultiDihedral.cpp Action.h ActionState.h Action_MultiDihedral.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DihedralSearch.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Vec3.h -Action_MultiVector.o : Action_MultiVector.cpp Action.h ActionState.h Action_MultiVector.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_NAstruct.o : Action_NAstruct.cpp Action.h ActionState.h Action_NAstruct.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h AxisType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_float.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_NMRrst.o : Action_NMRrst.cpp Action.h ActionState.h Action_NMRrst.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_float.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h ViewRst.h -Action_NativeContacts.o : Action_NativeContacts.cpp Action.h ActionState.h Action_NativeContacts.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_integer.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_OrderParameter.o : Action_OrderParameter.cpp Action.h ActionState.h Action_OrderParameter.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_Outtraj.o : Action_Outtraj.cpp Action.h ActionFrameCounter.h ActionState.h Action_Outtraj.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Vec3.h -Action_PairDist.o : Action_PairDist.cpp Action.h ActionState.h Action_PairDist.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_Pairwise.o : Action_Pairwise.cpp Action.h ActionFrameCounter.h ActionState.h Action_Pairwise.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Vec3.h -Action_Principal.o : Action_Principal.cpp Action.h ActionState.h Action_Principal.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_Projection.o : Action_Projection.cpp Action.h ActionFrameCounter.h ActionState.h Action_Projection.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_Pucker.o : Action_Pucker.cpp Action.h ActionState.h Action_Pucker.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Vec3.h -Action_Radgyr.o : Action_Radgyr.cpp Action.h ActionState.h Action_Radgyr.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_Radial.o : Action_Radial.cpp Action.h ActionState.h Action_Radial.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_RandomizeIons.o : Action_RandomizeIons.cpp Action.h ActionState.h Action_RandomizeIons.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_Remap.o : Action_Remap.cpp Action.h ActionState.h ActionTopWriter.h Action_Remap.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_ReplicateCell.o : Action_ReplicateCell.cpp Action.h ActionFrameCounter.h ActionState.h ActionTopWriter.h Action_ReplicateCell.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Vec3.h -Action_Rmsd.o : Action_Rmsd.cpp Action.h ActionState.h Action_Rmsd.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_Rotate.o : Action_Rotate.cpp Action.h ActionState.h Action_Rotate.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_RunningAvg.o : Action_RunningAvg.cpp Action.h ActionState.h Action_RunningAvg.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_STFC_Diffusion.o : Action_STFC_Diffusion.cpp Action.h ActionState.h Action_STFC_Diffusion.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_Scale.o : Action_Scale.cpp Action.h ActionState.h Action_Scale.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_SetVelocity.o : Action_SetVelocity.cpp Action.h ActionState.h Action_SetVelocity.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_Spam.o : Action_Spam.cpp Action.h ActionState.h Action_Spam.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_Peaks.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_Vector_Scalar.h DataSet_double.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h ImagedAction.h KDE.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_Strip.o : Action_Strip.cpp Action.h ActionState.h ActionTopWriter.h Action_Strip.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_Surf.o : Action_Surf.cpp Action.h ActionState.h Action_Surf.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_SymmetricRmsd.o : Action_SymmetricRmsd.cpp Action.h ActionState.h Action_SymmetricRmsd.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_Temperature.o : Action_Temperature.cpp Action.h ActionState.h Action_Temperature.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_Time.o : Action_Time.cpp Action.h ActionState.h Action_Time.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_Translate.o : Action_Translate.cpp Action.h ActionState.h Action_Translate.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_Unstrip.o : Action_Unstrip.cpp Action.h ActionState.h Action_Unstrip.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_Unwrap.o : Action_Unwrap.cpp Action.h ActionState.h Action_Unwrap.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h ImageRoutines.h ImageTypes.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_Vector.o : Action_Vector.cpp Action.h ActionState.h Action_Vector.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_VelocityAutoCorr.o : Action_VelocityAutoCorr.cpp Action.h ActionState.h Action_VelocityAutoCorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_Volmap.o : Action_Volmap.cpp Action.h ActionState.h Action_Volmap.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridDbl.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_Volume.o : Action_Volume.cpp Action.h ActionState.h Action_Volume.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_Watershell.o : Action_Watershell.cpp Action.h ActionState.h Action_Watershell.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageRoutines.h ImageTypes.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Action_XtalSymm.o : Action_XtalSymm.cpp Action.h ActionState.h Action_XtalSymm.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SpaceGroup.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -AnalysisList.o : AnalysisList.cpp ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Analysis_AmdBias.o : Analysis_AmdBias.cpp ActionState.h Analysis.h AnalysisState.h Analysis_AmdBias.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Analysis_AutoCorr.o : Analysis_AutoCorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_AutoCorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Analysis_Average.o : Analysis_Average.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Average.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Analysis_Clustering.o : Analysis_Clustering.cpp ActionFrameCounter.h ActionState.h Analysis.h AnalysisState.h Analysis_Clustering.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h ClusterDist.h ClusterList.h ClusterMatrix.h ClusterNode.h ClusterSieve.h Cluster_DBSCAN.h Cluster_DPeaks.h Cluster_HierAgglo.h Cluster_Kmeans.h Cluster_ReadInfo.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Cmatrix.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_float.h DataSet_integer.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Vec3.h -Analysis_ConstantPHStats.o : Analysis_ConstantPHStats.cpp ActionState.h Analysis.h AnalysisState.h Analysis_ConstantPHStats.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_pH.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Analysis_Corr.o : Analysis_Corr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Corr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Analysis_CrankShaft.o : Analysis_CrankShaft.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CrankShaft.h Analysis_Statistics.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_float.h DataSet_integer.h DataSet_string.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Analysis_CrdFluct.o : Analysis_CrdFluct.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CrdFluct.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Analysis_CrossCorr.o : Analysis_CrossCorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CrossCorr.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Analysis_CurveFit.o : Analysis_CurveFit.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CurveFit.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h CurveFit.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Analysis_Divergence.o : Analysis_Divergence.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Divergence.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Analysis_EvalPlateau.o : Analysis_EvalPlateau.cpp ActionState.h Analysis.h AnalysisState.h Analysis_EvalPlateau.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h CurveFit.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Analysis_FFT.o : Analysis_FFT.cpp ActionState.h Analysis.h AnalysisState.h Analysis_FFT.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Analysis_HausdorffDistance.o : Analysis_HausdorffDistance.cpp ActionState.h Analysis.h AnalysisState.h Analysis_HausdorffDistance.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Analysis_Hist.o : Analysis_Hist.cpp ActionFrameCounter.h ActionState.h Analysis.h AnalysisState.h Analysis_Hist.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h HistBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Vec3.h -Analysis_IRED.o : Analysis_IRED.cpp ActionState.h Analysis.h AnalysisState.h Analysis_IRED.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Analysis_Integrate.o : Analysis_Integrate.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Integrate.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Analysis_KDE.o : Analysis_KDE.cpp ActionState.h Analysis.h AnalysisState.h Analysis_KDE.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Analysis_Lifetime.o : Analysis_Lifetime.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Lifetime.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Analysis_LowestCurve.o : Analysis_LowestCurve.cpp ActionState.h Analysis.h AnalysisState.h Analysis_LowestCurve.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Analysis_Matrix.o : Analysis_Matrix.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Matrix.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Analysis_MeltCurve.o : Analysis_MeltCurve.cpp ActionState.h Analysis.h AnalysisState.h Analysis_MeltCurve.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Analysis_Modes.o : Analysis_Modes.cpp ActionFrameCounter.h ActionState.h Analysis.h AnalysisState.h Analysis_Modes.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Vec3.h -Analysis_MultiHist.o : Analysis_MultiHist.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Hist.h Analysis_KDE.h Analysis_MultiHist.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TypeNameHolder.h Vec3.h -Analysis_Multicurve.o : Analysis_Multicurve.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CurveFit.h Analysis_Multicurve.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Analysis_Overlap.o : Analysis_Overlap.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Overlap.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Analysis_PhiPsi.o : Analysis_PhiPsi.cpp ActionState.h Analysis.h AnalysisState.h Analysis_PhiPsi.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Analysis_Regression.o : Analysis_Regression.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Regression.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Analysis_RemLog.o : Analysis_RemLog.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Lifetime.h Analysis_RemLog.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_RemLog.h DataSet_integer.h DataSet_integer_mem.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Analysis_Rms2d.o : Analysis_Rms2d.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Rms2d.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TypeNameHolder.h Vec3.h -Analysis_RmsAvgCorr.o : Analysis_RmsAvgCorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_RmsAvgCorr.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Analysis_Rotdif.o : Analysis_Rotdif.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Rotdif.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h CurveFit.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_Mesh.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h PubFFT.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SimplexMin.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Analysis_RunningAvg.o : Analysis_RunningAvg.cpp ActionState.h Analysis.h AnalysisState.h Analysis_RunningAvg.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Analysis_Slope.o : Analysis_Slope.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Slope.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Analysis_Spline.o : Analysis_Spline.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Spline.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Analysis_State.o : Analysis_State.cpp ActionState.h Analysis.h AnalysisState.h Analysis_State.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Analysis_Statistics.o : Analysis_Statistics.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Statistics.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_float.h DataSet_integer.h DataSet_string.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Analysis_TI.o : Analysis_TI.cpp ActionState.h Analysis.h AnalysisState.h Analysis_TI.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Analysis_Timecorr.o : Analysis_Timecorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Timecorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Analysis_VectorMath.o : Analysis_VectorMath.cpp ActionState.h Analysis.h AnalysisState.h Analysis_VectorMath.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Analysis_Wavelet.o : Analysis_Wavelet.cpp ActionFrameCounter.h ActionState.h Analysis.h AnalysisState.h Analysis_Wavelet.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ClusterMap.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h ProgressBar.h ProgressTimer.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Vec3.h +ActionList.o : ActionList.cpp Action.h ActionList.h ActionState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +ActionTopWriter.o : ActionTopWriter.cpp ActionTopWriter.h ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_Align.o : Action_Align.cpp Action.h ActionState.h Action_Align.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_Angle.o : Action_Angle.cpp Action.h ActionState.h Action_Angle.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h +Action_AreaPerMol.o : Action_AreaPerMol.cpp Action.h ActionState.h Action_AreaPerMol.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_AtomMap.o : Action_AtomMap.cpp Action.h ActionState.h Action_AtomMap.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h StructureMapper.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_AtomicCorr.o : Action_AtomicCorr.cpp Action.h ActionState.h Action_AtomicCorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_AtomicFluct.o : Action_AtomicFluct.cpp Action.h ActionFrameCounter.h ActionState.h Action_AtomicFluct.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_AutoImage.o : Action_AutoImage.cpp Action.h ActionState.h Action_AutoImage.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageRoutines.h ImageTypes.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_Average.o : Action_Average.cpp Action.h ActionFrameCounter.h ActionState.h Action_Average.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h +Action_Bounds.o : Action_Bounds.cpp Action.h ActionState.h Action_Bounds.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_Box.o : Action_Box.cpp Action.h ActionState.h Action_Box.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_Center.o : Action_Center.cpp Action.h ActionState.h Action_Center.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_Channel.o : Action_Channel.cpp Action.h ActionState.h Action_Channel.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_CheckChirality.o : Action_CheckChirality.cpp Action.h ActionState.h Action_CheckChirality.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h +Action_CheckStructure.o : Action_CheckStructure.cpp Action.h ActionState.h Action_CheckStructure.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_integer.h DataSet_string.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_Closest.o : Action_Closest.cpp Action.h ActionState.h ActionTopWriter.h Action_Closest.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageRoutines.h ImageTypes.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_ClusterDihedral.o : Action_ClusterDihedral.cpp Action.h ActionState.h Action_ClusterDihedral.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h +Action_Contacts.o : Action_Contacts.cpp Action.h ActionState.h Action_Contacts.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_CreateCrd.o : Action_CreateCrd.cpp Action.h ActionState.h Action_CreateCrd.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_CreateReservoir.o : Action_CreateReservoir.cpp Action.h ActionState.h Action_CreateReservoir.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h NetcdfFile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_DNAionTracker.o : Action_DNAionTracker.cpp Action.h ActionState.h Action_DNAionTracker.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_DSSP.o : Action_DSSP.cpp Action.h ActionState.h Action_DSSP.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_Density.o : Action_Density.cpp Action.h ActionState.h Action_Density.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_Diffusion.o : Action_Diffusion.cpp Action.h ActionState.h Action_Diffusion.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_Dihedral.o : Action_Dihedral.cpp Action.h ActionState.h Action_Dihedral.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h +Action_DihedralRMS.o : Action_DihedralRMS.cpp Action.h ActionState.h Action_DihedralRMS.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h +Action_Dipole.o : Action_Dipole.cpp Action.h ActionState.h Action_Dipole.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridAction.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_DistRmsd.o : Action_DistRmsd.cpp Action.h ActionState.h Action_DistRmsd.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_Distance.o : Action_Distance.cpp Action.h ActionState.h Action_Distance.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_Energy.o : Action_Energy.cpp Action.h ActionState.h Action_Energy.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h Energy.h Ewald.h Ewald_ParticleMesh.h Ewald_Regular.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h helpme_standalone.h +Action_Esander.o : Action_Esander.cpp Action.h ActionState.h Action_Esander.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h Energy_Sander.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_FilterByData.o : Action_FilterByData.cpp Action.h ActionState.h Action_FilterByData.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_FixAtomOrder.o : Action_FixAtomOrder.cpp Action.h ActionState.h ActionTopWriter.h Action_FixAtomOrder.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomTopType.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_FixImagedBonds.o : Action_FixImagedBonds.cpp Action.h ActionState.h Action_FixImagedBonds.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_GIST.o : Action_GIST.cpp Action.h ActionState.h Action_GIST.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridDbl.h DataSet_GridFlt.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h ImagedAction.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/GistCudaSetup.cuh +Action_Grid.o : Action_Grid.cpp Action.h ActionState.h Action_Grid.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridAction.h GridBin.h MaskArray.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_GridFreeEnergy.o : Action_GridFreeEnergy.cpp Action.h ActionState.h Action_GridFreeEnergy.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridAction.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_HydrogenBond.o : Action_HydrogenBond.cpp Action.h ActionState.h Action_HydrogenBond.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h +Action_Image.o : Action_Image.cpp Action.h ActionState.h Action_Image.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h ImageRoutines.h ImageTypes.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_InfraredSpectrum.o : Action_InfraredSpectrum.cpp Action.h ActionState.h Action_InfraredSpectrum.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_Jcoupling.o : Action_Jcoupling.cpp Action.h ActionState.h Action_Jcoupling.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h +Action_LESsplit.o : Action_LESsplit.cpp Action.h ActionFrameCounter.h ActionState.h Action_LESsplit.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h +Action_LIE.o : Action_LIE.cpp Action.h ActionState.h Action_LIE.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_LipidOrder.o : Action_LipidOrder.cpp Action.h ActionState.h Action_LipidOrder.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_MakeStructure.o : Action_MakeStructure.cpp Action.h ActionState.h Action_MakeStructure.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h +Action_Mask.o : Action_Mask.cpp Action.h ActionFrameCounter.h ActionState.h Action_Mask.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h +Action_Matrix.o : Action_Matrix.cpp Action.h ActionFrameCounter.h ActionState.h Action_Matrix.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Vector.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_MinImage.o : Action_MinImage.cpp Action.h ActionState.h Action_MinImage.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_Molsurf.o : Action_Molsurf.cpp Action.h ActionState.h Action_Molsurf.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h molsurf.h +Action_MultiDihedral.o : Action_MultiDihedral.cpp Action.h ActionState.h Action_MultiDihedral.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DihedralSearch.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h +Action_MultiVector.o : Action_MultiVector.cpp Action.h ActionState.h Action_MultiVector.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_NAstruct.o : Action_NAstruct.cpp Action.h ActionState.h Action_NAstruct.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h AxisType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_float.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_NMRrst.o : Action_NMRrst.cpp Action.h ActionState.h Action_NMRrst.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_float.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h ViewRst.h +Action_NativeContacts.o : Action_NativeContacts.cpp Action.h ActionState.h Action_NativeContacts.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_integer.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_OrderParameter.o : Action_OrderParameter.cpp Action.h ActionState.h Action_OrderParameter.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_Outtraj.o : Action_Outtraj.cpp Action.h ActionFrameCounter.h ActionState.h Action_Outtraj.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h +Action_PairDist.o : Action_PairDist.cpp Action.h ActionState.h Action_PairDist.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_Pairwise.o : Action_Pairwise.cpp Action.h ActionFrameCounter.h ActionState.h Action_Pairwise.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h +Action_Principal.o : Action_Principal.cpp Action.h ActionState.h Action_Principal.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_Projection.o : Action_Projection.cpp Action.h ActionFrameCounter.h ActionState.h Action_Projection.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_Pucker.o : Action_Pucker.cpp Action.h ActionState.h Action_Pucker.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h +Action_Radgyr.o : Action_Radgyr.cpp Action.h ActionState.h Action_Radgyr.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_Radial.o : Action_Radial.cpp Action.h ActionState.h Action_Radial.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_RandomizeIons.o : Action_RandomizeIons.cpp Action.h ActionState.h Action_RandomizeIons.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_Remap.o : Action_Remap.cpp Action.h ActionState.h ActionTopWriter.h Action_Remap.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_ReplicateCell.o : Action_ReplicateCell.cpp Action.h ActionFrameCounter.h ActionState.h ActionTopWriter.h Action_ReplicateCell.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h +Action_Rmsd.o : Action_Rmsd.cpp Action.h ActionState.h Action_Rmsd.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_Rotate.o : Action_Rotate.cpp Action.h ActionState.h Action_Rotate.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_RunningAvg.o : Action_RunningAvg.cpp Action.h ActionState.h Action_RunningAvg.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_STFC_Diffusion.o : Action_STFC_Diffusion.cpp Action.h ActionState.h Action_STFC_Diffusion.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_Scale.o : Action_Scale.cpp Action.h ActionState.h Action_Scale.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_SetVelocity.o : Action_SetVelocity.cpp Action.h ActionState.h Action_SetVelocity.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_Spam.o : Action_Spam.cpp Action.h ActionState.h Action_Spam.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_Peaks.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_Vector_Scalar.h DataSet_double.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h ImagedAction.h KDE.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_Strip.o : Action_Strip.cpp Action.h ActionState.h ActionTopWriter.h Action_Strip.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_Surf.o : Action_Surf.cpp Action.h ActionState.h Action_Surf.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_SymmetricRmsd.o : Action_SymmetricRmsd.cpp Action.h ActionState.h Action_SymmetricRmsd.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_Temperature.o : Action_Temperature.cpp Action.h ActionState.h Action_Temperature.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_Time.o : Action_Time.cpp Action.h ActionState.h Action_Time.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_Translate.o : Action_Translate.cpp Action.h ActionState.h Action_Translate.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_Unstrip.o : Action_Unstrip.cpp Action.h ActionState.h Action_Unstrip.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_Unwrap.o : Action_Unwrap.cpp Action.h ActionState.h Action_Unwrap.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h ImageRoutines.h ImageTypes.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_Vector.o : Action_Vector.cpp Action.h ActionState.h Action_Vector.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_VelocityAutoCorr.o : Action_VelocityAutoCorr.cpp Action.h ActionState.h Action_VelocityAutoCorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_Volmap.o : Action_Volmap.cpp Action.h ActionState.h Action_Volmap.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridDbl.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_Volume.o : Action_Volume.cpp Action.h ActionState.h Action_Volume.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_Watershell.o : Action_Watershell.cpp Action.h ActionState.h Action_Watershell.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageRoutines.h ImageTypes.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_XtalSymm.o : Action_XtalSymm.cpp Action.h ActionState.h Action_XtalSymm.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SpaceGroup.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +AnalysisList.o : AnalysisList.cpp ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Analysis_AmdBias.o : Analysis_AmdBias.cpp ActionState.h Analysis.h AnalysisState.h Analysis_AmdBias.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Analysis_AutoCorr.o : Analysis_AutoCorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_AutoCorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Analysis_Average.o : Analysis_Average.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Average.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Analysis_Clustering.o : Analysis_Clustering.cpp ActionFrameCounter.h ActionState.h Analysis.h AnalysisState.h Analysis_Clustering.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h ClusterDist.h ClusterList.h ClusterMatrix.h ClusterNode.h ClusterSieve.h Cluster_DBSCAN.h Cluster_DPeaks.h Cluster_HierAgglo.h Cluster_Kmeans.h Cluster_ReadInfo.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Cmatrix.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_float.h DataSet_integer.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h +Analysis_ConstantPHStats.o : Analysis_ConstantPHStats.cpp ActionState.h Analysis.h AnalysisState.h Analysis_ConstantPHStats.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_pH.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Analysis_Corr.o : Analysis_Corr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Corr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Analysis_CrankShaft.o : Analysis_CrankShaft.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CrankShaft.h Analysis_Statistics.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_float.h DataSet_integer.h DataSet_string.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Analysis_CrdFluct.o : Analysis_CrdFluct.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CrdFluct.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Analysis_CrossCorr.o : Analysis_CrossCorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CrossCorr.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Analysis_CurveFit.o : Analysis_CurveFit.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CurveFit.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h CurveFit.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Analysis_Divergence.o : Analysis_Divergence.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Divergence.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Analysis_EvalPlateau.o : Analysis_EvalPlateau.cpp ActionState.h Analysis.h AnalysisState.h Analysis_EvalPlateau.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h CurveFit.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Analysis_FFT.o : Analysis_FFT.cpp ActionState.h Analysis.h AnalysisState.h Analysis_FFT.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Analysis_HausdorffDistance.o : Analysis_HausdorffDistance.cpp ActionState.h Analysis.h AnalysisState.h Analysis_HausdorffDistance.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Analysis_Hist.o : Analysis_Hist.cpp ActionFrameCounter.h ActionState.h Analysis.h AnalysisState.h Analysis_Hist.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h HistBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h +Analysis_IRED.o : Analysis_IRED.cpp ActionState.h Analysis.h AnalysisState.h Analysis_IRED.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Analysis_Integrate.o : Analysis_Integrate.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Integrate.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Analysis_KDE.o : Analysis_KDE.cpp ActionState.h Analysis.h AnalysisState.h Analysis_KDE.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Analysis_Lifetime.o : Analysis_Lifetime.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Lifetime.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Analysis_LowestCurve.o : Analysis_LowestCurve.cpp ActionState.h Analysis.h AnalysisState.h Analysis_LowestCurve.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Analysis_Matrix.o : Analysis_Matrix.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Matrix.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Analysis_MeltCurve.o : Analysis_MeltCurve.cpp ActionState.h Analysis.h AnalysisState.h Analysis_MeltCurve.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Analysis_Modes.o : Analysis_Modes.cpp ActionFrameCounter.h ActionState.h Analysis.h AnalysisState.h Analysis_Modes.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h +Analysis_MultiHist.o : Analysis_MultiHist.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Hist.h Analysis_KDE.h Analysis_MultiHist.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TypeNameHolder.h Unit.h Vec3.h +Analysis_Multicurve.o : Analysis_Multicurve.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CurveFit.h Analysis_Multicurve.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Analysis_Overlap.o : Analysis_Overlap.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Overlap.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Analysis_PhiPsi.o : Analysis_PhiPsi.cpp ActionState.h Analysis.h AnalysisState.h Analysis_PhiPsi.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Analysis_Regression.o : Analysis_Regression.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Regression.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Analysis_RemLog.o : Analysis_RemLog.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Lifetime.h Analysis_RemLog.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_RemLog.h DataSet_integer.h DataSet_integer_mem.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Analysis_Rms2d.o : Analysis_Rms2d.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Rms2d.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TypeNameHolder.h Unit.h Vec3.h +Analysis_RmsAvgCorr.o : Analysis_RmsAvgCorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_RmsAvgCorr.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Analysis_Rotdif.o : Analysis_Rotdif.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Rotdif.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h CurveFit.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_Mesh.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h PubFFT.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SimplexMin.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Analysis_RunningAvg.o : Analysis_RunningAvg.cpp ActionState.h Analysis.h AnalysisState.h Analysis_RunningAvg.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Analysis_Slope.o : Analysis_Slope.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Slope.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Analysis_Spline.o : Analysis_Spline.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Spline.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Analysis_State.o : Analysis_State.cpp ActionState.h Analysis.h AnalysisState.h Analysis_State.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Analysis_Statistics.o : Analysis_Statistics.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Statistics.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_float.h DataSet_integer.h DataSet_string.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Analysis_TI.o : Analysis_TI.cpp ActionState.h Analysis.h AnalysisState.h Analysis_TI.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Analysis_Timecorr.o : Analysis_Timecorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Timecorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Analysis_VectorMath.o : Analysis_VectorMath.cpp ActionState.h Analysis.h AnalysisState.h Analysis_VectorMath.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Analysis_Wavelet.o : Analysis_Wavelet.cpp ActionFrameCounter.h ActionState.h Analysis.h AnalysisState.h Analysis_Wavelet.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ClusterMap.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h ProgressBar.h ProgressTimer.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h ArgList.o : ArgList.cpp ArgList.h CpptrajStdio.h StringRoutines.h -Array1D.o : Array1D.cpp ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h +Array1D.o : Array1D.cpp ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h AssociatedData.o : AssociatedData.cpp ArgList.h AssociatedData.h CpptrajStdio.h Atom.o : Atom.cpp Atom.h CpptrajStdio.h NameType.h SymbolExporting.h -AtomMap.o : AtomMap.cpp Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h TypeNameHolder.h Vec3.h -AtomMask.o : AtomMask.cpp Atom.h AtomMask.h CpptrajStdio.h MaskToken.h Molecule.h NameType.h Residue.h SymbolExporting.h -AxisType.o : AxisType.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h AxisType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Vec3.h -BondSearch.o : BondSearch.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Vec3.h +AtomMap.o : AtomMap.cpp Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h +AtomMask.o : AtomMask.cpp Atom.h AtomMask.h CpptrajStdio.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h SymbolExporting.h Unit.h +AxisType.o : AxisType.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h AxisType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h +BondSearch.o : BondSearch.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h Box.o : Box.cpp Box.h Constants.h CpptrajStdio.h Matrix_3x3.h Parallel.h Vec3.h BufferedFrame.o : BufferedFrame.cpp BufferedFrame.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Parallel.h TextFormat.h BufferedLine.o : BufferedLine.cpp BufferedLine.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Parallel.h ByteRoutines.o : ByteRoutines.cpp CIFfile.o : CIFfile.cpp Atom.h BufferedLine.h CIFfile.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h SymbolExporting.h -CharMask.o : CharMask.cpp Atom.h CharMask.h CpptrajStdio.h MaskToken.h Molecule.h NameType.h Residue.h SymbolExporting.h +CharMask.o : CharMask.cpp Atom.h CharMask.h CpptrajStdio.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h SymbolExporting.h Unit.h CharmmParamFile.o : CharmmParamFile.cpp ArgList.h AtomType.h BufferedLine.h CharmmParamFile.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h StringRoutines.h TypeNameHolder.h -ClusterDist.o : ClusterDist.cpp ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h ClusterDist.h Constants.h CoordinateInfo.h CpptrajFile.h DataSet.h DataSet_1D.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Topology.h TypeNameHolder.h Vec3.h -ClusterList.o : ClusterList.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h ClusterDist.h ClusterList.h ClusterNode.h ClusterSieve.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_Cmatrix.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Topology.h TypeNameHolder.h Vec3.h +ClusterDist.o : ClusterDist.cpp ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h ClusterDist.h Constants.h CoordinateInfo.h CpptrajFile.h DataSet.h DataSet_1D.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h +ClusterList.o : ClusterList.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h ClusterDist.h ClusterList.h ClusterNode.h ClusterSieve.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_Cmatrix.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h ClusterMap.o : ClusterMap.cpp AssociatedData.h ClusterMap.h Constants.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_2D.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h ProgressBar.h ProgressTimer.h Range.h TextFormat.h Timer.h ClusterMatrix.o : ClusterMatrix.cpp ArrayIterator.h ClusterMatrix.h CpptrajStdio.h Matrix.h -ClusterNode.o : ClusterNode.cpp ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h ClusterDist.h ClusterNode.h ClusterSieve.h Constants.h CoordinateInfo.h CpptrajFile.h DataSet.h DataSet_1D.h DataSet_Cmatrix.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Topology.h TypeNameHolder.h Vec3.h +ClusterNode.o : ClusterNode.cpp ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h ClusterDist.h ClusterNode.h ClusterSieve.h Constants.h CoordinateInfo.h CpptrajFile.h DataSet.h DataSet_1D.h DataSet_Cmatrix.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h ClusterSieve.o : ClusterSieve.cpp ClusterSieve.h Random.h -Cluster_DBSCAN.o : Cluster_DBSCAN.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h ClusterDist.h ClusterList.h ClusterNode.h ClusterSieve.h Cluster_DBSCAN.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Cmatrix.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Cluster_DPeaks.o : Cluster_DPeaks.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h ClusterDist.h ClusterList.h ClusterNode.h ClusterSieve.h Cluster_DPeaks.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_Cmatrix.h DataSet_Coords.h DataSet_Mesh.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReplicaDimArray.h Residue.h Spline.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Topology.h TypeNameHolder.h Vec3.h -Cluster_HierAgglo.o : Cluster_HierAgglo.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h ClusterDist.h ClusterList.h ClusterMatrix.h ClusterNode.h ClusterSieve.h Cluster_HierAgglo.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_Cmatrix.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Cluster_Kmeans.o : Cluster_Kmeans.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h ClusterDist.h ClusterList.h ClusterNode.h ClusterSieve.h Cluster_Kmeans.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_Cmatrix.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Random.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Topology.h TypeNameHolder.h Vec3.h -Cluster_ReadInfo.o : Cluster_ReadInfo.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h BufferedLine.h ClusterDist.h ClusterList.h ClusterNode.h ClusterSieve.h Cluster_ReadInfo.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_Cmatrix.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Topology.h TypeNameHolder.h Vec3.h +Cluster_DBSCAN.o : Cluster_DBSCAN.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h ClusterDist.h ClusterList.h ClusterNode.h ClusterSieve.h Cluster_DBSCAN.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Cmatrix.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Cluster_DPeaks.o : Cluster_DPeaks.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h ClusterDist.h ClusterList.h ClusterNode.h ClusterSieve.h Cluster_DPeaks.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_Cmatrix.h DataSet_Coords.h DataSet_Mesh.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Cluster_HierAgglo.o : Cluster_HierAgglo.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h ClusterDist.h ClusterList.h ClusterMatrix.h ClusterNode.h ClusterSieve.h Cluster_HierAgglo.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_Cmatrix.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Cluster_Kmeans.o : Cluster_Kmeans.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h ClusterDist.h ClusterList.h ClusterNode.h ClusterSieve.h Cluster_Kmeans.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_Cmatrix.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Random.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Cluster_ReadInfo.o : Cluster_ReadInfo.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h BufferedLine.h ClusterDist.h ClusterList.h ClusterNode.h ClusterSieve.h Cluster_ReadInfo.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_Cmatrix.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h Cmd.o : Cmd.cpp Cmd.h DispatchObject.h CmdInput.o : CmdInput.cpp CmdInput.h StringRoutines.h CmdList.o : CmdList.cpp Cmd.h CmdList.h DispatchObject.h -Command.o : Command.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h ActionTopWriter.h Action_Align.h Action_Angle.h Action_AreaPerMol.h Action_AtomMap.h Action_AtomicCorr.h Action_AtomicFluct.h Action_AutoImage.h Action_Average.h Action_Bounds.h Action_Box.h Action_Center.h Action_Channel.h Action_CheckChirality.h Action_CheckStructure.h Action_Closest.h Action_ClusterDihedral.h Action_Contacts.h Action_CreateCrd.h Action_CreateReservoir.h Action_DNAionTracker.h Action_DSSP.h Action_Density.h Action_Diffusion.h Action_Dihedral.h Action_DihedralRMS.h Action_Dipole.h Action_DistRmsd.h Action_Distance.h Action_Energy.h Action_Esander.h Action_FilterByData.h Action_FixAtomOrder.h Action_FixImagedBonds.h Action_GIST.h Action_Grid.h Action_GridFreeEnergy.h Action_HydrogenBond.h Action_Image.h Action_InfraredSpectrum.h Action_Jcoupling.h Action_LESsplit.h Action_LIE.h Action_LipidOrder.h Action_MakeStructure.h Action_Mask.h Action_Matrix.h Action_MinImage.h Action_Molsurf.h Action_MultiDihedral.h Action_MultiVector.h Action_NAstruct.h Action_NMRrst.h Action_NativeContacts.h Action_OrderParameter.h Action_Outtraj.h Action_PairDist.h Action_Pairwise.h Action_Principal.h Action_Projection.h Action_Pucker.h Action_Radgyr.h Action_Radial.h Action_RandomizeIons.h Action_Remap.h Action_ReplicateCell.h Action_Rmsd.h Action_Rotate.h Action_RunningAvg.h Action_STFC_Diffusion.h Action_Scale.h Action_SetVelocity.h Action_Spam.h Action_Strip.h Action_Surf.h Action_SymmetricRmsd.h Action_Temperature.h Action_Time.h Action_Translate.h Action_Unstrip.h Action_Unwrap.h Action_Vector.h Action_VelocityAutoCorr.h Action_Volmap.h Action_Volume.h Action_Watershell.h Action_XtalSymm.h Analysis.h AnalysisList.h AnalysisState.h Analysis_AmdBias.h Analysis_AutoCorr.h Analysis_Average.h Analysis_Clustering.h Analysis_ConstantPHStats.h Analysis_Corr.h Analysis_CrankShaft.h Analysis_CrdFluct.h Analysis_CrossCorr.h Analysis_CurveFit.h Analysis_Divergence.h Analysis_EvalPlateau.h Analysis_FFT.h Analysis_HausdorffDistance.h Analysis_Hist.h Analysis_IRED.h Analysis_Integrate.h Analysis_KDE.h Analysis_Lifetime.h Analysis_LowestCurve.h Analysis_Matrix.h Analysis_MeltCurve.h Analysis_Modes.h Analysis_MultiHist.h Analysis_Multicurve.h Analysis_Overlap.h Analysis_PhiPsi.h Analysis_Regression.h Analysis_RemLog.h Analysis_Rms2d.h Analysis_RmsAvgCorr.h Analysis_Rotdif.h Analysis_RunningAvg.h Analysis_Slope.h Analysis_Spline.h Analysis_State.h Analysis_Statistics.h Analysis_TI.h Analysis_Timecorr.h Analysis_VectorMath.h Analysis_Wavelet.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h AxisType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h ClusterDist.h ClusterList.h ClusterMap.h ClusterNode.h ClusterSieve.h Cmd.h CmdInput.h CmdList.h Command.h ComplexArray.h Constants.h Constraints.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h Corr.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Cmatrix.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_RemLog.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h Deprecated.h DihedralSearch.h Dimension.h DispatchObject.h DistRoutines.h Energy.h Energy_Sander.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_AddMissingRes.h Exec_Analyze.h Exec_Calc.h Exec_CatCrd.h Exec_Change.h Exec_ClusterMap.h Exec_CombineCoords.h Exec_Commands.h Exec_CompareTop.h Exec_CrdAction.h Exec_CrdOut.h Exec_CreateSet.h Exec_DataFile.h Exec_DataFilter.h Exec_DataSetCmd.h Exec_Emin.h Exec_GenerateAmberRst.h Exec_Graft.h Exec_Help.h Exec_LoadCrd.h Exec_LoadTraj.h Exec_ParallelAnalysis.h Exec_ParmBox.h Exec_ParmSolvent.h Exec_ParmStrip.h Exec_ParmWrite.h Exec_PermuteDihedrals.h Exec_Precision.h Exec_PrepareForLeap.h Exec_PrintData.h Exec_ReadData.h Exec_ReadEnsembleData.h Exec_ReadInput.h Exec_RotateDihedral.h Exec_RunAnalysis.h Exec_ScaleDihedralK.h Exec_SequenceAlign.h Exec_Set.h Exec_Show.h Exec_SortEnsembleData.h Exec_SplitCoords.h Exec_System.h Exec_Top.h Exec_Traj.h Exec_UpdateParameters.h Exec_ViewRst.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h Grid.h GridAction.h GridBin.h HistBin.h Hungarian.h ImageTypes.h ImagedAction.h InputTrajCommon.h MapAtom.h MaskArray.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h NetcdfFile.h OnlineVarT.h OutputTrajCommon.h PDBfile.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h RPNcalc.h Random.h Range.h ReferenceAction.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h ReplicaInfo.h Residue.h Spline.h StructureCheck.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Vec3.h cuda_kernels/GistCudaSetup.cuh molsurf.h +Command.o : Command.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h ActionTopWriter.h Action_Align.h Action_Angle.h Action_AreaPerMol.h Action_AtomMap.h Action_AtomicCorr.h Action_AtomicFluct.h Action_AutoImage.h Action_Average.h Action_Bounds.h Action_Box.h Action_Center.h Action_Channel.h Action_CheckChirality.h Action_CheckStructure.h Action_Closest.h Action_ClusterDihedral.h Action_Contacts.h Action_CreateCrd.h Action_CreateReservoir.h Action_DNAionTracker.h Action_DSSP.h Action_Density.h Action_Diffusion.h Action_Dihedral.h Action_DihedralRMS.h Action_Dipole.h Action_DistRmsd.h Action_Distance.h Action_Energy.h Action_Esander.h Action_FilterByData.h Action_FixAtomOrder.h Action_FixImagedBonds.h Action_GIST.h Action_Grid.h Action_GridFreeEnergy.h Action_HydrogenBond.h Action_Image.h Action_InfraredSpectrum.h Action_Jcoupling.h Action_LESsplit.h Action_LIE.h Action_LipidOrder.h Action_MakeStructure.h Action_Mask.h Action_Matrix.h Action_MinImage.h Action_Molsurf.h Action_MultiDihedral.h Action_MultiVector.h Action_NAstruct.h Action_NMRrst.h Action_NativeContacts.h Action_OrderParameter.h Action_Outtraj.h Action_PairDist.h Action_Pairwise.h Action_Principal.h Action_Projection.h Action_Pucker.h Action_Radgyr.h Action_Radial.h Action_RandomizeIons.h Action_Remap.h Action_ReplicateCell.h Action_Rmsd.h Action_Rotate.h Action_RunningAvg.h Action_STFC_Diffusion.h Action_Scale.h Action_SetVelocity.h Action_Spam.h Action_Strip.h Action_Surf.h Action_SymmetricRmsd.h Action_Temperature.h Action_Time.h Action_Translate.h Action_Unstrip.h Action_Unwrap.h Action_Vector.h Action_VelocityAutoCorr.h Action_Volmap.h Action_Volume.h Action_Watershell.h Action_XtalSymm.h Analysis.h AnalysisList.h AnalysisState.h Analysis_AmdBias.h Analysis_AutoCorr.h Analysis_Average.h Analysis_Clustering.h Analysis_ConstantPHStats.h Analysis_Corr.h Analysis_CrankShaft.h Analysis_CrdFluct.h Analysis_CrossCorr.h Analysis_CurveFit.h Analysis_Divergence.h Analysis_EvalPlateau.h Analysis_FFT.h Analysis_HausdorffDistance.h Analysis_Hist.h Analysis_IRED.h Analysis_Integrate.h Analysis_KDE.h Analysis_Lifetime.h Analysis_LowestCurve.h Analysis_Matrix.h Analysis_MeltCurve.h Analysis_Modes.h Analysis_MultiHist.h Analysis_Multicurve.h Analysis_Overlap.h Analysis_PhiPsi.h Analysis_Regression.h Analysis_RemLog.h Analysis_Rms2d.h Analysis_RmsAvgCorr.h Analysis_Rotdif.h Analysis_RunningAvg.h Analysis_Slope.h Analysis_Spline.h Analysis_State.h Analysis_Statistics.h Analysis_TI.h Analysis_Timecorr.h Analysis_VectorMath.h Analysis_Wavelet.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h AxisType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h ClusterDist.h ClusterList.h ClusterMap.h ClusterNode.h ClusterSieve.h Cmd.h CmdInput.h CmdList.h Command.h ComplexArray.h Constants.h Constraints.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h Corr.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Cmatrix.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_RemLog.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h Deprecated.h DihedralSearch.h Dimension.h DispatchObject.h DistRoutines.h Energy.h Energy_Sander.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_AddMissingRes.h Exec_Analyze.h Exec_Calc.h Exec_CatCrd.h Exec_Change.h Exec_ClusterMap.h Exec_CombineCoords.h Exec_Commands.h Exec_CompareTop.h Exec_CrdAction.h Exec_CrdOut.h Exec_CreateSet.h Exec_DataFile.h Exec_DataFilter.h Exec_DataSetCmd.h Exec_Emin.h Exec_GenerateAmberRst.h Exec_Graft.h Exec_Help.h Exec_LoadCrd.h Exec_LoadTraj.h Exec_ParallelAnalysis.h Exec_ParmBox.h Exec_ParmSolvent.h Exec_ParmStrip.h Exec_ParmWrite.h Exec_PermuteDihedrals.h Exec_Precision.h Exec_PrepareForLeap.h Exec_PrintData.h Exec_ReadData.h Exec_ReadEnsembleData.h Exec_ReadInput.h Exec_RotateDihedral.h Exec_RunAnalysis.h Exec_ScaleDihedralK.h Exec_SequenceAlign.h Exec_Set.h Exec_Show.h Exec_SortEnsembleData.h Exec_SplitCoords.h Exec_System.h Exec_Top.h Exec_Traj.h Exec_UpdateParameters.h Exec_ViewRst.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h Grid.h GridAction.h GridBin.h HistBin.h Hungarian.h ImageTypes.h ImagedAction.h InputTrajCommon.h MapAtom.h MaskArray.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h NetcdfFile.h OnlineVarT.h OutputTrajCommon.h PDBfile.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h RPNcalc.h Random.h Range.h ReferenceAction.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h StructureCheck.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/GistCudaSetup.cuh molsurf.h ComplexArray.o : ComplexArray.cpp ArrayIterator.h ComplexArray.h -Constraints.o : Constraints.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h TypeNameHolder.h Vec3.h -ControlBlock_For.o : ControlBlock_For.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_dataSetBlocks.h ForLoop_integer.h ForLoop_list.h ForLoop_mask.h ForLoop_overSets.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h +Constraints.o : Constraints.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h +ControlBlock_For.o : ControlBlock_For.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_dataSetBlocks.h ForLoop_integer.h ForLoop_list.h ForLoop_mask.h ForLoop_overSets.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h CoordinateInfo.o : CoordinateInfo.cpp Box.h CoordinateInfo.h CpptrajStdio.h Matrix_3x3.h Parallel.h ReplicaDimArray.h Vec3.h Corr.o : Corr.cpp ArrayIterator.h ComplexArray.h Corr.h PubFFT.h Cph.o : Cph.cpp Cph.h NameType.h -Cpptraj.o : Cpptraj.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdInput.h CmdList.h Command.h Constants.h CoordinateInfo.h Cpptraj.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReadLine.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h TopInfo.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h Version.h +Cpptraj.o : Cpptraj.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdInput.h CmdList.h Command.h Constants.h CoordinateInfo.h Cpptraj.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReadLine.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h TopInfo.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h Version.h CpptrajFile.o : CpptrajFile.cpp CpptrajFile.h CpptrajStdio.h FileIO.h FileIO_Bzip2.h FileIO_Gzip.h FileIO_Mpi.h FileIO_MpiShared.h FileIO_Std.h FileName.h Parallel.h StringRoutines.h -CpptrajState.o : CpptrajState.cpp Action.h ActionList.h ActionState.h Action_CreateCrd.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleNavigator.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h +CpptrajState.o : CpptrajState.cpp Action.h ActionList.h ActionState.h Action_CreateCrd.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleNavigator.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h CpptrajStdio.o : CpptrajStdio.cpp Parallel.h CurveFit.o : CurveFit.cpp CurveFit.h -DataFile.o : DataFile.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h ClusterDist.h ClusterSieve.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataFile.h DataIO.h DataIO_CCP4.h DataIO_CharmmFastRep.h DataIO_CharmmOutput.h DataIO_CharmmRepLog.h DataIO_CharmmRtfPrm.h DataIO_Cmatrix.h DataIO_Cpout.h DataIO_Evecs.h DataIO_Gnuplot.h DataIO_Grace.h DataIO_Mdout.h DataIO_NC_Cmatrix.h DataIO_OpenDx.h DataIO_Peaks.h DataIO_RemLog.h DataIO_Std.h DataIO_VecTraj.h DataIO_XVG.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Cmatrix.h DataSet_Cmatrix_MEM.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Cmatrix.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TypeNameHolder.h Vec3.h -DataFileList.o : DataFileList.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -DataIO.o : DataIO.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -DataIO_CCP4.o : DataIO_CCP4.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ByteRoutines.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CCP4.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -DataIO_CharmmFastRep.o : DataIO_CharmmFastRep.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmFastRep.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -DataIO_CharmmOutput.o : DataIO_CharmmOutput.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmOutput.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -DataIO_CharmmRepLog.o : DataIO_CharmmRepLog.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmRepLog.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -DataIO_CharmmRtfPrm.o : DataIO_CharmmRtfPrm.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharmmParamFile.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmRtfPrm.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h DataSet_Topology.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -DataIO_Cmatrix.o : DataIO_Cmatrix.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h ClusterDist.h ClusterSieve.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Cmatrix.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Cmatrix.h DataSet_Cmatrix_MEM.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -DataIO_Cpout.o : DataIO_Cpout.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Cpout.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_pH.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -DataIO_Evecs.o : DataIO_Evecs.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Evecs.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -DataIO_Gnuplot.o : DataIO_Gnuplot.cpp ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Gnuplot.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -DataIO_Grace.o : DataIO_Grace.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Grace.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -DataIO_Mdout.o : DataIO_Mdout.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Mdout.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -DataIO_NC_Cmatrix.o : DataIO_NC_Cmatrix.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h ClusterDist.h ClusterSieve.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_NC_Cmatrix.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Cmatrix.h DataSet_Cmatrix_MEM.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Cmatrix.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -DataIO_OpenDx.o : DataIO_OpenDx.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_OpenDx.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridDbl.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -DataIO_Peaks.o : DataIO_Peaks.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Peaks.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector_Scalar.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -DataIO_RemLog.o : DataIO_RemLog.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_RemLog.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -DataIO_Std.o : DataIO_Std.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h ClusterDist.h ClusterSieve.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Std.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Cmatrix.h DataSet_Cmatrix_MEM.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -DataIO_VecTraj.o : DataIO_VecTraj.cpp ActionFrameCounter.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_VecTraj.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Vec3.h -DataIO_XVG.o : DataIO_XVG.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_XVG.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -DataIO_Xplor.o : DataIO_Xplor.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h +DataFile.o : DataFile.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h ClusterDist.h ClusterSieve.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataFile.h DataIO.h DataIO_CCP4.h DataIO_CharmmFastRep.h DataIO_CharmmOutput.h DataIO_CharmmRepLog.h DataIO_CharmmRtfPrm.h DataIO_Cmatrix.h DataIO_Cpout.h DataIO_Evecs.h DataIO_Gnuplot.h DataIO_Grace.h DataIO_Mdout.h DataIO_NC_Cmatrix.h DataIO_OpenDx.h DataIO_Peaks.h DataIO_RemLog.h DataIO_Std.h DataIO_VecTraj.h DataIO_XVG.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Cmatrix.h DataSet_Cmatrix_MEM.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Cmatrix.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TypeNameHolder.h Unit.h Vec3.h +DataFileList.o : DataFileList.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +DataIO.o : DataIO.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +DataIO_CCP4.o : DataIO_CCP4.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ByteRoutines.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CCP4.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +DataIO_CharmmFastRep.o : DataIO_CharmmFastRep.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmFastRep.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +DataIO_CharmmOutput.o : DataIO_CharmmOutput.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmOutput.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +DataIO_CharmmRepLog.o : DataIO_CharmmRepLog.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmRepLog.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +DataIO_CharmmRtfPrm.o : DataIO_CharmmRtfPrm.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharmmParamFile.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmRtfPrm.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h DataSet_Topology.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +DataIO_Cmatrix.o : DataIO_Cmatrix.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h ClusterDist.h ClusterSieve.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Cmatrix.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Cmatrix.h DataSet_Cmatrix_MEM.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +DataIO_Cpout.o : DataIO_Cpout.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Cpout.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_pH.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +DataIO_Evecs.o : DataIO_Evecs.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Evecs.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +DataIO_Gnuplot.o : DataIO_Gnuplot.cpp ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Gnuplot.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +DataIO_Grace.o : DataIO_Grace.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Grace.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +DataIO_Mdout.o : DataIO_Mdout.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Mdout.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +DataIO_NC_Cmatrix.o : DataIO_NC_Cmatrix.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h ClusterDist.h ClusterSieve.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_NC_Cmatrix.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Cmatrix.h DataSet_Cmatrix_MEM.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Cmatrix.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +DataIO_OpenDx.o : DataIO_OpenDx.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_OpenDx.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridDbl.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +DataIO_Peaks.o : DataIO_Peaks.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Peaks.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector_Scalar.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +DataIO_RemLog.o : DataIO_RemLog.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_RemLog.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +DataIO_Std.o : DataIO_Std.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h ClusterDist.h ClusterSieve.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Std.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Cmatrix.h DataSet_Cmatrix_MEM.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +DataIO_VecTraj.o : DataIO_VecTraj.cpp ActionFrameCounter.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_VecTraj.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h +DataIO_XVG.o : DataIO_XVG.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_XVG.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +DataIO_Xplor.o : DataIO_Xplor.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h DataSet.o : DataSet.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h -DataSetList.o : DataSetList.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h ClusterDist.h ClusterSieve.h ComplexArray.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Cmatrix.h DataSet_Cmatrix_DISK.h DataSet_Cmatrix_MEM.h DataSet_Cmatrix_NOMEM.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_GridDbl.h DataSet_GridFlt.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_Parameters.h DataSet_RemLog.h DataSet_StringVar.h DataSet_Tensor.h DataSet_Topology.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_disk.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h Hungarian.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Cmatrix.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h SymmetricTensor.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TypeNameHolder.h Vec3.h +DataSetList.o : DataSetList.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h ClusterDist.h ClusterSieve.h ComplexArray.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Cmatrix.h DataSet_Cmatrix_DISK.h DataSet_Cmatrix_MEM.h DataSet_Cmatrix_NOMEM.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_GridDbl.h DataSet_GridFlt.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_Parameters.h DataSet_RemLog.h DataSet_StringVar.h DataSet_Tensor.h DataSet_Topology.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_disk.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h Hungarian.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Cmatrix.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h SymmetricTensor.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TypeNameHolder.h Unit.h Vec3.h DataSet_1D.o : DataSet_1D.cpp ArrayIterator.h AssociatedData.h ComplexArray.h Constants.h Corr.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h PubFFT.h Range.h TextFormat.h DataSet_3D.o : DataSet_3D.cpp AssociatedData.h Box.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_3D.h Dimension.h FileIO.h FileName.h GridBin.h Matrix_3x3.h MetaData.h Parallel.h Range.h TextFormat.h Vec3.h -DataSet_Cmatrix.o : DataSet_Cmatrix.cpp ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h ClusterDist.h ClusterSieve.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_Cmatrix.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Topology.h TypeNameHolder.h Vec3.h -DataSet_Cmatrix_DISK.o : DataSet_Cmatrix_DISK.cpp ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h ClusterDist.h ClusterSieve.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_Cmatrix.h DataSet_Cmatrix_DISK.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Cmatrix.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Topology.h TypeNameHolder.h Vec3.h -DataSet_Cmatrix_MEM.o : DataSet_Cmatrix_MEM.cpp ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h ClusterDist.h ClusterSieve.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_Cmatrix.h DataSet_Cmatrix_MEM.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Topology.h TypeNameHolder.h Vec3.h -DataSet_Cmatrix_NOMEM.o : DataSet_Cmatrix_NOMEM.cpp ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h ClusterDist.h ClusterSieve.h Constants.h CoordinateInfo.h CpptrajFile.h DataSet.h DataSet_1D.h DataSet_Cmatrix.h DataSet_Cmatrix_NOMEM.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Topology.h TypeNameHolder.h Vec3.h -DataSet_Coords.o : DataSet_Coords.cpp AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Vec3.h -DataSet_Coords_CRD.o : DataSet_Coords_CRD.cpp AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_CRD.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Vec3.h -DataSet_Coords_REF.o : DataSet_Coords_REF.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Topology.h TrajFrameCounter.h Trajin.h Trajin_Single.h TypeNameHolder.h Vec3.h -DataSet_Coords_TRJ.o : DataSet_Coords_TRJ.cpp AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_TRJ.h Dimension.h FileIO.h FileName.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h Trajin_Single.h TypeNameHolder.h Vec3.h +DataSet_Cmatrix.o : DataSet_Cmatrix.cpp ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h ClusterDist.h ClusterSieve.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_Cmatrix.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h +DataSet_Cmatrix_DISK.o : DataSet_Cmatrix_DISK.cpp ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h ClusterDist.h ClusterSieve.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_Cmatrix.h DataSet_Cmatrix_DISK.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Cmatrix.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h +DataSet_Cmatrix_MEM.o : DataSet_Cmatrix_MEM.cpp ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h ClusterDist.h ClusterSieve.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_Cmatrix.h DataSet_Cmatrix_MEM.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h +DataSet_Cmatrix_NOMEM.o : DataSet_Cmatrix_NOMEM.cpp ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h ClusterDist.h ClusterSieve.h Constants.h CoordinateInfo.h CpptrajFile.h DataSet.h DataSet_1D.h DataSet_Cmatrix.h DataSet_Cmatrix_NOMEM.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h +DataSet_Coords.o : DataSet_Coords.cpp AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h +DataSet_Coords_CRD.o : DataSet_Coords_CRD.cpp AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_CRD.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h +DataSet_Coords_REF.o : DataSet_Coords_REF.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TrajFrameCounter.h Trajin.h Trajin_Single.h TypeNameHolder.h Unit.h Vec3.h +DataSet_Coords_TRJ.o : DataSet_Coords_TRJ.cpp AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_TRJ.h Dimension.h FileIO.h FileName.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h Trajin_Single.h TypeNameHolder.h Unit.h Vec3.h DataSet_GridDbl.o : DataSet_GridDbl.cpp ArrayIterator.h AssociatedData.h Box.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_3D.h DataSet_GridDbl.h Dimension.h FileIO.h FileName.h Grid.h GridBin.h Matrix_3x3.h MetaData.h Parallel.h Range.h StringRoutines.h TextFormat.h Vec3.h DataSet_GridFlt.o : DataSet_GridFlt.cpp ArrayIterator.h AssociatedData.h Box.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_3D.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Grid.h GridBin.h Matrix_3x3.h MetaData.h Parallel.h Range.h StringRoutines.h TextFormat.h Vec3.h DataSet_Mat3x3.o : DataSet_Mat3x3.cpp AssociatedData.h CpptrajFile.h DataSet.h DataSet_Mat3x3.h Dimension.h FileIO.h FileName.h Matrix_3x3.h MetaData.h Parallel.h Range.h TextFormat.h Vec3.h DataSet_MatrixDbl.o : DataSet_MatrixDbl.cpp ArrayIterator.h AssociatedData.h CpptrajFile.h DataSet.h DataSet_2D.h DataSet_MatrixDbl.h Dimension.h FileIO.h FileName.h Matrix.h MetaData.h Parallel.h Range.h TextFormat.h DataSet_MatrixFlt.o : DataSet_MatrixFlt.cpp ArrayIterator.h AssociatedData.h CpptrajFile.h DataSet.h DataSet_2D.h DataSet_MatrixFlt.h Dimension.h FileIO.h FileName.h Matrix.h MetaData.h Parallel.h Range.h TextFormat.h DataSet_Mesh.o : DataSet_Mesh.cpp AssociatedData.h Constants.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_Mesh.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h Spline.h TextFormat.h -DataSet_Modes.o : DataSet_Modes.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_2D.h DataSet_MatrixDbl.h DataSet_Modes.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Vec3.h +DataSet_Modes.o : DataSet_Modes.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_2D.h DataSet_MatrixDbl.h DataSet_Modes.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Unit.h Vec3.h DataSet_PHREMD_Explicit.o : DataSet_PHREMD_Explicit.cpp AssociatedData.h Cph.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h Dimension.h FileIO.h FileName.h MetaData.h NameType.h Parallel.h Range.h TextFormat.h DataSet_PHREMD_Implicit.o : DataSet_PHREMD_Implicit.cpp AssociatedData.h Cph.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_PHREMD.h DataSet_PHREMD_Implicit.h Dimension.h FileIO.h FileName.h MetaData.h NameType.h Parallel.h Range.h TextFormat.h DataSet_Parameters.o : DataSet_Parameters.cpp AssociatedData.h AtomType.h Constants.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h MetaData.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h TextFormat.h TypeNameHolder.h DataSet_RemLog.o : DataSet_RemLog.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h ReplicaDimArray.h TextFormat.h DataSet_StringVar.o : DataSet_StringVar.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_StringVar.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h DataSet_Tensor.o : DataSet_Tensor.cpp AssociatedData.h CpptrajFile.h DataSet.h DataSet_Tensor.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h SymmetricTensor.h TextFormat.h -DataSet_Topology.o : DataSet_Topology.cpp AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Topology.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Vec3.h +DataSet_Topology.o : DataSet_Topology.cpp AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Topology.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h DataSet_Vector.o : DataSet_Vector.cpp ArrayIterator.h AssociatedData.h ComplexArray.h Constants.h Corr.h CpptrajFile.h DataSet.h DataSet_1D.h DataSet_Vector.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h PubFFT.h Range.h SymbolExporting.h TextFormat.h Vec3.h DataSet_Vector_Scalar.o : DataSet_Vector_Scalar.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Vector_Scalar.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h Vec3.h DataSet_double.o : DataSet_double.cpp AssociatedData.h CpptrajFile.h DataSet.h DataSet_1D.h DataSet_double.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h @@ -228,68 +228,68 @@ DataSet_integer_mem.o : DataSet_integer_mem.cpp AssociatedData.h CpptrajFile.h D DataSet_pH.o : DataSet_pH.cpp AssociatedData.h Cph.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_pH.h Dimension.h FileIO.h FileName.h MetaData.h NameType.h Parallel.h Range.h TextFormat.h DataSet_string.o : DataSet_string.cpp AssociatedData.h CpptrajFile.h DataSet.h DataSet_string.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h Deprecated.o : Deprecated.cpp CpptrajStdio.h Deprecated.h DispatchObject.h -DihedralSearch.o : DihedralSearch.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DihedralSearch.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Vec3.h +DihedralSearch.o : DihedralSearch.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DihedralSearch.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h DistRoutines.o : DistRoutines.cpp Box.h DistRoutines.h Matrix_3x3.h Parallel.h Vec3.h -Energy.o : Energy.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h Energy.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Vec3.h +Energy.o : Energy.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h Energy.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h EnergyArray.o : EnergyArray.cpp CpptrajFile.h CpptrajStdio.h EnergyArray.h FileIO.h FileName.h Parallel.h -Energy_Sander.o : Energy_Sander.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy_Sander.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h TypeNameHolder.h Vec3.h -EnsembleIn.o : EnsembleIn.cpp Atom.h AtomMask.h Box.h CoordinateInfo.h CpptrajStdio.h EnsembleIn.h FileName.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h Timer.h TrajFrameCounter.h Vec3.h -EnsembleIn_Multi.o : EnsembleIn_Multi.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h EnsembleIn.h EnsembleIn_Multi.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryIO.h TypeNameHolder.h Vec3.h -EnsembleIn_Single.o : EnsembleIn_Single.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleIn.h EnsembleIn_Single.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Vec3.h -EnsembleNavigator.o : EnsembleNavigator.cpp Atom.h AtomMask.h Box.h CoordinateInfo.h CpptrajStdio.h EnsembleIn.h EnsembleNavigator.h FileName.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h Timer.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TrajinList.h Vec3.h +Energy_Sander.o : Energy_Sander.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy_Sander.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h +EnsembleIn.o : EnsembleIn.cpp Atom.h AtomMask.h Box.h CoordinateInfo.h CpptrajStdio.h EnsembleIn.h FileName.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h Timer.h TrajFrameCounter.h Unit.h Vec3.h +EnsembleIn_Multi.o : EnsembleIn_Multi.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h EnsembleIn.h EnsembleIn_Multi.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h +EnsembleIn_Single.o : EnsembleIn_Single.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleIn.h EnsembleIn_Single.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h +EnsembleNavigator.o : EnsembleNavigator.cpp Atom.h AtomMask.h Box.h CoordinateInfo.h CpptrajStdio.h EnsembleIn.h EnsembleNavigator.h FileName.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h Timer.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TrajinList.h Unit.h Vec3.h EnsembleOut.o : EnsembleOut.cpp ActionFrameCounter.h BaseIOtype.h Box.h CoordinateInfo.h CpptrajStdio.h EnsembleOut.h FileName.h FileTypes.h FramePtrArray.h Matrix_3x3.h OutputTrajCommon.h Parallel.h Range.h ReplicaDimArray.h TrajectoryFile.h Vec3.h -EnsembleOutList.o : EnsembleOutList.cpp ActionFrameCounter.h ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleOut.h EnsembleOutList.h EnsembleOut_Multi.h EnsembleOut_Single.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h TrajectoryFile.h TypeNameHolder.h Vec3.h -EnsembleOut_Multi.o : EnsembleOut_Multi.cpp ActionFrameCounter.h ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleOut.h EnsembleOut_Multi.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Vec3.h -EnsembleOut_Single.o : EnsembleOut_Single.cpp ActionFrameCounter.h ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleOut.h EnsembleOut_Single.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Vec3.h -Ewald.o : Ewald.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h EnergyKernel_Adjust.h EnergyKernel_Nonbond.h Ewald.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h PairListLoop.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Spline.h StringRoutines.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Ewald_ParticleMesh.o : Ewald_ParticleMesh.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Ewald.h Ewald_ParticleMesh.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Vec3.h helpme_standalone.h -Ewald_Regular.o : Ewald_Regular.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Ewald.h Ewald_Regular.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Exec_AddMissingRes.o : Exec_AddMissingRes.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_AddMissingRes.h Exec_AddMissingRes_Pres.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Vec3.h -Exec_Analyze.o : Exec_Analyze.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Analyze.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -Exec_Calc.o : Exec_Calc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Calc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CatCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -Exec_ClusterMap.o : Exec_ClusterMap.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ClusterMap.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ClusterMap.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -Exec_CombineCoords.o : Exec_CombineCoords.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CombineCoords.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -Exec_Commands.o : Exec_Commands.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Commands.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -Exec_CompareTop.o : Exec_CompareTop.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CompareTop.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -Exec_CrdAction.o : Exec_CrdAction.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CrdAction.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -Exec_CrdOut.o : Exec_CrdOut.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CrdOut.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Vec3.h -Exec_CreateSet.o : Exec_CreateSet.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CreateSet.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -Exec_DataFile.o : Exec_DataFile.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_DataFile.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -Exec_DataFilter.o : Exec_DataFilter.cpp Action.h ActionList.h ActionState.h Action_FilterByData.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_DataFilter.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -Exec_DataSetCmd.o : Exec_DataSetCmd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Vector.h DataSet_string.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_DataSetCmd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -Exec_Emin.o : Exec_Emin.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Emin.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -Exec_GenerateAmberRst.o : Exec_GenerateAmberRst.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_GenerateAmberRst.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -Exec_Graft.o : Exec_Graft.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Graft.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -Exec_Help.o : Exec_Help.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Help.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -Exec_LoadCrd.o : Exec_LoadCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_LoadCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h TypeNameHolder.h Vec3.h -Exec_LoadTraj.o : Exec_LoadTraj.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_LoadTraj.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -Exec_ParallelAnalysis.o : Exec_ParallelAnalysis.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParallelAnalysis.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -Exec_ParmBox.o : Exec_ParmBox.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmBox.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -Exec_ParmSolvent.o : Exec_ParmSolvent.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmSolvent.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -Exec_ParmStrip.o : Exec_ParmStrip.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmStrip.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -Exec_ParmWrite.o : Exec_ParmWrite.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmWrite.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -Exec_PermuteDihedrals.o : Exec_PermuteDihedrals.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h DistRoutines.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_PermuteDihedrals.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImagedAction.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Vec3.h -Exec_Precision.o : Exec_Precision.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Precision.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -Exec_PrepareForLeap.o : Exec_PrepareForLeap.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_PrepareForLeap.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -Exec_PrintData.o : Exec_PrintData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_PrintData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -Exec_ReadData.o : Exec_ReadData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ReadData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -Exec_ReadEnsembleData.o : Exec_ReadEnsembleData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ReadEnsembleData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -Exec_ReadInput.o : Exec_ReadInput.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ReadInput.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -Exec_RotateDihedral.o : Exec_RotateDihedral.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_RotateDihedral.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -Exec_RunAnalysis.o : Exec_RunAnalysis.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_RunAnalysis.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -Exec_ScaleDihedralK.o : Exec_ScaleDihedralK.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ScaleDihedralK.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -Exec_SequenceAlign.o : Exec_SequenceAlign.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SequenceAlign.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Vec3.h -Exec_Set.o : Exec_Set.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Set.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -Exec_Show.o : Exec_Show.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Show.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -Exec_SortEnsembleData.o : Exec_SortEnsembleData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_pH.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SortEnsembleData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -Exec_SplitCoords.o : Exec_SplitCoords.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SplitCoords.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -Exec_System.o : Exec_System.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_System.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -Exec_Top.o : Exec_Top.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Top.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h TopInfo.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -Exec_Traj.o : Exec_Traj.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Traj.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -Exec_UpdateParameters.o : Exec_UpdateParameters.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_UpdateParameters.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -Exec_ViewRst.o : Exec_ViewRst.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ViewRst.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h ViewRst.h +EnsembleOutList.o : EnsembleOutList.cpp ActionFrameCounter.h ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleOut.h EnsembleOutList.h EnsembleOut_Multi.h EnsembleOut_Single.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TrajectoryFile.h TypeNameHolder.h Unit.h Vec3.h +EnsembleOut_Multi.o : EnsembleOut_Multi.cpp ActionFrameCounter.h ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleOut.h EnsembleOut_Multi.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h +EnsembleOut_Single.o : EnsembleOut_Single.cpp ActionFrameCounter.h ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleOut.h EnsembleOut_Single.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h +Ewald.o : Ewald.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h EnergyKernel_Adjust.h EnergyKernel_Nonbond.h Ewald.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h PairListLoop.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Ewald_ParticleMesh.o : Ewald_ParticleMesh.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Ewald.h Ewald_ParticleMesh.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h helpme_standalone.h +Ewald_Regular.o : Ewald_Regular.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Ewald.h Ewald_Regular.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Exec_AddMissingRes.o : Exec_AddMissingRes.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_AddMissingRes.h Exec_AddMissingRes_Pres.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h +Exec_Analyze.o : Exec_Analyze.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Analyze.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +Exec_Calc.o : Exec_Calc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Calc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CatCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +Exec_ClusterMap.o : Exec_ClusterMap.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ClusterMap.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ClusterMap.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +Exec_CombineCoords.o : Exec_CombineCoords.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CombineCoords.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +Exec_Commands.o : Exec_Commands.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Commands.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +Exec_CompareTop.o : Exec_CompareTop.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CompareTop.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +Exec_CrdAction.o : Exec_CrdAction.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CrdAction.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +Exec_CrdOut.o : Exec_CrdOut.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CrdOut.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h +Exec_CreateSet.o : Exec_CreateSet.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CreateSet.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +Exec_DataFile.o : Exec_DataFile.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_DataFile.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +Exec_DataFilter.o : Exec_DataFilter.cpp Action.h ActionList.h ActionState.h Action_FilterByData.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_DataFilter.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +Exec_DataSetCmd.o : Exec_DataSetCmd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Vector.h DataSet_string.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_DataSetCmd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +Exec_Emin.o : Exec_Emin.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Emin.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +Exec_GenerateAmberRst.o : Exec_GenerateAmberRst.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_GenerateAmberRst.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +Exec_Graft.o : Exec_Graft.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Graft.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +Exec_Help.o : Exec_Help.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Help.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +Exec_LoadCrd.o : Exec_LoadCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_LoadCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +Exec_LoadTraj.o : Exec_LoadTraj.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_LoadTraj.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +Exec_ParallelAnalysis.o : Exec_ParallelAnalysis.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParallelAnalysis.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +Exec_ParmBox.o : Exec_ParmBox.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmBox.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +Exec_ParmSolvent.o : Exec_ParmSolvent.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmSolvent.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +Exec_ParmStrip.o : Exec_ParmStrip.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmStrip.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +Exec_ParmWrite.o : Exec_ParmWrite.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmWrite.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +Exec_PermuteDihedrals.o : Exec_PermuteDihedrals.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h DistRoutines.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_PermuteDihedrals.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImagedAction.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h +Exec_Precision.o : Exec_Precision.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Precision.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +Exec_PrepareForLeap.o : Exec_PrepareForLeap.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_PrepareForLeap.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +Exec_PrintData.o : Exec_PrintData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_PrintData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +Exec_ReadData.o : Exec_ReadData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ReadData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +Exec_ReadEnsembleData.o : Exec_ReadEnsembleData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ReadEnsembleData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +Exec_ReadInput.o : Exec_ReadInput.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ReadInput.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +Exec_RotateDihedral.o : Exec_RotateDihedral.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_RotateDihedral.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +Exec_RunAnalysis.o : Exec_RunAnalysis.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_RunAnalysis.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +Exec_ScaleDihedralK.o : Exec_ScaleDihedralK.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ScaleDihedralK.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +Exec_SequenceAlign.o : Exec_SequenceAlign.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SequenceAlign.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h +Exec_Set.o : Exec_Set.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Set.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +Exec_Show.o : Exec_Show.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Show.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +Exec_SortEnsembleData.o : Exec_SortEnsembleData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_pH.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SortEnsembleData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +Exec_SplitCoords.o : Exec_SplitCoords.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SplitCoords.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +Exec_System.o : Exec_System.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_System.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +Exec_Top.o : Exec_Top.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Top.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h TopInfo.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +Exec_Traj.o : Exec_Traj.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Traj.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +Exec_UpdateParameters.o : Exec_UpdateParameters.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_UpdateParameters.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +Exec_ViewRst.o : Exec_ViewRst.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ViewRst.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h ViewRst.h FileIO_Bzip2.o : FileIO_Bzip2.cpp CpptrajStdio.h FileIO.h FileIO_Bzip2.h FileIO_Gzip.o : FileIO_Gzip.cpp CpptrajStdio.h FileIO.h FileIO_Gzip.h FileIO_Mpi.o : FileIO_Mpi.cpp FileIO.h FileIO_Mpi.h Parallel.h @@ -299,107 +299,107 @@ FileName.o : FileName.cpp CpptrajStdio.h FileName.h StringRoutines.h FileType.o : FileType.cpp FileType.h FileTypes.o : FileTypes.cpp ArgList.h BaseIOtype.h CpptrajStdio.h FileTypes.h File_TempName.o : File_TempName.cpp CpptrajStdio.h FileName.h File_TempName.h StringRoutines.h -ForLoop.o : ForLoop.cpp AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h ForLoop.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h -ForLoop_dataSetBlocks.o : ForLoop_dataSetBlocks.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_dataSetBlocks.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -ForLoop_integer.o : ForLoop_integer.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_integer.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -ForLoop_list.o : ForLoop_list.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_list.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -ForLoop_mask.o : ForLoop_mask.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_mask.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -ForLoop_overSets.o : ForLoop_overSets.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_overSets.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -Frame.o : Frame.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h Residue.h SymbolExporting.h Vec3.h -GridAction.o : GridAction.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridAction.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h +ForLoop.o : ForLoop.cpp AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h ForLoop.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +ForLoop_dataSetBlocks.o : ForLoop_dataSetBlocks.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_dataSetBlocks.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +ForLoop_integer.o : ForLoop_integer.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_integer.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +ForLoop_list.o : ForLoop_list.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_list.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +ForLoop_mask.o : ForLoop_mask.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_mask.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +ForLoop_overSets.o : ForLoop_overSets.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_overSets.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +Frame.o : Frame.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Unit.h Vec3.h +GridAction.o : GridAction.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridAction.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h HistBin.o : HistBin.cpp Constants.h CpptrajStdio.h Dimension.h HistBin.h Hungarian.o : Hungarian.cpp ArrayIterator.h Constants.h CpptrajStdio.h Hungarian.h Matrix.h -ImageRoutines.o : ImageRoutines.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h DistRoutines.h FileName.h Frame.h ImageRoutines.h ImageTypes.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h TypeNameHolder.h Vec3.h +ImageRoutines.o : ImageRoutines.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h DistRoutines.h FileName.h Frame.h ImageRoutines.h ImageTypes.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h InputTrajCommon.o : InputTrajCommon.cpp CpptrajStdio.h FileName.h InputTrajCommon.h TrajFrameCounter.h KDE.o : KDE.cpp AssociatedData.h Constants.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_double.h Dimension.h FileIO.h FileName.h HistBin.h KDE.h MetaData.h Parallel.h Range.h TextFormat.h MapAtom.o : MapAtom.cpp Atom.h MapAtom.h NameType.h SymbolExporting.h -MaskArray.o : MaskArray.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h TypeNameHolder.h Vec3.h -MaskToken.o : MaskToken.cpp ArgList.h Atom.h Box.h CpptrajStdio.h DistRoutines.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h Residue.h StringRoutines.h SymbolExporting.h Vec3.h +MaskArray.o : MaskArray.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h +MaskToken.o : MaskToken.cpp ArgList.h Atom.h Box.h CpptrajStdio.h DistRoutines.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Unit.h Vec3.h Matrix_3x3.o : Matrix_3x3.cpp Constants.h CpptrajStdio.h Matrix_3x3.h Vec3.h MetaData.o : MetaData.cpp CpptrajStdio.h FileName.h MetaData.h Range.h StringRoutines.h -Minimize_SteepestDescent.o : Minimize_SteepestDescent.cpp ActionFrameCounter.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h EnergyArray.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Vec3.h -Mol.o : Mol.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Mol.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h TypeNameHolder.h Vec3.h +Minimize_SteepestDescent.o : Minimize_SteepestDescent.cpp ActionFrameCounter.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h EnergyArray.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h +Mol.o : Mol.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Mol.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h Mol2File.o : Mol2File.cpp Atom.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Mol2File.h NameType.h Parallel.h Residue.h StringRoutines.h SymbolExporting.h NC_Cmatrix.o : NC_Cmatrix.cpp CpptrajStdio.h FileName.h NC_Cmatrix.h NC_Routines.h NC_Routines.o : NC_Routines.cpp CpptrajStdio.h NC_Routines.h NameType.o : NameType.cpp CpptrajStdio.h NameType.h -NetcdfFile.o : NetcdfFile.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h ParallelNetcdf.h ReplicaDimArray.h Residue.h SymbolExporting.h Vec3.h Version.h -OutputTrajCommon.o : OutputTrajCommon.cpp ActionFrameCounter.h ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Vec3.h +NetcdfFile.o : NetcdfFile.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h ParallelNetcdf.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Unit.h Vec3.h Version.h +OutputTrajCommon.o : OutputTrajCommon.cpp ActionFrameCounter.h ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h PDBfile.o : PDBfile.cpp Atom.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h PDBfile.h Parallel.h Residue.h SymbolExporting.h -PairList.o : PairList.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Vec3.h +PairList.o : PairList.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h Parallel.o : Parallel.cpp Parallel.h ParallelNetcdf.o : ParallelNetcdf.cpp CpptrajStdio.h Parallel.h ParallelNetcdf.h ParameterSet.o : ParameterSet.cpp AtomType.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h TypeNameHolder.h UpdateParameters.h -ParmFile.o : ParmFile.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h ParmIO.h Parm_Amber.h Parm_CIF.h Parm_CharmmPsf.h Parm_Gromacs.h Parm_Mol2.h Parm_PDB.h Parm_SDF.h Parm_Tinker.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Vec3.h -Parm_Amber.o : Parm_Amber.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_Amber.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Vec3.h -Parm_CIF.o : Parm_CIF.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h CIFfile.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_CIF.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Vec3.h -Parm_CharmmPsf.o : Parm_CharmmPsf.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h CharmmParamFile.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Mol.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_CharmmPsf.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Vec3.h -Parm_Gromacs.o : Parm_Gromacs.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_Gromacs.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Vec3.h -Parm_Mol2.o : Parm_Mol2.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Mol2File.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_Mol2.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h TypeNameHolder.h Vec3.h -Parm_PDB.o : Parm_PDB.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_PDB.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Vec3.h -Parm_SDF.o : Parm_SDF.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_SDF.h Range.h ReplicaDimArray.h Residue.h SDFfile.h SymbolExporting.h Topology.h TypeNameHolder.h Vec3.h -Parm_Tinker.o : Parm_Tinker.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_Tinker.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h TinkerFile.h Topology.h TypeNameHolder.h Vec3.h -PotentialFunction.o : PotentialFunction.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h EnergyArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PotentialFunction.h PotentialTerm.h PotentialTerm_Bond.h PotentialTerm_LJ_Coulomb.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h TypeNameHolder.h Vec3.h -PotentialTerm_Bond.o : PotentialTerm_Bond.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h EnergyArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PotentialTerm.h PotentialTerm_Bond.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h TypeNameHolder.h Vec3.h -PotentialTerm_LJ_Coulomb.o : PotentialTerm_LJ_Coulomb.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h EnergyArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PotentialTerm.h PotentialTerm_LJ_Coulomb.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h TypeNameHolder.h Vec3.h +ParmFile.o : ParmFile.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h ParmIO.h Parm_Amber.h Parm_CIF.h Parm_CharmmPsf.h Parm_Gromacs.h Parm_Mol2.h Parm_PDB.h Parm_SDF.h Parm_Tinker.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Parm_Amber.o : Parm_Amber.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_Amber.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Parm_CIF.o : Parm_CIF.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h CIFfile.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_CIF.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Parm_CharmmPsf.o : Parm_CharmmPsf.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h CharmmParamFile.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Mol.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_CharmmPsf.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Parm_Gromacs.o : Parm_Gromacs.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_Gromacs.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Parm_Mol2.o : Parm_Mol2.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Mol2File.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_Mol2.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Parm_PDB.o : Parm_PDB.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_PDB.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Parm_SDF.o : Parm_SDF.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_SDF.h Range.h ReplicaDimArray.h Residue.h SDFfile.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Parm_Tinker.o : Parm_Tinker.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmIO.h Parm_Tinker.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TinkerFile.h Topology.h TypeNameHolder.h Unit.h Vec3.h +PotentialFunction.o : PotentialFunction.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h EnergyArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PotentialFunction.h PotentialTerm.h PotentialTerm_Bond.h PotentialTerm_LJ_Coulomb.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h +PotentialTerm_Bond.o : PotentialTerm_Bond.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h EnergyArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PotentialTerm.h PotentialTerm_Bond.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h +PotentialTerm_LJ_Coulomb.o : PotentialTerm_LJ_Coulomb.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h EnergyArray.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PotentialTerm.h PotentialTerm_LJ_Coulomb.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h ProgressBar.o : ProgressBar.cpp CpptrajStdio.h ProgressBar.h ProgressTimer.o : ProgressTimer.cpp CpptrajStdio.h ProgressTimer.h Timer.h PubFFT.o : PubFFT.cpp ArrayIterator.h ComplexArray.h CpptrajStdio.h PubFFT.h -RPNcalc.o : RPNcalc.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_Vector.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h +RPNcalc.o : RPNcalc.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_Vector.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h Random.o : Random.cpp CpptrajStdio.h Random.h Range.o : Range.cpp ArgList.h CpptrajStdio.h Range.h -ReadLine.o : ReadLine.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdInput.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReadLine.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h -ReferenceAction.o : ReferenceAction.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h Dimension.h FileIO.h FileName.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TypeNameHolder.h Vec3.h -RemdReservoirNC.o : RemdReservoirNC.cpp Atom.h AtomMask.h Box.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h RemdReservoirNC.h ReplicaDimArray.h Residue.h SymbolExporting.h Vec3.h +ReadLine.o : ReadLine.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdInput.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReadLine.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h +ReferenceAction.o : ReferenceAction.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h Dimension.h FileIO.h FileName.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TypeNameHolder.h Unit.h Vec3.h +RemdReservoirNC.o : RemdReservoirNC.cpp Atom.h AtomMask.h Box.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h RemdReservoirNC.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Unit.h Vec3.h Residue.o : Residue.cpp NameType.h Residue.h SDFfile.o : SDFfile.cpp Atom.h CpptrajFile.h FileIO.h FileName.h NameType.h Parallel.h SDFfile.h StringRoutines.h SymbolExporting.h SimplexMin.o : SimplexMin.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Random.h Range.h SimplexMin.h TextFormat.h SpaceGroup.o : SpaceGroup.cpp Matrix_3x3.h SpaceGroup.h Vec3.h Spline.o : Spline.cpp CpptrajStdio.h Spline.h StringRoutines.o : StringRoutines.cpp CpptrajStdio.h StringRoutines.h -StructureCheck.o : StructureCheck.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StructureCheck.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Vec3.h -StructureMapper.o : StructureMapper.cpp AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StructureMapper.h SymbolExporting.h TextFormat.h Topology.h TorsionRoutines.h TypeNameHolder.h Vec3.h -SymmetricRmsdCalc.o : SymmetricRmsdCalc.cpp ArrayIterator.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h SymmetricRmsdCalc.h Topology.h TypeNameHolder.h Vec3.h +StructureCheck.o : StructureCheck.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StructureCheck.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +StructureMapper.o : StructureMapper.cpp AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StructureMapper.h SymbolExporting.h TextFormat.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h +SymmetricRmsdCalc.o : SymmetricRmsdCalc.cpp ArrayIterator.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h Topology.h TypeNameHolder.h Unit.h Vec3.h TextFormat.o : TextFormat.cpp StringRoutines.h TextFormat.h Timer.o : Timer.cpp CpptrajStdio.h Timer.h -TinkerFile.o : TinkerFile.cpp ArgList.h Atom.h AtomMask.h Box.h BufferedLine.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TinkerFile.h Vec3.h -TopInfo.o : TopInfo.cpp AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h DistRoutines.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Mol.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h TopInfo.h Topology.h TorsionRoutines.h TypeNameHolder.h Vec3.h -Topology.o : Topology.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h UpdateParameters.h Vec3.h +TinkerFile.o : TinkerFile.cpp ArgList.h Atom.h AtomMask.h Box.h BufferedLine.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TinkerFile.h Unit.h Vec3.h +TopInfo.o : TopInfo.cpp AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h DistRoutines.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Mol.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h TopInfo.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h +Topology.o : Topology.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h UpdateParameters.h Vec3.h TorsionRoutines.o : TorsionRoutines.cpp Constants.h TorsionRoutines.h Vec3.h TrajFrameCounter.o : TrajFrameCounter.cpp ArgList.h CpptrajStdio.h TrajFrameCounter.h -TrajIOarray.o : TrajIOarray.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Vec3.h -Traj_AmberCoord.o : Traj_AmberCoord.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Topology.h Traj_AmberCoord.h TrajectoryIO.h TypeNameHolder.h Vec3.h -Traj_AmberNetcdf.o : Traj_AmberNetcdf.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h ParallelNetcdf.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h Traj_AmberNetcdf.h TrajectoryIO.h TypeNameHolder.h Vec3.h -Traj_AmberRestart.o : Traj_AmberRestart.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Traj_AmberRestart.h TrajectoryIO.h TypeNameHolder.h Vec3.h -Traj_AmberRestartNC.o : Traj_AmberRestartNC.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h Topology.h Traj_AmberRestartNC.h TrajectoryIO.h TypeNameHolder.h Vec3.h -Traj_Binpos.o : Traj_Binpos.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h Traj_Binpos.h TrajectoryIO.h TypeNameHolder.h Vec3.h -Traj_CIF.o : Traj_CIF.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CIFfile.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h Topology.h Traj_CIF.h TrajectoryIO.h TypeNameHolder.h Vec3.h -Traj_CharmmCor.o : Traj_CharmmCor.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h Topology.h Traj_CharmmCor.h TrajectoryIO.h TypeNameHolder.h Vec3.h -Traj_CharmmDcd.o : Traj_CharmmDcd.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ByteRoutines.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h Traj_CharmmDcd.h TrajectoryIO.h TypeNameHolder.h Vec3.h -Traj_CharmmRestart.o : Traj_CharmmRestart.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedFrame.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Traj_CharmmRestart.h TrajectoryIO.h TypeNameHolder.h Vec3.h -Traj_Conflib.o : Traj_Conflib.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h Traj_Conflib.h TrajectoryIO.h TypeNameHolder.h Vec3.h -Traj_DTR.o : Traj_DTR.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h Traj_DTR.h TrajectoryIO.h TypeNameHolder.h Vec3.h vmdplugin/dtrplugin.hxx -Traj_GmxDump.o : Traj_GmxDump.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h Traj_GmxDump.h TrajectoryIO.h TypeNameHolder.h Vec3.h -Traj_GmxTng.o : Traj_GmxTng.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h Traj_GmxTng.h TrajectoryIO.h TypeNameHolder.h Vec3.h -Traj_GmxTrX.o : Traj_GmxTrX.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ByteRoutines.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h Traj_GmxTrX.h TrajectoryIO.h TypeNameHolder.h Vec3.h -Traj_GmxXtc.o : Traj_GmxXtc.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h Traj_GmxXtc.h TrajectoryIO.h TypeNameHolder.h Vec3.h -Traj_Gro.o : Traj_Gro.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h Topology.h Traj_Gro.h TrajectoryIO.h TypeNameHolder.h Vec3.h -Traj_Mol2File.o : Traj_Mol2File.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Mol2File.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h Traj_Mol2File.h TrajectoryIO.h TypeNameHolder.h Vec3.h -Traj_NcEnsemble.o : Traj_NcEnsemble.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FrameArray.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h ParallelNetcdf.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h Traj_NcEnsemble.h TrajectoryIO.h TypeNameHolder.h Vec3.h -Traj_PDBfile.o : Traj_PDBfile.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Tensor.h Dimension.h DistRoutines.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h SymmetricTensor.h TextFormat.h Timer.h Topology.h Traj_PDBfile.h TrajectoryIO.h TypeNameHolder.h Vec3.h -Traj_SDF.o : Traj_SDF.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SDFfile.h SymbolExporting.h Topology.h Traj_SDF.h TrajectoryIO.h TypeNameHolder.h Vec3.h -Traj_SQM.o : Traj_SQM.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h Topology.h Traj_SQM.h TrajectoryIO.h TypeNameHolder.h Vec3.h -Traj_Tinker.o : Traj_Tinker.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h TinkerFile.h Topology.h Traj_Tinker.h TrajectoryIO.h TypeNameHolder.h Vec3.h -Traj_XYZ.o : Traj_XYZ.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Traj_XYZ.h TrajectoryIO.h TypeNameHolder.h Vec3.h -TrajectoryFile.o : TrajectoryFile.cpp Atom.h AtomMask.h BaseIOtype.h Box.h BufferedFrame.h BufferedLine.h CIFfile.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Mol2File.h Molecule.h NameType.h NetcdfFile.h PDBfile.h Parallel.h ReplicaDimArray.h Residue.h SDFfile.h SymbolExporting.h TextFormat.h TinkerFile.h Traj_AmberCoord.h Traj_AmberNetcdf.h Traj_AmberRestart.h Traj_AmberRestartNC.h Traj_Binpos.h Traj_CIF.h Traj_CharmmCor.h Traj_CharmmDcd.h Traj_CharmmRestart.h Traj_Conflib.h Traj_DTR.h Traj_GmxDump.h Traj_GmxTng.h Traj_GmxTrX.h Traj_GmxXtc.h Traj_Gro.h Traj_Mol2File.h Traj_NcEnsemble.h Traj_PDBfile.h Traj_SDF.h Traj_SQM.h Traj_Tinker.h Traj_XYZ.h TrajectoryFile.h TrajectoryIO.h Vec3.h +TrajIOarray.o : TrajIOarray.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h +Traj_AmberCoord.o : Traj_AmberCoord.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h Traj_AmberCoord.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h +Traj_AmberNetcdf.o : Traj_AmberNetcdf.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h ParallelNetcdf.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_AmberNetcdf.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h +Traj_AmberRestart.o : Traj_AmberRestart.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedFrame.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Traj_AmberRestart.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h +Traj_AmberRestartNC.o : Traj_AmberRestartNC.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_AmberRestartNC.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h +Traj_Binpos.o : Traj_Binpos.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_Binpos.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h +Traj_CIF.o : Traj_CIF.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CIFfile.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_CIF.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h +Traj_CharmmCor.o : Traj_CharmmCor.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_CharmmCor.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h +Traj_CharmmDcd.o : Traj_CharmmDcd.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ByteRoutines.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_CharmmDcd.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h +Traj_CharmmRestart.o : Traj_CharmmRestart.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedFrame.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Traj_CharmmRestart.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h +Traj_Conflib.o : Traj_Conflib.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_Conflib.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h +Traj_DTR.o : Traj_DTR.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_DTR.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h vmdplugin/dtrplugin.hxx +Traj_GmxDump.o : Traj_GmxDump.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_GmxDump.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h +Traj_GmxTng.o : Traj_GmxTng.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_GmxTng.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h +Traj_GmxTrX.o : Traj_GmxTrX.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ByteRoutines.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_GmxTrX.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h +Traj_GmxXtc.o : Traj_GmxXtc.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_GmxXtc.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h +Traj_Gro.o : Traj_Gro.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_Gro.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h +Traj_Mol2File.o : Traj_Mol2File.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Mol2File.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_Mol2File.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h +Traj_NcEnsemble.o : Traj_NcEnsemble.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FrameArray.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h ParallelNetcdf.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Traj_NcEnsemble.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h +Traj_PDBfile.o : Traj_PDBfile.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Tensor.h Dimension.h DistRoutines.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricTensor.h TextFormat.h Timer.h Topology.h Traj_PDBfile.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h +Traj_SDF.o : Traj_SDF.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SDFfile.h Segment.h SymbolExporting.h Topology.h Traj_SDF.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h +Traj_SQM.o : Traj_SQM.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Traj_SQM.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h +Traj_Tinker.o : Traj_Tinker.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TinkerFile.h Topology.h Traj_Tinker.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h +Traj_XYZ.o : Traj_XYZ.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Traj_XYZ.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h +TrajectoryFile.o : TrajectoryFile.cpp Atom.h AtomMask.h BaseIOtype.h Box.h BufferedFrame.h BufferedLine.h CIFfile.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Mol2File.h Molecule.h NameType.h NetcdfFile.h PDBfile.h Parallel.h ReplicaDimArray.h Residue.h SDFfile.h Segment.h SymbolExporting.h TextFormat.h TinkerFile.h Traj_AmberCoord.h Traj_AmberNetcdf.h Traj_AmberRestart.h Traj_AmberRestartNC.h Traj_Binpos.h Traj_CIF.h Traj_CharmmCor.h Traj_CharmmDcd.h Traj_CharmmRestart.h Traj_Conflib.h Traj_DTR.h Traj_GmxDump.h Traj_GmxTng.h Traj_GmxTrX.h Traj_GmxXtc.h Traj_Gro.h Traj_Mol2File.h Traj_NcEnsemble.h Traj_PDBfile.h Traj_SDF.h Traj_SQM.h Traj_Tinker.h Traj_XYZ.h TrajectoryFile.h TrajectoryIO.h Unit.h Vec3.h TrajectoryIO.o : TrajectoryIO.cpp BaseIOtype.h Box.h CoordinateInfo.h FramePtrArray.h Matrix_3x3.h Parallel.h ReplicaDimArray.h TrajectoryIO.h Vec3.h -TrajinList.o : TrajinList.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_RemLog.h Dimension.h EnsembleIn.h EnsembleIn_Multi.h EnsembleIn_Single.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h ReplicaInfo.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h Trajin_Multi.h Trajin_Single.h TypeNameHolder.h Vec3.h -Trajin_Multi.o : Trajin_Multi.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h ReplicaInfo.h Residue.h StringRoutines.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryIO.h Trajin.h Trajin_Multi.h TypeNameHolder.h Vec3.h -Trajin_Single.o : Trajin_Single.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Trajin.h Trajin_Single.h TypeNameHolder.h Vec3.h -TrajoutList.o : TrajoutList.cpp ActionFrameCounter.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Vec3.h -Trajout_Single.o : Trajout_Single.cpp ActionFrameCounter.h ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h Trajout_Single.h TypeNameHolder.h Vec3.h +TrajinList.o : TrajinList.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_RemLog.h Dimension.h EnsembleIn.h EnsembleIn_Multi.h EnsembleIn_Single.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h Trajin_Multi.h Trajin_Single.h TypeNameHolder.h Unit.h Vec3.h +Trajin_Multi.o : Trajin_Multi.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryIO.h Trajin.h Trajin_Multi.h TypeNameHolder.h Unit.h Vec3.h +Trajin_Single.o : Trajin_Single.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Trajin.h Trajin_Single.h TypeNameHolder.h Unit.h Vec3.h +TrajoutList.o : TrajoutList.cpp ActionFrameCounter.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h +Trajout_Single.o : Trajout_Single.cpp ActionFrameCounter.h ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h Vec3.o : Vec3.cpp Constants.h CpptrajStdio.h Vec3.h -ViewRst.o : ViewRst.cpp ActionFrameCounter.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Vec3.h ViewRst.h -main.o : main.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h Cpptraj.h CpptrajFile.h CpptrajState.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h +ViewRst.o : ViewRst.cpp ActionFrameCounter.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h ViewRst.h +main.o : main.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h Cpptraj.h CpptrajFile.h CpptrajState.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h molsurf.o : molsurf.c molsurf.h vmdplugin/dtrplugin.o : vmdplugin/dtrplugin.cpp vmdplugin/../ByteRoutines.h vmdplugin/dtrplugin.hxx vmdplugin/vmddir.h From 6fd80c0aba56aef622759949b3df4060548cf07b Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Sun, 6 Sep 2020 07:25:41 -0400 Subject: [PATCH 05/65] Report non-contiguous molecules as a warning --- src/Topology.cpp | 22 +++++++++++++++++++++- 1 file changed, 21 insertions(+), 1 deletion(-) diff --git a/src/Topology.cpp b/src/Topology.cpp index 99f4e8f995..7801442f45 100644 --- a/src/Topology.cpp +++ b/src/Topology.cpp @@ -997,6 +997,10 @@ int Topology::DetermineMolecules() { numberOfMolecules = NonrecursiveMolSearch(); else numberOfMolecules = RecursiveMolSearch(); + if (numberOfMolecules < 1) { + mprinterr("Internal Error: Could not determine molecules.\n"); + return 1; + } /*// DEBUG Compare both methods int test_nmol = NonrecursiveMolSearch(); std::vector molNums( atoms_.size() ); @@ -1027,16 +1031,32 @@ int Topology::DetermineMolecules() { molecules_[atom.MolNum()].ModifyUnit().AddIndex( atomIdx ); } mprintf("Molecule information:\n"); + std::vector< std::vector::const_iterator > nonContiguousMols; for (std::vector::const_iterator mol = molecules_.begin(); mol != molecules_.end(); ++mol) { + if (mol->MolUnit().nSegments() > 1) + nonContiguousMols.push_back( mol ); mprintf("\t%8li %8u segments:", mol - molecules_.begin(), mol->MolUnit().nSegments()); for (Unit::const_iterator seg = mol->MolUnit().segBegin(); seg != mol->MolUnit().segEnd(); ++seg) mprintf(" %i-%i (%i) ", seg->Begin(), seg->End(), seg->Size()); mprintf("\n"); } + if (!nonContiguousMols.empty()) { + mprintf("Warning: %zu molecules have non-contiguous segments of atoms.\n", nonContiguousMols.size()); + for (std::vector< std::vector::const_iterator >::const_iterator it = nonContiguousMols.begin(); + it != nonContiguousMols.end(); ++it) + { + mprintf("\t%8li %8u segments:", *it - molecules_.begin() + 1, (*it)->MolUnit().nSegments()); + for (Unit::const_iterator seg = (*it)->MolUnit().segBegin(); + seg != (*it)->MolUnit().segEnd(); ++seg) + mprintf(" %i-%i (%i) ", seg->Begin()+1, seg->End(), seg->Size()); + mprintf("\n"); + } + mprintf("Warning: The 'fixatomorder' command can be used to reorder the topology and any\n" + "Warning: associated coordinates.\n"); + } - if (numberOfMolecules == 0) return 0; std::vector::iterator molecule = molecules_.begin(); molecule->SetFirst(0); std::vector::const_iterator atom = atoms_.begin(); From 2c43119de59ff8146dc9b4f72517b81ccdd0f3ba Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Sun, 6 Sep 2020 09:48:26 -0400 Subject: [PATCH 06/65] Start removing begin/end atom for molecule --- src/Action_AreaPerMol.cpp | 2 +- src/CharMask.cpp | 8 ++++++++ src/CharMask.h | 3 +++ src/Molecule.h | 27 ++++++++------------------- src/Unit.h | 10 +++++++++- 5 files changed, 29 insertions(+), 21 deletions(-) diff --git a/src/Action_AreaPerMol.cpp b/src/Action_AreaPerMol.cpp index a7be12eec9..3d045de4b7 100644 --- a/src/Action_AreaPerMol.cpp +++ b/src/Action_AreaPerMol.cpp @@ -77,7 +77,7 @@ Action::RetType Action_AreaPerMol::Setup(ActionSetup& setup) { for (Topology::mol_iterator mol = setup.Top().MolStart(); mol != setup.Top().MolEnd(); ++mol) { - if (Mask1_.AtomsInCharMask(mol->BeginAtom(), mol->EndAtom())) + if (Mask1_.AtomsInCharMask(mol->MolUnit())) Nmols_ += 1.0; } mprintf("\tMask '%s' selects %.0f molecules.\n", Mask1_.MaskString(), Nmols_); diff --git a/src/CharMask.cpp b/src/CharMask.cpp index e230b36ea1..a90b9a4372 100644 --- a/src/CharMask.cpp +++ b/src/CharMask.cpp @@ -1,5 +1,6 @@ #include "CharMask.h" #include "CpptrajStdio.h" // PrintMaskAtoms +#include "Unit.h" /** Use to initialize the mask without a mask expression. */ void CharMask::InitCharMask(int natoms, bool initSelected) { @@ -83,6 +84,13 @@ bool CharMask::AtomsInCharMask(int startatom, int endatom) const { return false; } +// AtomsInCharMask() +bool CharMask::AtomsInCharMask(Unit const& unitIn) const { + for (Unit::const_iterator it = unitIn.segBegin(); it != unitIn.segEnd(); ++it) + if (AtomsInCharMask(it->Begin(), it->End())) return true; + return false; +} + /** This routine can be used to convert a CharMask to an AtomMask, e.g. * AtomMask mask( CharMask.ConvertToIntMask(), CharMask.Natom() ) */ diff --git a/src/CharMask.h b/src/CharMask.h index 02f6755fd5..fc73986a40 100644 --- a/src/CharMask.h +++ b/src/CharMask.h @@ -1,6 +1,7 @@ #ifndef INC_CHARMASK_H #define INC_CHARMASK_H #include "MaskToken.h" +class Unit; /// Atom mask using character array. /** This is the original way to use the atom mask, useful e.g. when * you need to know what atoms are not selected as well as what atoms @@ -23,6 +24,8 @@ class CharMask : public MaskTokenArray { bool AtomInCharMask(int) const; /// \return true if any atoms within given range are selected. bool AtomsInCharMask(int,int) const; + /// \return true if any atoms of the unit are selected. + bool AtomsInCharMask(Unit const&) const; /// \return Integer array of selected atoms. std::vector ConvertToIntMask() const; /// \return size of char mask diff --git a/src/Molecule.h b/src/Molecule.h index fb67139262..31e780a612 100644 --- a/src/Molecule.h +++ b/src/Molecule.h @@ -5,29 +5,18 @@ /// Hold information for a molecule class Molecule { public: - Molecule() : beginAtom_(0), endAtom_(0), isSolvent_(false) {} - Molecule(int begin, int end) : - beginAtom_(begin), - endAtom_(end), - isSolvent_(false) - {} + Molecule() : isSolvent_(false) {} - void SetFirst(int begin) { beginAtom_ = begin; } - void SetLast(int last) { endAtom_ = last; } - void SetSolvent() { isSolvent_ = true; } - void SetNoSolvent() { isSolvent_ = false; } - Unit& ModifyUnit() { return unit_; } + void SetSolvent() { isSolvent_ = true; } + void SetNoSolvent() { isSolvent_ = false; } + Unit& ModifyUnit() { return unit_; } - inline int BeginAtom() const { return beginAtom_; } - inline int EndAtom() const { return endAtom_; } - inline bool IsSolvent() const { return isSolvent_; } - inline int NumAtoms() const { return (endAtom_ - beginAtom_); } - Unit const& MolUnit() const { return unit_; } + bool IsSolvent() const { return isSolvent_; } + unsigned int NumAtoms() const { return unit_.Size(); } + Unit const& MolUnit() const { return unit_; } private: - int beginAtom_; - int endAtom_; bool isSolvent_; - Unit unit_; ///< Hold all molecule segments. + Unit unit_; ///< Hold all molecule segments. }; #endif diff --git a/src/Unit.h b/src/Unit.h index 711f146bf2..ef432bc0e5 100644 --- a/src/Unit.h +++ b/src/Unit.h @@ -5,6 +5,7 @@ //namespace Cpptraj { /// Hold 1 or more contiguous segments of atoms class Unit { + typedef std::vector SegArrayType; public: /// CONSTRUCTOR - Set last index to large negative so first AddIndex() call creates a Segment Unit() : lastIdx_(-9999) {} @@ -14,6 +15,14 @@ class Unit { const_iterator segEnd() const { return segArray_.end(); } unsigned int nSegments() const { return segArray_.size(); } + /// \return Total unit size + unsigned int Size() const { + unsigned int total = 0; + for (SegArrayType::const_iterator it = segArray_.begin(); it != segArray_.end(); ++it) + total += it->Size(); + return total; + } + /// Add index to the unit int AddIndex(int idx) { int delta = idx - lastIdx_; @@ -27,7 +36,6 @@ class Unit { return 0; } private: - typedef std::vector SegArrayType; SegArrayType segArray_; ///< Array of segments that make up the Unit int lastIdx_; ///< The last index added to the Unit }; From df5f3608af4426eb0f542a47b81d021e10ef62b7 Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Sun, 6 Sep 2020 10:11:43 -0400 Subject: [PATCH 07/65] Start converting imaging routines to use Unit --- src/Action_AutoImage.cpp | 50 +++++++++++++++------------------------- src/Action_AutoImage.h | 9 ++++---- src/AtomMask.cpp | 7 ++++++ src/AtomMask.h | 3 +++ src/Unit.h | 3 +++ 5 files changed, 36 insertions(+), 36 deletions(-) diff --git a/src/Action_AutoImage.cpp b/src/Action_AutoImage.cpp index af50e65c89..f83f9f4196 100644 --- a/src/Action_AutoImage.cpp +++ b/src/Action_AutoImage.cpp @@ -4,6 +4,7 @@ #include "DistRoutines.h" #include "ImageRoutines.h" #include "CharMask.h" +#include "Unit.h" // CONSTRUCTOR Action_AutoImage::Action_AutoImage() : @@ -78,35 +79,23 @@ Action::RetType Action_AutoImage::Init(ArgList& actionArgs, ActionInit& init, in /** Based on the given atom mask expression determine what molecules are * selected by the mask. If a mask selects any part of a molecule the * entire molecule will be selected. - * \return A list of atom pairs that mark the beginning and end of each - * selected molecule. + * \return A list of Units for each selected molecule. */ -Action_AutoImage::pairList +Action_AutoImage::Uarray Action_AutoImage::SetupAtomRanges(Topology const& currentParm, std::string const& maskexpr) { - pairList imageList; + Uarray imageList; CharMask Mask1( maskexpr.c_str() ); if (currentParm.SetupCharMask( Mask1 )) return imageList; if (Mask1.None()) return imageList; for (Topology::mol_iterator mol = currentParm.MolStart(); mol != currentParm.MolEnd(); mol++) { - int firstAtom = mol->BeginAtom(); - int lastAtom = mol->EndAtom(); - bool rangeIsValid = false; // Check that any atom in the range is in Mask1 - for (int atom = firstAtom; atom < lastAtom; ++atom) { - if (Mask1.AtomInCharMask(atom)) { - rangeIsValid = true; - break; - } - } - if (rangeIsValid) { - imageList.push_back( firstAtom ); - imageList.push_back( lastAtom ); - } + if (Mask1.AtomsInCharMask(mol->MolUnit())) + imageList.push_back( mol->MolUnit() ); } - mprintf("\tMask [%s] corresponds to %zu molecules\n", Mask1.MaskString(), imageList.size()/2); + mprintf("\tMask [%s] corresponds to %zu molecules\n", Mask1.MaskString(), imageList.size()); return imageList; } @@ -159,8 +148,7 @@ Action::RetType Action_AutoImage::Setup(ActionSetup& setup) { // No anchor specified. Use first molecule as anchor. anchormolnum = 0; mprintf("\tUsing first molecule as anchor.\n"); - anchorMask_.AddAtomRange( setup.Top().Mol(0).BeginAtom(), - setup.Top().Mol(0).EndAtom() ); + anchorMask_.AddUnit( setup.Top().Mol(0).MolUnit() ); } // Set up fixed region @@ -189,13 +177,11 @@ Action::RetType Action_AutoImage::Setup(ActionSetup& setup) { // everything else into fixed list. if ( mol->IsSolvent() || mol->NumAtoms() == 1 ) { if (mobileauto) { - mobileList_.push_back( mol->BeginAtom() ); - mobileList_.push_back( mol->EndAtom() ); + mobileList_.push_back( mol->MolUnit() ); } } else { if (fixedauto) { - fixedList_.push_back( mol->BeginAtom() ); - fixedList_.push_back( mol->EndAtom() ); + fixedList_.push_back( mol->MolUnit() ); } } } @@ -204,18 +190,18 @@ Action::RetType Action_AutoImage::Setup(ActionSetup& setup) { } // Print fixed and mobile lists if (!fixedList_.empty()) { - mprintf("\t%zu molecules are fixed to anchor:", fixedList_.size() / 2); - for (pairList::const_iterator atom = fixedList_.begin(); - atom != fixedList_.end(); atom += 2) - mprintf(" %i", setup.Top()[ *atom ].MolNum()+1 ); + mprintf("\t%zu molecules are fixed to anchor:", fixedList_.size()); + for (Uarray::const_iterator it = fixedList_.begin(); + it != fixedList_.end(); ++it) + mprintf(" %i", setup.Top()[ it->Front() ].MolNum()+1 ); mprintf("\n"); } - mprintf("\t%zu molecules are mobile.\n", mobileList_.size() / 2 ); + mprintf("\t%zu molecules are mobile.\n", mobileList_.size() ); if (debug_ > 1) { mprintf("\tThe following molecules are mobile:\n"); - for (pairList::const_iterator atom = mobileList_.begin(); - atom != mobileList_.end(); atom += 2) - mprintf(" %i\n", setup.Top()[ *atom ].MolNum()+1 ); + for (Uarray::const_iterator it = mobileList_.begin(); + it != mobileList_.end(); ++it) + mprintf(" %i\n", setup.Top()[ it->Front() ].MolNum()+1 ); mprintf("\n"); } diff --git a/src/Action_AutoImage.h b/src/Action_AutoImage.h index 16594f2bcb..109fa3bea9 100644 --- a/src/Action_AutoImage.h +++ b/src/Action_AutoImage.h @@ -1,6 +1,7 @@ #ifndef INC_ACTION_AUTOIMAGE_H #define INC_ACTION_AUTOIMAGE_H #include "Action.h" +class Unit; class Action_AutoImage : public Action { public: Action_AutoImage(); @@ -12,9 +13,9 @@ class Action_AutoImage : public Action { Action::RetType DoAction(int, ActionFrame&); void Print() {} - typedef std::vector pairList; + typedef std::vector Uarray; - static pairList SetupAtomRanges(Topology const&, std::string const&); + static Uarray SetupAtomRanges(Topology const&, std::string const&); AtomMask anchorMask_; ///< Used to center anchor region. std::string anchor_; ///< Mask expression for anchor region. @@ -30,7 +31,7 @@ class Action_AutoImage : public Action { enum TriclinicArg {OFF, FORCE, FAMILIAR}; TriclinicArg triclinic_; ///< Determine whether triclinic code should be used. - pairList fixedList_; ///< Contain first and last atom indices for fixed elements - pairList mobileList_; ///< Contain first and last atom indices for mobile elements. + Uarray fixedList_; ///< Contain atom indices for fixed elements + Uarray mobileList_; ///< Contain atom indices for mobile elements. }; #endif diff --git a/src/AtomMask.cpp b/src/AtomMask.cpp index d963c19306..6e32acdea1 100644 --- a/src/AtomMask.cpp +++ b/src/AtomMask.cpp @@ -1,6 +1,7 @@ #include // sort, unique #include "AtomMask.h" #include "CpptrajStdio.h" +#include "Unit.h" // CONSTRUCTOR AtomMask::AtomMask(int beginAtom, int endAtom) : Natom_(0), maskChar_(SelectedChar_) @@ -158,6 +159,12 @@ void AtomMask::AddAtomRange(int minAtom, int maxAtom) { //mprintf("]\n"); } +/** Add atoms in given unit to mask. */ +void AtomMask::AddUnit(Unit const& unitIn) { + for (Unit::const_iterator it = unitIn.segBegin(); it != unitIn.segEnd(); ++it) + AddAtomRange( it->Begin(), it->End() ); +} + // AtomMask::AddMaskAtPosition() /** Add the atoms in Mask to this mask starting at the specified positon. * Currently only used by Closest for modifying the original stripped diff --git a/src/AtomMask.h b/src/AtomMask.h index 57b43c454d..fc648e68e3 100644 --- a/src/AtomMask.h +++ b/src/AtomMask.h @@ -1,6 +1,7 @@ #ifndef INC_ATOMMASK_H #define INC_ATOMMASK_H #include "MaskToken.h" +class Unit; /// Atom mask using integer array. /** AtomMask is used to hold an array of integers that represent atom numbers * of atoms selected based on a mask expression set via SetMaskString. @@ -57,6 +58,8 @@ class AtomMask : public MaskTokenArray { void AddAtoms(std::vector const&); /// Add minAtom <= atom < maxAtom to mask void AddAtomRange(int,int); + /// Add atoms in given unit to mask + void AddUnit(Unit const&); /// Add atoms in given mask to this mask at positon, update position void AddMaskAtPosition(AtomMask const&, int); /// Convert from integer mask to char mask. diff --git a/src/Unit.h b/src/Unit.h index ef432bc0e5..64160e97de 100644 --- a/src/Unit.h +++ b/src/Unit.h @@ -23,6 +23,9 @@ class Unit { return total; } + /// \return First index in the unit + int Front() const { return segArray_.front().Begin(); } + /// Add index to the unit int AddIndex(int idx) { int delta = idx - lastIdx_; From cb6ced30b96322bad2438137e727e20e586ac78e Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Mon, 7 Sep 2020 19:15:37 -0400 Subject: [PATCH 08/65] Add abstract base class for image list --- src/Image_List.h | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 src/Image_List.h diff --git a/src/Image_List.h b/src/Image_List.h new file mode 100644 index 0000000000..c4d7e08e2d --- /dev/null +++ b/src/Image_List.h @@ -0,0 +1,23 @@ +#ifndef INC_IMAGE_LIST_H +#define INC_IMAGE_LIST_H +#include +class Topology; +class Frame; +class Vec3; +namespace Image { +/// Abstract base class for holding entities to be imaged +class List { + public: + List() {} + virtual ~List() {} + /// \return Number of entities to be imaged + virtual unsigned int nEntities() const = 0; + /// Set up the list according to Topology and mask expression + virtual int SetupList(Topology const&, std::string const&) = 0; + /// \return Coordinates of specified entity + virtual Vec3 GetCoord(unsigned int) const = 0; + /// Do translation of specified entity according to given translation vector. + virtual void DoTranslation(Frame&, unsigned int, Vec3 const&) const = 0; +}; +} +#endif From a0b172cedba2e12750f7e2ce1954a58564a67aaa Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Mon, 7 Sep 2020 19:32:56 -0400 Subject: [PATCH 09/65] Add Image::List_Pair --- src/Image_List_Pair.cpp | 19 +++++++++++++++++++ src/Image_List_Pair.h | 17 +++++++++++++++++ 2 files changed, 36 insertions(+) create mode 100644 src/Image_List_Pair.cpp create mode 100644 src/Image_List_Pair.h diff --git a/src/Image_List_Pair.cpp b/src/Image_List_Pair.cpp new file mode 100644 index 0000000000..aeb7a57fa2 --- /dev/null +++ b/src/Image_List_Pair.cpp @@ -0,0 +1,19 @@ +#include "Image_List_Pair.h" +#include "AtomMask.h" +#include "Topology.h" + +int Image::List_Pair::SetupList(Topology const& Parm, std::string const& maskExpression) +{ + AtomMask mask; + if (mask.SetMaskString(maskExpression)) return 1; + if ( Parm.SetupIntegerMask( mask ) ) return 1; + mask.MaskInfo(); + if (mask.None()) return -1; + std::vector resnums = Parm.ResnumsSelectedBy( mask ); + for (std::vector::const_iterator it = resnums.begin(); it != resnums.end(); ++it) + { + begin_.push_back( Parm.Res(*it).FirstAtom() ); + end_.push_back( Parm.Res(*it).LastAtom() ); + } + return 0; +} diff --git a/src/Image_List_Pair.h b/src/Image_List_Pair.h new file mode 100644 index 0000000000..583d4881dc --- /dev/null +++ b/src/Image_List_Pair.h @@ -0,0 +1,17 @@ +#ifndef INC_IMAGE_LIST_PAIR_H +#define INC_IMAGE_LIST_PAIR_H +#include "Image_List.h" +#include +namespace Image { +/// List with entities defined by a single range +class List_Pair : public List { + public: + List_Pair() {} + int SetupList(Topology const&, std::string const&); + private: + typedef std::vector Iarray; + Iarray begin_; + Iarray end_; +}; +} +#endif From 2435d490835897ba2fbce56cf409a0b776120b65 Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Mon, 7 Sep 2020 19:36:53 -0400 Subject: [PATCH 10/65] Add translation --- src/Image_List_Pair.h | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/src/Image_List_Pair.h b/src/Image_List_Pair.h index 583d4881dc..b7b76f83d6 100644 --- a/src/Image_List_Pair.h +++ b/src/Image_List_Pair.h @@ -1,6 +1,8 @@ #ifndef INC_IMAGE_LIST_PAIR_H #define INC_IMAGE_LIST_PAIR_H #include "Image_List.h" +#include "Frame.h" +#include "Vec3.h" #include namespace Image { /// List with entities defined by a single range @@ -8,6 +10,9 @@ class List_Pair : public List { public: List_Pair() {} int SetupList(Topology const&, std::string const&); + void DoTranslation(Frame& frm, unsigned int idx, Vec3 const& boxTrans) const { + frm.Translate(boxTrans, begin_[idx], end_[idx]); + } private: typedef std::vector Iarray; Iarray begin_; From 0a8dbe601beb3f8f86edc746a051218891a3ff84 Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Tue, 8 Sep 2020 19:20:25 -0400 Subject: [PATCH 11/65] Add center of mass version of Image::List_Pair --- src/Image_List.h | 2 +- src/Image_List_Pair.h | 4 +++- src/Image_List_Pair_CoM.h | 11 +++++++++++ 3 files changed, 15 insertions(+), 2 deletions(-) create mode 100644 src/Image_List_Pair_CoM.h diff --git a/src/Image_List.h b/src/Image_List.h index c4d7e08e2d..e68e50d369 100644 --- a/src/Image_List.h +++ b/src/Image_List.h @@ -15,7 +15,7 @@ class List { /// Set up the list according to Topology and mask expression virtual int SetupList(Topology const&, std::string const&) = 0; /// \return Coordinates of specified entity - virtual Vec3 GetCoord(unsigned int) const = 0; + virtual Vec3 GetCoord(unsigned int, Frame const&) const = 0; /// Do translation of specified entity according to given translation vector. virtual void DoTranslation(Frame&, unsigned int, Vec3 const&) const = 0; }; diff --git a/src/Image_List_Pair.h b/src/Image_List_Pair.h index b7b76f83d6..38d98df210 100644 --- a/src/Image_List_Pair.h +++ b/src/Image_List_Pair.h @@ -9,11 +9,13 @@ namespace Image { class List_Pair : public List { public: List_Pair() {} + virtual ~List_Pair() {} + unsigned int nEntities() const { return begin_.size(); } int SetupList(Topology const&, std::string const&); void DoTranslation(Frame& frm, unsigned int idx, Vec3 const& boxTrans) const { frm.Translate(boxTrans, begin_[idx], end_[idx]); } - private: + protected: typedef std::vector Iarray; Iarray begin_; Iarray end_; diff --git a/src/Image_List_Pair_CoM.h b/src/Image_List_Pair_CoM.h new file mode 100644 index 0000000000..491bf58649 --- /dev/null +++ b/src/Image_List_Pair_CoM.h @@ -0,0 +1,11 @@ +#ifndef INC_IMAGE_LIST_PAIR_COM_H +#define INC_IMAGE_LIST_PAIR_COM_H +#include "Image_List_Pair.h" +namespace Image { +class List_Pair_CoM : public List_Pair { + public: + List_Pair_CoM() {} + Vec3 GetCoord(unsigned int idx, Frame const& frm) const { return frm.VCenterOfMass(begin_[idx], end_[idx]); } +}; +} +#endif From 68063173c584ec00ceb3e9dc5c9dd61ac2e6ba8c Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Tue, 8 Sep 2020 19:24:40 -0400 Subject: [PATCH 12/65] Add geometric and first atom versions --- src/Image_List_Pair_First.h | 11 +++++++++++ src/Image_List_Pair_Geom.h | 11 +++++++++++ 2 files changed, 22 insertions(+) create mode 100644 src/Image_List_Pair_First.h create mode 100644 src/Image_List_Pair_Geom.h diff --git a/src/Image_List_Pair_First.h b/src/Image_List_Pair_First.h new file mode 100644 index 0000000000..8d2638df5a --- /dev/null +++ b/src/Image_List_Pair_First.h @@ -0,0 +1,11 @@ +#ifndef INC_IMAGE_LIST_PAIR_FIRST_H +#define INC_IMAGE_LIST_PAIR_FIRST_H +#include "Image_List_Pair.h" +namespace Image { +class List_Pair_First : public List_Pair { + public: + List_Pair_First() {} + Vec3 GetCoord(unsigned int idx, Frame const& frm) const { return frm.XYZ(begin_[idx]); } +}; +} +#endif diff --git a/src/Image_List_Pair_Geom.h b/src/Image_List_Pair_Geom.h new file mode 100644 index 0000000000..5758afa4e0 --- /dev/null +++ b/src/Image_List_Pair_Geom.h @@ -0,0 +1,11 @@ +#ifndef INC_IMAGE_LIST_PAIR_GEOM_H +#define INC_IMAGE_LIST_PAIR_GEOM_H +#include "Image_List_Pair.h" +namespace Image { +class List_Pair_Geom : public List_Pair { + public: + List_Pair_Geom() {} + Vec3 GetCoord(unsigned int idx, Frame const& frm) const { return frm.VGeometricCenter(begin_[idx], end_[idx]); } +}; +} +#endif From 8fd66302bde5e99e62f549b44c508f20414acc8a Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Tue, 8 Sep 2020 19:29:02 -0400 Subject: [PATCH 13/65] Take into account molecules with non-consecutive segments --- src/Topology.cpp | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/src/Topology.cpp b/src/Topology.cpp index 7801442f45..67178958ad 100644 --- a/src/Topology.cpp +++ b/src/Topology.cpp @@ -1268,18 +1268,22 @@ std::vector Topology::ResnumsSelectedBy(AtomMask const& mask) const { // Topology::MolnumsSelectedBy() std::vector Topology::MolnumsSelectedBy(AtomMask const& mask) const { - std::vector molnums; + std::set molnums; if (molecules_.empty()) { mprintf("Warning: Topology has no molecule information.\n"); } else { int mol = -1; for (AtomMask::const_iterator at = mask.begin(); at != mask.end(); ++at) - if (atoms_[*at].MolNum() > mol) { + if (atoms_[*at].MolNum() != mol) { mol = atoms_[*at].MolNum(); molnums.push_back( mol ); } } - return molnums; + std::vector tmp; + tmp.reserve( molnums.size() ); + for (std::set::const_iterator it = molnums.begin(); it != molnums.end(); ++it) + tmp.push_back( *it ); + return tmp; } // ----------------------------------------------------------------------------- From 2c8a8616b2e0159708c9171078c7a3934eeca3ca Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Wed, 9 Sep 2020 13:08:20 -0400 Subject: [PATCH 14/65] Fix for molecule changes --- src/Topology.cpp | 45 ++++++++++++++++++++++++--------------------- src/Topology.h | 2 +- 2 files changed, 25 insertions(+), 22 deletions(-) diff --git a/src/Topology.cpp b/src/Topology.cpp index 67178958ad..f8ba27ce9f 100644 --- a/src/Topology.cpp +++ b/src/Topology.cpp @@ -327,7 +327,7 @@ int Topology::AddTopAtom(Atom const& atomIn, Residue const& resIn) residues_.back().SetLastAtom( atoms_.size() ); return 0; } - +/* // Topology::StartNewMol() void Topology::StartNewMol() { // No atoms, so no need to do anything. @@ -354,7 +354,7 @@ void Topology::StartNewMol() { residues_.push_back( Residue("MOL",0,atoms_.size(),1,' ',' ') ); } residues_.back().SetTerminal( true ); -} +}*/ /** Common setup with common excluded distance. */ int Topology::CommonSetup(bool molsearch) { @@ -381,8 +381,8 @@ int Topology::CommonSetup(bool molsearch, int excludedDist) { for (std::vector::const_iterator mol = molecules_.begin() + 1; mol != molecules_.end(); ++mol) { - int m0_resnum = atoms_[(mol-1)->BeginAtom()].ResNum(); - int m1_resnum = atoms_[ mol->BeginAtom()].ResNum(); + int m0_resnum = atoms_[(mol-1)->MolUnit().Front()].ResNum(); + int m1_resnum = atoms_[ mol->MolUnit().Front()].ResNum(); if (m0_resnum == m1_resnum) { mols_share_residues = true; unsigned int molnum = mol - molecules_.begin(); @@ -478,20 +478,24 @@ int Topology::Setup_NoResInfo() { { // Try to detect at least water as solvent. Assume CommonSetup will be // run after this to set up molecule solvent info. - if (mol->NumAtoms() == 3) { + if (mol->MolUnit().nSegments() == 1 && mol->NumAtoms() == 3) { int nH = 0; int nO = 0; - for (int atnum = mol->BeginAtom(); atnum != mol->EndAtom(); atnum++) + for (Unit::const_iterator seg = mol->MolUnit().segBegin(); + seg != mol->MolUnit().segEnd(); ++seg) { - if (atoms_[atnum].Element() == Atom::HYDROGEN) nH++; - if (atoms_[atnum].Element() == Atom::OXYGEN) nO++; + for (int atnum = seg->Begin(); atnum != seg->End(); atnum++) + { + if (atoms_[atnum].Element() == Atom::HYDROGEN) nH++; + if (atoms_[atnum].Element() == Atom::OXYGEN) nO++; + } } if (nO == 1 && nH == 2) res_name = "HOH"; } else res_name = default_res_name; residues_.push_back( Residue(res_name, resnum+1, ' ', ' ') ); - residues_.back().SetFirstAtom( mol->BeginAtom() ); - residues_.back().SetLastAtom( mol->EndAtom() ); + residues_.back().SetFirstAtom( mol->MolUnit().Front() ); + residues_.back().SetLastAtom( mol->MolUnit().Back() ); // Update atom residue numbers for (int atnum = residues_.back().FirstAtom(); atnum != residues_.back().LastAtom(); ++atnum) @@ -1056,7 +1060,7 @@ int Topology::DetermineMolecules() { mprintf("Warning: The 'fixatomorder' command can be used to reorder the topology and any\n" "Warning: associated coordinates.\n"); } - +/* std::vector::iterator molecule = molecules_.begin(); molecule->SetFirst(0); std::vector::const_iterator atom = atoms_.begin(); @@ -1090,6 +1094,7 @@ int Topology::DetermineMolecules() { ++atomNum; } molecule->SetLast( atoms_.size() ); +*/ return 0; } @@ -1184,13 +1189,11 @@ int Topology::SetSolvent(std::string const& maskexpr) { mol->SetNoSolvent(); // If any atoms in this molecule are selected by mask, make entire // molecule solvent. - for (int atom = mol->BeginAtom(); atom < mol->EndAtom(); ++atom) { - if ( mask.AtomInCharMask( atom ) ) { - mol->SetSolvent(); - ++NsolventMolecules_; - numSolvAtoms += mol->NumAtoms(); - break; - } + if ( mask.AtomsInCharMask( mol->MolUnit() ) ) { + mol->SetSolvent(); + ++NsolventMolecules_; + numSolvAtoms += mol->NumAtoms(); + break; } } @@ -1213,7 +1216,7 @@ int Topology::SetSolventInfo() { for (std::vector::iterator mol = molecules_.begin(); mol != molecules_.end(); mol++) { - int firstRes = atoms_[ mol->BeginAtom() ].ResNum(); + int firstRes = atoms_[ mol->MolUnit().Front() ].ResNum(); if ( residues_[firstRes].NameIsSolvent() ) { mol->SetSolvent(); ++NsolventMolecules_; @@ -1276,7 +1279,7 @@ std::vector Topology::MolnumsSelectedBy(AtomMask const& mask) const { for (AtomMask::const_iterator at = mask.begin(); at != mask.end(); ++at) if (atoms_[*at].MolNum() != mol) { mol = atoms_[*at].MolNum(); - molnums.push_back( mol ); + molnums.insert( mol ); } } std::vector tmp; @@ -1449,7 +1452,7 @@ Topology* Topology::ModifyByMap(std::vector const& MapIn, bool setupFullPar for (std::vector::iterator mol = newParm->molecules_.begin(); mol != newParm->molecules_.end(); ++mol) { - if ( isSolvent[ mol->BeginAtom() ] ) { + if ( isSolvent[ mol->MolUnit().Front() ] ) { mol->SetSolvent(); newParm->NsolventMolecules_++; } else diff --git a/src/Topology.h b/src/Topology.h index 9e6e137294..a7b5c67116 100644 --- a/src/Topology.h +++ b/src/Topology.h @@ -165,7 +165,7 @@ class Topology { // ----- Setup routines ---------------------- int AddTopAtom(Atom const&, Residue const&); void AddExtraAtomInfo(AtomExtra const& ex) { extra_.push_back(ex); } // FIXME bounds check - void StartNewMol(); + //void StartNewMol(); /// Perform common final setup: optional molecule determination, excluded distance int CommonSetup(bool, int); /// Perform common final setup: optional molecule determination From d55f392928cdb80ee42486a68aa4fc65ea84b753 Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Wed, 9 Sep 2020 13:09:12 -0400 Subject: [PATCH 15/65] Constructor for a single segment --- src/Molecule.h | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/Molecule.h b/src/Molecule.h index 31e780a612..8a7e54f6c9 100644 --- a/src/Molecule.h +++ b/src/Molecule.h @@ -6,6 +6,8 @@ class Molecule { public: Molecule() : isSolvent_(false) {} + /// CONSTRUCTOR - Single segment from beg to end + Molecule(int beg, int end) : isSolvent_(false), unit_(Unit(beg, end)) {} void SetSolvent() { isSolvent_ = true; } void SetNoSolvent() { isSolvent_ = false; } From bfcab2a50bd5dea83dc0f79ec7dafbd7cc8b9e0c Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Wed, 9 Sep 2020 13:09:57 -0400 Subject: [PATCH 16/65] Add new constructors and functions --- src/Segment.h | 2 ++ src/Unit.h | 3 +++ 2 files changed, 5 insertions(+) diff --git a/src/Segment.h b/src/Segment.h index 85b094544b..1273064ea6 100644 --- a/src/Segment.h +++ b/src/Segment.h @@ -8,6 +8,8 @@ class Segment { Segment() : begin_(-1), end_(-1) {} /// CONSTRUCTOR - Segment size of 1 Segment(int idx) : begin_(idx), end_(idx+1) {} + /// CONSTRUCTOR - Beginning and end + Segment(int beg, int end) : begin_(beg), end_(end) {} int Begin() const { return begin_; } int End() const { return end_; } diff --git a/src/Unit.h b/src/Unit.h index 64160e97de..403460f60f 100644 --- a/src/Unit.h +++ b/src/Unit.h @@ -9,6 +9,8 @@ class Unit { public: /// CONSTRUCTOR - Set last index to large negative so first AddIndex() call creates a Segment Unit() : lastIdx_(-9999) {} + /// CONSTRUCTOR - Single segment + Unit(int beg, int end) : segArray_(SegArrayType(1, Segment(beg, end))), lastIdx_(end-1) {} typedef std::vector::const_iterator const_iterator; const_iterator segBegin() const { return segArray_.begin(); } @@ -25,6 +27,7 @@ class Unit { /// \return First index in the unit int Front() const { return segArray_.front().Begin(); } + int Back() const { return segArray_.back().End(); } /// Add index to the unit int AddIndex(int idx) { From 6e337122d24a9c052d22282548611e80c306fa60 Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Wed, 9 Sep 2020 13:10:21 -0400 Subject: [PATCH 17/65] Set terminal status directly --- src/Parm_PDB.cpp | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/Parm_PDB.cpp b/src/Parm_PDB.cpp index f1fbe0ae06..da0d24160c 100644 --- a/src/Parm_PDB.cpp +++ b/src/Parm_PDB.cpp @@ -151,7 +151,8 @@ int Parm_PDB::ReadParm(FileName const& fname, Topology &TopIn) { infile.RecType() == PDBfile::END ) { // Indicate end of molecule for TER/END. Finish if END. - TopIn.StartNewMol(); + //TopIn.StartNewMol(); + TopIn.SetRes( TopIn.Nres()-1 ).SetTerminal( true ); if (infile.RecType() == PDBfile::END) break; } else if ( !missingResidues && infile.RecType() == PDBfile::MISSING_RES ) { missingResidues = true; From b7556e1ec11cd7be006f575efe997edadee933f4 Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Wed, 9 Sep 2020 19:13:20 -0400 Subject: [PATCH 18/65] Remove unneeded dependency --- src/Image_List_Pair.h | 1 - 1 file changed, 1 deletion(-) diff --git a/src/Image_List_Pair.h b/src/Image_List_Pair.h index 38d98df210..c248951084 100644 --- a/src/Image_List_Pair.h +++ b/src/Image_List_Pair.h @@ -2,7 +2,6 @@ #define INC_IMAGE_LIST_PAIR_H #include "Image_List.h" #include "Frame.h" -#include "Vec3.h" #include namespace Image { /// List with entities defined by a single range From ad2b27cc73c9c16138bbf15c5d931465683b86a7 Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Thu, 10 Sep 2020 08:58:05 -0400 Subject: [PATCH 19/65] Add Unit Translate function --- src/Frame.h | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/src/Frame.h b/src/Frame.h index f30cc5f8a5..bfa7d66bac 100644 --- a/src/Frame.h +++ b/src/Frame.h @@ -211,6 +211,8 @@ class Frame { inline void Translate(Vec3 const&, AtomMask const&); /// Translate atoms in range by Vec inline void Translate(Vec3 const&, int, int); + /// Translate atoms in Unit by Vec + inline void Translate(Vec3 const&, Unit const&); /// Translate atom by Vec inline void Translate(Vec3 const&, int); /// Translate all atoms by Vec @@ -390,6 +392,11 @@ void Frame::Translate(Vec3 const& Vec, int firstAtom, int lastAtom) { } } +void Frame::Translate(Vec3 const& Vec, Unit const& unit) { + for (Unit::const_iterator seg = unit.segBegin(); seg != unit.segEnd(); ++seg) + Translate(Vec, seg->Begin(), seg->End()); +} + void Frame::Translate(Vec3 const& Vec, int atom) { int icrd = atom * 3; X_[icrd ] += Vec[0]; From 1ae177b69914e43a73cafc0080bf6c4f749977d9 Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Thu, 10 Sep 2020 09:08:16 -0400 Subject: [PATCH 20/65] Add Image_List_Unit --- src/Image_List_Unit.cpp | 18 ++++++++++++++++++ src/Image_List_Unit.h | 23 +++++++++++++++++++++++ 2 files changed, 41 insertions(+) create mode 100644 src/Image_List_Unit.cpp create mode 100644 src/Image_List_Unit.h diff --git a/src/Image_List_Unit.cpp b/src/Image_List_Unit.cpp new file mode 100644 index 0000000000..b1fbc02e19 --- /dev/null +++ b/src/Image_List_Unit.cpp @@ -0,0 +1,18 @@ +#include "Image_List_Unit.h" +#include "AtomMask.h" +#include "Topology.h" + +int Image::List_Unit::SetupList(Topology const& Parm, std::string const& maskExpression) +{ + AtomMask mask; + if (mask.SetMaskString(maskExpression)) return 1; + if ( Parm.SetupIntegerMask( mask ) ) return 1; + mask.MaskInfo(); + if (mask.None()) return -1; + std::vector molnums = Parm.MolnumsSelectedBy( mask ); + for (std::vector::const_iterator it = molnums.begin(); it != molnums.end(); ++it) + { + units_.push_back( Parm.Mol(*it).MolUnit() ); + } + return 0; +} diff --git a/src/Image_List_Unit.h b/src/Image_List_Unit.h new file mode 100644 index 0000000000..b3345e2bdb --- /dev/null +++ b/src/Image_List_Unit.h @@ -0,0 +1,23 @@ +#ifndef INC_IMAGE_LIST_UNIT_H +#define INC_IMAGE_LIST_UNIT_H +#include "Image_List.h" +#include "Frame.h" +#include +class Unit; +namespace Image { +/// List with entities defined by Units +class List_Unit : public List { + public: + List_Unit() {} + virtual ~List_Unit() {} + unsigned int nEntities() const { return units_.size(); } + int SetupList(Topology const&, std::string const&); + void DoTranslation(Frame& frm, unsigned int idx, Vec3 const& boxTrans) const { + frm.Translate(boxTrans, units_[idx]); + } + protected: + typedef std::vector Uarray; + Uarray units_; +}; +} +#endif From a6cdb4ee5449de13882e8698ea1920154e112599 Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Thu, 10 Sep 2020 19:12:59 -0400 Subject: [PATCH 21/65] Add Unit center calc routines --- src/Frame.h | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/src/Frame.h b/src/Frame.h index bfa7d66bac..0550e3fa95 100644 --- a/src/Frame.h +++ b/src/Frame.h @@ -207,6 +207,10 @@ class Frame { inline Vec3 VCenterOfMass(int, int) const; /// \return Geometric center of atoms in range. inline Vec3 VGeometricCenter(int, int) const; + /// \return Center of mass of atoms in Unit + inline Vec3 VCenterOfMass(Unit const&) const; + /// \return Geometric center of atoms in Unit + inline Vec3 VGeometricCenter(Unit const&) const; /// Translate atoms in mask by Vec inline void Translate(Vec3 const&, AtomMask const&); /// Translate atoms in range by Vec @@ -356,6 +360,13 @@ Vec3 Frame::VCenterOfMass(int startAtom, int stopAtom) const { return Vec3( Coord0 / sumMass, Coord1 / sumMass, Coord2 / sumMass ); } +Vec3 Frame::VCenterOfMass(Unit const& unit) const { + Vec3 out(0.0); + for (Unit::const_iterator seg = unit.segBegin(); seg != unit.segEnd(); ++seg) + out += VCenterOfMass(seg->Begin(), seg->End()); + return out; +} + Vec3 Frame::VGeometricCenter(int startAtom, int stopAtom) const { double Coord0 = 0.0; double Coord1 = 0.0; @@ -372,6 +383,13 @@ Vec3 Frame::VGeometricCenter(int startAtom, int stopAtom) const { return Vec3( Coord0 / sumMass, Coord1 / sumMass, Coord2 / sumMass ); } +Vec3 Frame::VGeometricCenter(Unit const& unit) const { + Vec3 out(0.0); + for (Unit::const_iterator seg = unit.segBegin(); seg != unit.segEnd(); ++seg) + out += VGeometricCenter(seg->Begin(), seg->End()); + return out; +} + void Frame::Translate(Vec3 const& Vec, AtomMask const& maskIn) { for (AtomMask::const_iterator atm = maskIn.begin(); atm != maskIn.end(); ++atm) { From deeee3ab7674f76548cd23d0e00edd804e8237bc Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Thu, 10 Sep 2020 19:14:53 -0400 Subject: [PATCH 22/65] Image unit com class --- src/Image_List_Unit_CoM.h | 11 +++++++++++ 1 file changed, 11 insertions(+) create mode 100644 src/Image_List_Unit_CoM.h diff --git a/src/Image_List_Unit_CoM.h b/src/Image_List_Unit_CoM.h new file mode 100644 index 0000000000..dc7ceeebd3 --- /dev/null +++ b/src/Image_List_Unit_CoM.h @@ -0,0 +1,11 @@ +#ifndef INC_IMAGE_LIST_UNIT_COM_H +#define INC_IMAGE_LIST_UNIT_COM_H +#include "Image_List_Unit.h" +namespace Image { +class List_Unit_CoM : public List_Unit { + public: + List_Unit_CoM() {} + Vec3 GetCoord(unsigned int idx, Frame const& frm) const { return frm.VCenterOfMass(units_[idx]); } +}; +} +#endif From 7bf46f10ae1181120cca270237ea33a0f936541a Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Thu, 10 Sep 2020 19:19:29 -0400 Subject: [PATCH 23/65] Add Geom and First versions --- src/Image_List_Unit_First.h | 11 +++++++++++ src/Image_List_Unit_Geom.h | 11 +++++++++++ 2 files changed, 22 insertions(+) create mode 100644 src/Image_List_Unit_First.h create mode 100644 src/Image_List_Unit_Geom.h diff --git a/src/Image_List_Unit_First.h b/src/Image_List_Unit_First.h new file mode 100644 index 0000000000..743bcbf91f --- /dev/null +++ b/src/Image_List_Unit_First.h @@ -0,0 +1,11 @@ +#ifndef INC_IMAGE_LIST_UNIT_FIRST_H +#define INC_IMAGE_LIST_UNIT_FIRST_H +#include "Image_List_Unit.h" +namespace Image { +class List_Unit_First : public List_Unit { + public: + List_Unit_First() {} + Vec3 GetCoord(unsigned int idx, Frame const& frm) const { return frm.XYZ(units_[idx].Front()); } +}; +} +#endif diff --git a/src/Image_List_Unit_Geom.h b/src/Image_List_Unit_Geom.h new file mode 100644 index 0000000000..a6363e22bd --- /dev/null +++ b/src/Image_List_Unit_Geom.h @@ -0,0 +1,11 @@ +#ifndef INC_IMAGE_LIST_UNIT_GEOM_H +#define INC_IMAGE_LIST_UNIT_GEOM_H +#include "Image_List_Unit.h" +namespace Image { +class List_Unit_Geom : public List_Unit { + public: + List_Unit_Geom() {} + Vec3 GetCoord(unsigned int idx, Frame const& frm) const { return frm.VGeometricCenter(units_[idx]); } +}; +} +#endif From 44c7ba914d9dcadc948b08b74c02390333ad3b78 Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Thu, 10 Sep 2020 20:49:54 -0400 Subject: [PATCH 24/65] Add image list based on atom mask --- src/Image_List_Mask.cpp | 12 ++++++++++++ src/Image_List_Mask.h | 22 ++++++++++++++++++++++ 2 files changed, 34 insertions(+) create mode 100644 src/Image_List_Mask.cpp create mode 100644 src/Image_List_Mask.h diff --git a/src/Image_List_Mask.cpp b/src/Image_List_Mask.cpp new file mode 100644 index 0000000000..f7a6619b8c --- /dev/null +++ b/src/Image_List_Mask.cpp @@ -0,0 +1,12 @@ +#include "Image_List_Mask.h" +#include "Topology.h" + +int Image::List_Mask::SetupList(Topology const& Parm, std::string const& maskExpression) +{ + mask_.ResetMask(); + if (mask_.SetMaskString(maskExpression)) return 1; + if ( Parm.SetupIntegerMask( mask_ ) ) return 1; + mask_.MaskInfo(); + if (mask_.None()) return -1; + return 0; +} diff --git a/src/Image_List_Mask.h b/src/Image_List_Mask.h new file mode 100644 index 0000000000..9ad9827095 --- /dev/null +++ b/src/Image_List_Mask.h @@ -0,0 +1,22 @@ +#ifndef INC_IMAGE_LIST_MASK_H +#define INC_IMAGE_LIST_MASK_H +#include "Image_List.h" +#include "Frame.h" +#include "AtomMask.h" +namespace Image { +/// List with entities defined by atom mask +class List_Mask : public List { + public: + List_Mask() {} + virtual ~List_Mask() {} + unsigned int nEntities() const { return mask_.Nselected(); } + int SetupList(Topology const&, std::string const&); + Vec3 GetCoord(unsigned int idx, Frame const& frm) { return frm.XYZ(mask_[idx]); } + void DoTranslation(Frame& frm, unsigned int idx, Vec3 const& boxTrans) const { + frm.Translate(boxTrans, mask_[idx]); + } + protected: + AtomMask mask_; +}; +} +#endif From 6ba4e75c9fa0a6c0399a1a9170ba0bcd82a5d83c Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Fri, 11 Sep 2020 09:30:40 -0400 Subject: [PATCH 25/65] Add missing const --- src/Image_List_Mask.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/Image_List_Mask.h b/src/Image_List_Mask.h index 9ad9827095..8020fd4d4b 100644 --- a/src/Image_List_Mask.h +++ b/src/Image_List_Mask.h @@ -11,7 +11,7 @@ class List_Mask : public List { virtual ~List_Mask() {} unsigned int nEntities() const { return mask_.Nselected(); } int SetupList(Topology const&, std::string const&); - Vec3 GetCoord(unsigned int idx, Frame const& frm) { return frm.XYZ(mask_[idx]); } + Vec3 GetCoord(unsigned int idx, Frame const& frm) const { return frm.XYZ(mask_[idx]); } void DoTranslation(Frame& frm, unsigned int idx, Vec3 const& boxTrans) const { frm.Translate(boxTrans, mask_[idx]); } From 3c53cd7aca4d643edc5a729365fef40d28f9407f Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Fri, 11 Sep 2020 09:33:57 -0400 Subject: [PATCH 26/65] Change CreateAtomPairList to CreateImageList --- src/ImageRoutines.cpp | 104 +++++++++++++++++++----------------------- src/ImageRoutines.h | 3 +- src/ImageTypes.h | 1 - 3 files changed, 50 insertions(+), 58 deletions(-) diff --git a/src/ImageRoutines.cpp b/src/ImageRoutines.cpp index a63b880306..00de956f24 100644 --- a/src/ImageRoutines.cpp +++ b/src/ImageRoutines.cpp @@ -1,68 +1,60 @@ #include // floor #include "ImageRoutines.h" #include "DistRoutines.h" -#include "Topology.h" -#include "CharMask.h" +#include "CpptrajStdio.h" +#include "Image_List.h" +#include "Image_List_Pair_CoM.h" +#include "Image_List_Pair_Geom.h" +#include "Image_List_Pair_First.h" +#include "Image_List_Unit_CoM.h" +#include "Image_List_Unit_Geom.h" +#include "Image_List_Unit_First.h" +#include "Image_List_Mask.h" -/** Check that at least 1 atom in the range is in Mask1 */ -static inline void CheckRange(Image::PairType& atomPairs, CharMask const& MaskIn, - int firstAtom, int lastAtom) +// Image::CreateImageList() +/** \return list of entities to be imaged based on given mode. + */ +Image::List* Image::CreateImageList(Topology const& Parm, Mode modeIn, + std::string const& maskExpression, + bool useMass, bool center) { - bool rangeIsValid = false; - for (int atom = firstAtom; atom < lastAtom; ++atom) { - if (MaskIn.AtomInCharMask(atom)) { - rangeIsValid = true; + Image::List* listOut = 0; + switch (modeIn) { + case BYMOL : + if (center) { + if (useMass) + listOut = new Image::List_Unit_CoM(); + else + listOut = new Image::List_Unit_Geom(); + } else + listOut = new Image::List_Unit_First(); + break; + case BYRES : + if (center) { + if (useMass) + listOut = new Image::List_Pair_CoM(); + else + listOut = new Image::List_Pair_Geom(); + } else + listOut = new Image::List_Pair_First(); + break; + case BYATOM : + listOut = new Image::List_Mask(); break; - } - } - if (rangeIsValid) { - atomPairs.push_back( firstAtom ); - atomPairs.push_back( lastAtom ); } -} - -// Image::CreateAtomPairList() -/** An atom pair list consists of 2 values for each entry, a beginning - * index and ending index. For molecules and residues this is the first - * and just beyond the last atom; for atoms it is just the atom itself - * twice. - */ -Image::PairType Image::CreateAtomPairList(Topology const& Parm, Mode modeIn, - std::string const& maskExpression) -{ - PairType atomPairs; - // Set up mask based on desired imaging mode. - if ( modeIn == BYMOL || modeIn == BYRES ) { - CharMask cmask( maskExpression ); - if ( Parm.SetupCharMask( cmask ) ) return atomPairs; - cmask.MaskInfo(); - if (cmask.None()) return atomPairs; - // Set up atom range for each entity to be imaged. - if (modeIn == BYMOL) { - atomPairs.reserve( Parm.Nmol()*2 ); - for (Topology::mol_iterator mol = Parm.MolStart(); - mol != Parm.MolEnd(); ++mol) - CheckRange( atomPairs, cmask, mol->BeginAtom(), mol->EndAtom()); - } else { // BYRES - atomPairs.reserve( Parm.Nres()*2 ); - for (Topology::res_iterator residue = Parm.ResStart(); - residue != Parm.ResEnd(); ++residue) - CheckRange( atomPairs, cmask, residue->FirstAtom(), residue->LastAtom() ); - } - } else { // BYATOM - AtomMask imask( maskExpression ); - if ( Parm.SetupIntegerMask( imask ) ) return atomPairs; - imask.MaskInfo(); - if (imask.None()) return atomPairs; - atomPairs.reserve( Parm.Natom()*2 ); - for (AtomMask::const_iterator atom = imask.begin(); atom != imask.end(); ++atom) { - atomPairs.push_back( *atom ); - atomPairs.push_back( (*atom)+1 ); + if (listOut != 0) { + if (listOut->SetupList(Parm, maskExpression)) { + mprinterr("Error: Could not set up image list for '%s'\n", maskExpression.c_str()); + delete listOut; + return 0; } + } else { + mprinterr("Internal Error: Could not allocate image list for '%s'\n", maskExpression.c_str()); + return 0; } -// mprintf("\tNumber of %ss to be imaged is %zu based on mask '%s'\n", -// ModeString[modeIn], atomPairs.size()/2, maskIn.MaskString()); - return atomPairs; + mprintf("DEBUG: Image list for '%s' over %u %ss.\n", + maskExpression.c_str(), listOut->nEntities(), ModeString(modeIn)); + return listOut; } // ----------------------------------------------------------------------------- diff --git a/src/ImageRoutines.h b/src/ImageRoutines.h index 5159e594a4..e31fe6e1fe 100644 --- a/src/ImageRoutines.h +++ b/src/ImageRoutines.h @@ -9,8 +9,9 @@ class Vec3; class Box; #include "ImageTypes.h" namespace Image { + class List; /// Create an atom pair list by molecule, residue, or atom. - PairType CreateAtomPairList(Topology const&, Mode, std::string const&); + List* CreateImageList(Topology const&, Mode, std::string const&, bool, bool); /// \return Coordinates of center if wrapping molecules into truncated oct. shape. Vec3 SetupTruncoct( Frame const&, AtomMask*, bool, bool); /// Perform non-orthogonal imaging on given pair list, optionally into trunc. oct. shape. diff --git a/src/ImageTypes.h b/src/ImageTypes.h index 2efc06f4f5..cbe2ffca66 100644 --- a/src/ImageTypes.h +++ b/src/ImageTypes.h @@ -5,7 +5,6 @@ */ #include namespace Image { - typedef std::vector PairType; enum Mode { BYMOL = 0, BYRES, BYATOM }; inline const char* ModeString(Mode m) { if (m == BYMOL) return "molecule"; From 0ea190a9c96ec14138131b6f5234781d15a88983 Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Fri, 11 Sep 2020 13:04:06 -0400 Subject: [PATCH 27/65] Use Image::List --- src/ImageRoutines.cpp | 46 ++++++++----------------------------------- src/ImageRoutines.h | 4 ++-- 2 files changed, 10 insertions(+), 40 deletions(-) diff --git a/src/ImageRoutines.cpp b/src/ImageRoutines.cpp index 00de956f24..f4e4965157 100644 --- a/src/ImageRoutines.cpp +++ b/src/ImageRoutines.cpp @@ -95,8 +95,7 @@ Vec3 Image::SetupTruncoct( Frame const& frameIn, AtomMask* ComMask, bool useMass */ void Image::Nonortho(Frame& frameIn, bool origin, Vec3 const& fcom, Vec3 const& offIn, Matrix_3x3 const& ucell, Matrix_3x3 const& recip, - bool truncoct, bool center, - bool useMass, PairType const& AtomPairs) + bool truncoct, List const& AtomPairs) { Vec3 Coord; Vec3 offset = ucell.TransposeMult( offIn ); @@ -108,29 +107,14 @@ void Image::Nonortho(Frame& frameIn, bool origin, Vec3 const& fcom, Vec3 const& frameIn.BoxCrd().BoxZ()*frameIn.BoxCrd().BoxZ()); // Loop over atom pairs - for (PairType::const_iterator atom = AtomPairs.begin(); - atom != AtomPairs.end(); ++atom) + for (unsigned int idx = 0; idx != AtomPairs.nEntities(); idx++) { - int firstAtom = *atom; - ++atom; - int lastAtom = *atom; - //if (debug>2) - // mprintf( " IMAGE processing atoms %i to %i\n", firstAtom+1, lastAtom); - // Set up Coord with position to check for imaging based on first atom or - // center of mass of atoms first to last. - if (center) { - if (useMass) - Coord = frameIn.VCenterOfMass(firstAtom,lastAtom); - else - Coord = frameIn.VGeometricCenter(firstAtom,lastAtom); - } else - Coord = frameIn.XYZ( firstAtom ); + Coord = AtomPairs.GetCoord( idx, frameIn ); // boxTrans will hold calculated translation needed to move atoms back into box Vec3 boxTrans = Nonortho(Coord, truncoct, origin, ucell, recip, fcom, min) + offset; - frameIn.Translate(boxTrans, firstAtom, lastAtom); - + AtomPairs.DoTranslation( frameIn, idx, boxTrans ); } // END loop over atom pairs } @@ -207,36 +191,22 @@ int Image::SetupOrtho(Box const& boxIn, Vec3& bp, Vec3& bm, bool origin) { * \param useMass If true calc center of mass, otherwise geometric center. */ void Image::Ortho(Frame& frameIn, Vec3 const& bp, Vec3 const& bm, Vec3 const& offIn, - bool center, bool useMass, PairType const& AtomPairs) + List const& AtomPairs) { Vec3 Coord; Vec3 offset(offIn[0] * frameIn.BoxCrd()[0], offIn[1] * frameIn.BoxCrd()[1], offIn[2] * frameIn.BoxCrd()[2]); // Loop over atom pairs - for (PairType::const_iterator atom = AtomPairs.begin(); - atom != AtomPairs.end(); atom++) + for (unsigned int idx = 0; idx != AtomPairs.nEntities(); idx++) { - int firstAtom = *atom; - ++atom; - int lastAtom = *atom; - //if (debug>2) - // mprintf( " IMAGE processing atoms %i to %i\n", firstAtom+1, lastAtom); - // Set up Coord with position to check for imaging based on first atom or - // center of mass of atoms first to last. - if (center) { - if (useMass) - Coord = frameIn.VCenterOfMass(firstAtom,lastAtom); - else - Coord = frameIn.VGeometricCenter(firstAtom,lastAtom); - } else - Coord = frameIn.XYZ( firstAtom ); + Coord = AtomPairs.GetCoord(idx, frameIn); // boxTrans will hold calculated translation needed to move atoms back into box Vec3 boxTrans = Ortho(Coord, bp, bm, frameIn.BoxCrd()) + offset; // Translate atoms according to Coord - frameIn.Translate(boxTrans, firstAtom, lastAtom); + AtomPairs.DoTranslation(frameIn, idx, boxTrans); } // END loop over atom pairs } diff --git a/src/ImageRoutines.h b/src/ImageRoutines.h index e31fe6e1fe..bf2c4644dd 100644 --- a/src/ImageRoutines.h +++ b/src/ImageRoutines.h @@ -16,14 +16,14 @@ namespace Image { Vec3 SetupTruncoct( Frame const&, AtomMask*, bool, bool); /// Perform non-orthogonal imaging on given pair list, optionally into trunc. oct. shape. void Nonortho(Frame&, bool, Vec3 const&, Vec3 const&, Matrix_3x3 const&, Matrix_3x3 const&, - bool, bool, bool, PairType const&); + bool, List const&); /// Perform non-orthogonal imaging on given coordinates, optionally into trunc. oct. shape. Vec3 Nonortho(Vec3 const&, bool, bool, Matrix_3x3 const&, Matrix_3x3 const&, Vec3 const&, double); /// Setup box boundaries based on centering type. int SetupOrtho(Box const&, Vec3&, Vec3&, bool); /// Perform orthogonal imaging on given pair list using given box boundaries - void Ortho(Frame&, Vec3 const&, Vec3 const&, Vec3 const&, bool, bool, PairType const&); + void Ortho(Frame&, Vec3 const&, Vec3 const&, Vec3 const&, List const&); /// Perform orthogonal imaging on given coordinates using given box boundaries Vec3 Ortho(Vec3 const&, Vec3 const&, Vec3 const&, Box const&); /// Perform unwrap of non-orthogonal cell using given reference. From f55c2d0b75b346dd53858e56a639bc6eb0b199e0 Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Fri, 11 Sep 2020 13:27:53 -0400 Subject: [PATCH 28/65] Add function to copy things from Frame to this Frame. --- src/Frame.cpp | 15 ++++++++++++++- src/Frame.h | 4 ++++ 2 files changed, 18 insertions(+), 1 deletion(-) diff --git a/src/Frame.cpp b/src/Frame.cpp index 00a57b608d..9300cab1b4 100644 --- a/src/Frame.cpp +++ b/src/Frame.cpp @@ -415,7 +415,20 @@ void Frame::SetMass(std::vector const& atoms) { Mass_[i] = atoms[i].Mass(); } } - + +/** Copy from firstAtom to lastAtom in tgtIn to this Frame. */ +void Frame::CopyFrom(Frame const& tgtIn, int firstAtom, int lastAtom) +{ + int i3 = firstAtom * 3; + std::copy( tgtIn.xAddress()+i3, tgtIn.xAddress()+(lastAtom*3), xAddress()+i3 ); +} + +/** Copy unit in tgtIn to this Frame. */ +void Frame::CopyFrom(Frame const& tgtIn, Unit const& unit) { + for (Unit::const_iterator seg = unit.segBegin(); seg != unit.segEnd(); ++seg) + CopyFrom( tgtIn, seg->Begin(), seg->End() ); +} + // ---------- FRAME MEMORY ALLOCATION/REALLOCATION ----------------------------- /** \return True if reallocation of coordinate arrray must occur based on * given number of atoms. diff --git a/src/Frame.h b/src/Frame.h index 0550e3fa95..e27c1a7e24 100644 --- a/src/Frame.h +++ b/src/Frame.h @@ -122,6 +122,10 @@ class Frame { void SetTime(double tIn) { time_ = tIn; } /// Set masses void SetMass(std::vector const&); + /// Copy atoms from input frame to here + void CopyFrom(Frame const&, int, int); + /// Copy unit from input frame to here + void CopyFrom(Frame const&, Unit const&); // ----- Access to internal data pointers ---- inline double* xAddress() { return X_; } inline double* vAddress() { return V_; } From 706e5d2ccdb9c1c72054891c05adf66de81cbb7d Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Fri, 11 Sep 2020 13:30:25 -0400 Subject: [PATCH 29/65] Use List in unwrap functions --- src/ImageRoutines.cpp | 56 ++++++++++--------------------------------- src/ImageRoutines.h | 6 ++--- 2 files changed, 15 insertions(+), 47 deletions(-) diff --git a/src/ImageRoutines.cpp b/src/ImageRoutines.cpp index f4e4965157..d07380acde 100644 --- a/src/ImageRoutines.cpp +++ b/src/ImageRoutines.cpp @@ -238,32 +238,16 @@ Vec3 Image::Ortho(Vec3 const& Coord, Vec3 const& bp, Vec3 const& bm, Box const& // ----------------------------------------------------------------------------- // Image::UnwrapNonortho() -void Image::UnwrapNonortho( Frame& tgtIn, Frame& refIn, PairType const& AtomPairs, - Matrix_3x3 const& ucell, Matrix_3x3 const& recip, - bool center, bool useMass ) +void Image::UnwrapNonortho( Frame& tgtIn, Frame& refIn, List const& AtomPairs, + Matrix_3x3 const& ucell, Matrix_3x3 const& recip) { Vec3 vtgt, vref, boxTrans; // Loop over atom pairs - for (PairType::const_iterator atom = AtomPairs.begin(); - atom != AtomPairs.end(); ++atom) + for (unsigned int idx = 0; idx != AtomPairs.nEntities(); idx++) { - int firstAtom = *atom; - ++atom; - int lastAtom = *atom; - if (center) { - // Use center of coordinates between first and last atoms. - if (useMass) { - vtgt = tgtIn.VCenterOfMass(firstAtom, lastAtom); - vref = refIn.VCenterOfMass(firstAtom, lastAtom); - } else { - vtgt = tgtIn.VGeometricCenter(firstAtom, lastAtom); - vref = refIn.VGeometricCenter(firstAtom, lastAtom); - } - } else { - // Use position first atom only. - vtgt = tgtIn.XYZ( firstAtom ); - vref = refIn.XYZ( firstAtom ); - } + vtgt = AtomPairs.GetCoord(idx, tgtIn); + vref = AtomPairs.GetCoord(idx, refIn); + boxTrans.Zero(); // Calculate original distance from the ref (previous) position. Vec3 vd = vtgt - vref; // dx dy dz @@ -296,7 +280,7 @@ void Image::UnwrapNonortho( Frame& tgtIn, Frame& refIn, PairType const& AtomPair } // Translate tgt atoms boxTrans.Neg(); - tgtIn.Translate( boxTrans, firstAtom, lastAtom ); + AtomPairs.DoTranslation( tgtIn, idx, boxTrans ); // Save new ref positions int i3 = firstAtom * 3; std::copy( tgtIn.xAddress()+i3, tgtIn.xAddress()+(lastAtom*3), refIn.xAddress()+i3 ); @@ -304,32 +288,16 @@ void Image::UnwrapNonortho( Frame& tgtIn, Frame& refIn, PairType const& AtomPair } // Image::UnwrapOrtho() -void Image::UnwrapOrtho( Frame& tgtIn, Frame& refIn, PairType const& AtomPairs, - bool center, bool useMass ) +void Image::UnwrapOrtho( Frame& tgtIn, Frame& refIn, List const& AtomPairs) { Vec3 vtgt, vref, boxTrans; Vec3 boxVec = tgtIn.BoxCrd().Lengths(); // Loop over atom pairs - for (PairType::const_iterator atom = AtomPairs.begin(); - atom != AtomPairs.end(); ++atom) + for (unsigned int idx = 0; idx != AtomPairs.nEntities(); idx++) { - int firstAtom = *atom; - ++atom; - int lastAtom = *atom; - if (center) { - // Use center of coordinates between first and last atoms. - if (useMass) { - vtgt = tgtIn.VCenterOfMass(firstAtom, lastAtom); - vref = refIn.VCenterOfMass(firstAtom, lastAtom); - } else { - vtgt = tgtIn.VGeometricCenter(firstAtom, lastAtom); - vref = refIn.VGeometricCenter(firstAtom, lastAtom); - } - } else { - // Use position first atom only. - vtgt = tgtIn.XYZ( firstAtom ); - vref = refIn.XYZ( firstAtom ); - } + vtgt = AtomPairs.GetCoord(idx, tgtIn); + vref = AtomPairs.GetCoord(idx, refIn); + Vec3 dxyz = vtgt - vref; boxTrans[0] = -floor( dxyz[0] / boxVec[0] + 0.5 ) * boxVec[0]; boxTrans[1] = -floor( dxyz[1] / boxVec[1] + 0.5 ) * boxVec[1]; diff --git a/src/ImageRoutines.h b/src/ImageRoutines.h index bf2c4644dd..d43f6a87dc 100644 --- a/src/ImageRoutines.h +++ b/src/ImageRoutines.h @@ -27,10 +27,10 @@ namespace Image { /// Perform orthogonal imaging on given coordinates using given box boundaries Vec3 Ortho(Vec3 const&, Vec3 const&, Vec3 const&, Box const&); /// Perform unwrap of non-orthogonal cell using given reference. - void UnwrapNonortho( Frame&, Frame&, PairType const&, - Matrix_3x3 const&, Matrix_3x3 const&, bool, bool ); + void UnwrapNonortho( Frame&, Frame&, List const&, + Matrix_3x3 const&, Matrix_3x3 const& ); /// Perform unwrap of orthogonal cell using given reference. - void UnwrapOrtho( Frame&, Frame&, PairType const&, bool, bool ); + void UnwrapOrtho( Frame&, Frame&, List const& ); /// Wrap selected atom coords from given frame into primary cell, store in result. void WrapToCell0(std::vector&, Frame const&, AtomMask const&, Matrix_3x3 const&, Matrix_3x3 const&); From 09f3214b96a482a0fe7ecd339ade4cecc034a388 Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Fri, 11 Sep 2020 13:41:29 -0400 Subject: [PATCH 30/65] Finish up Image routines. --- src/ImageRoutines.cpp | 8 +++----- src/Image_List.h | 2 ++ src/Image_List_Mask.h | 3 +++ src/Image_List_Pair.h | 3 +++ src/Image_List_Unit.h | 3 +++ src/cpptrajdepend | 2 +- 6 files changed, 15 insertions(+), 6 deletions(-) diff --git a/src/ImageRoutines.cpp b/src/ImageRoutines.cpp index d07380acde..80d93ca7dd 100644 --- a/src/ImageRoutines.cpp +++ b/src/ImageRoutines.cpp @@ -282,8 +282,7 @@ void Image::UnwrapNonortho( Frame& tgtIn, Frame& refIn, List const& AtomPairs, boxTrans.Neg(); AtomPairs.DoTranslation( tgtIn, idx, boxTrans ); // Save new ref positions - int i3 = firstAtom * 3; - std::copy( tgtIn.xAddress()+i3, tgtIn.xAddress()+(lastAtom*3), refIn.xAddress()+i3 ); + AtomPairs.CopyFrame(refIn, idx, tgtIn); } // END loop over atom pairs } @@ -303,10 +302,9 @@ void Image::UnwrapOrtho( Frame& tgtIn, Frame& refIn, List const& AtomPairs) boxTrans[1] = -floor( dxyz[1] / boxVec[1] + 0.5 ) * boxVec[1]; boxTrans[2] = -floor( dxyz[2] / boxVec[2] + 0.5 ) * boxVec[2]; // Translate atoms from first to last - tgtIn.Translate(boxTrans, firstAtom, lastAtom); + AtomPairs.DoTranslation( tgtIn, idx, boxTrans ); // Save new ref positions - int i3 = firstAtom * 3; - std::copy( tgtIn.xAddress()+i3, tgtIn.xAddress()+(lastAtom*3), refIn.xAddress()+i3 ); + AtomPairs.CopyFrame(refIn, idx, tgtIn); } // END loop over atom pairs } diff --git a/src/Image_List.h b/src/Image_List.h index e68e50d369..b0697d2dfe 100644 --- a/src/Image_List.h +++ b/src/Image_List.h @@ -18,6 +18,8 @@ class List { virtual Vec3 GetCoord(unsigned int, Frame const&) const = 0; /// Do translation of specified entity according to given translation vector. virtual void DoTranslation(Frame&, unsigned int, Vec3 const&) const = 0; + /// Copy specified entity from Frame to another Frame + virtual void CopyFrame(Frame&, unsigned int, Frame const&) const = 0; }; } #endif diff --git a/src/Image_List_Mask.h b/src/Image_List_Mask.h index 8020fd4d4b..abe62166d1 100644 --- a/src/Image_List_Mask.h +++ b/src/Image_List_Mask.h @@ -15,6 +15,9 @@ class List_Mask : public List { void DoTranslation(Frame& frm, unsigned int idx, Vec3 const& boxTrans) const { frm.Translate(boxTrans, mask_[idx]); } + void CopyFrame(Frame& refIn, unsigned int idx, Frame const& tgtIn) const { + refIn.CopyFrom(tgtIn, mask_[idx], mask_[idx]); + } protected: AtomMask mask_; }; diff --git a/src/Image_List_Pair.h b/src/Image_List_Pair.h index c248951084..7c64c59eb1 100644 --- a/src/Image_List_Pair.h +++ b/src/Image_List_Pair.h @@ -14,6 +14,9 @@ class List_Pair : public List { void DoTranslation(Frame& frm, unsigned int idx, Vec3 const& boxTrans) const { frm.Translate(boxTrans, begin_[idx], end_[idx]); } + void CopyFrame(Frame& refIn, unsigned int idx, Frame const& tgtIn) const { + refIn.CopyFrom(tgtIn, begin_[idx], end_[idx]); + } protected: typedef std::vector Iarray; Iarray begin_; diff --git a/src/Image_List_Unit.h b/src/Image_List_Unit.h index b3345e2bdb..48ac2f89b0 100644 --- a/src/Image_List_Unit.h +++ b/src/Image_List_Unit.h @@ -15,6 +15,9 @@ class List_Unit : public List { void DoTranslation(Frame& frm, unsigned int idx, Vec3 const& boxTrans) const { frm.Translate(boxTrans, units_[idx]); } + void CopyFrame(Frame& refIn, unsigned int idx, Frame const& tgtIn) const { + refIn.CopyFrom(tgtIn, units_[idx]); + } protected: typedef std::vector Uarray; Uarray units_; diff --git a/src/cpptrajdepend b/src/cpptrajdepend index 9e77f0d1d7..d7d549feda 100644 --- a/src/cpptrajdepend +++ b/src/cpptrajdepend @@ -309,7 +309,7 @@ Frame.o : Frame.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h Cpptraj GridAction.o : GridAction.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridAction.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h HistBin.o : HistBin.cpp Constants.h CpptrajStdio.h Dimension.h HistBin.h Hungarian.o : Hungarian.cpp ArrayIterator.h Constants.h CpptrajStdio.h Hungarian.h Matrix.h -ImageRoutines.o : ImageRoutines.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h DistRoutines.h FileName.h Frame.h ImageRoutines.h ImageTypes.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h +ImageRoutines.o : ImageRoutines.cpp Atom.h AtomMask.h Box.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h Frame.h ImageRoutines.h ImageTypes.h Image_List.h Image_List_Mask.h Image_List_Pair.h Image_List_Pair_CoM.h Image_List_Pair_First.h Image_List_Pair_Geom.h Image_List_Unit.h Image_List_Unit_CoM.h Image_List_Unit_First.h Image_List_Unit_Geom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Unit.h Vec3.h InputTrajCommon.o : InputTrajCommon.cpp CpptrajStdio.h FileName.h InputTrajCommon.h TrajFrameCounter.h KDE.o : KDE.cpp AssociatedData.h Constants.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_double.h Dimension.h FileIO.h FileName.h HistBin.h KDE.h MetaData.h Parallel.h Range.h TextFormat.h MapAtom.o : MapAtom.cpp Atom.h MapAtom.h NameType.h SymbolExporting.h From 8f2fce2f6f8b8a0b672001c994b2e6826bc8f461 Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Sat, 12 Sep 2020 13:32:58 -0400 Subject: [PATCH 31/65] Add separate routine for creating empty image list --- src/ImageRoutines.cpp | 30 ++++++++++++++++++------------ src/ImageRoutines.h | 4 +++- 2 files changed, 21 insertions(+), 13 deletions(-) diff --git a/src/ImageRoutines.cpp b/src/ImageRoutines.cpp index 80d93ca7dd..7f19f9fef6 100644 --- a/src/ImageRoutines.cpp +++ b/src/ImageRoutines.cpp @@ -11,13 +11,8 @@ #include "Image_List_Unit_First.h" #include "Image_List_Mask.h" -// Image::CreateImageList() -/** \return list of entities to be imaged based on given mode. - */ -Image::List* Image::CreateImageList(Topology const& Parm, Mode modeIn, - std::string const& maskExpression, - bool useMass, bool center) -{ +/** \return Empty list for imaging. */ +Image::List* Image::CreateImageList(Mode modeIn, bool useMass, bool center) { Image::List* listOut = 0; switch (modeIn) { case BYMOL : @@ -42,18 +37,29 @@ Image::List* Image::CreateImageList(Topology const& Parm, Mode modeIn, listOut = new Image::List_Mask(); break; } + if (listOut == 0) { + mprinterr("Internal Error: Could not allocate image list over %ss\n", ModeString(modeIn)); + } + return listOut; +} + +// Image::CreateImageList() +/** \return list of entities to be imaged based on given mode. + */ +Image::List* Image::CreateImageList(Topology const& Parm, Mode modeIn, + std::string const& maskExpression, + bool useMass, bool center) +{ + Image::List* listOut = CreateImageList(modeIn, useMass, center); if (listOut != 0) { if (listOut->SetupList(Parm, maskExpression)) { mprinterr("Error: Could not set up image list for '%s'\n", maskExpression.c_str()); delete listOut; return 0; } - } else { - mprinterr("Internal Error: Could not allocate image list for '%s'\n", maskExpression.c_str()); - return 0; + mprintf("DEBUG: Image list for '%s' over %u %ss.\n", + maskExpression.c_str(), listOut->nEntities(), ModeString(modeIn)); } - mprintf("DEBUG: Image list for '%s' over %u %ss.\n", - maskExpression.c_str(), listOut->nEntities(), ModeString(modeIn)); return listOut; } diff --git a/src/ImageRoutines.h b/src/ImageRoutines.h index d43f6a87dc..baeaf14bbb 100644 --- a/src/ImageRoutines.h +++ b/src/ImageRoutines.h @@ -10,7 +10,9 @@ class Box; #include "ImageTypes.h" namespace Image { class List; - /// Create an atom pair list by molecule, residue, or atom. + /// \return empty image list for given mode, optionally using mass and centering + List* CreateImageList(Mode, bool, bool); + /// \return an image list for given Top, mode, mask, optionally using mass and centering List* CreateImageList(Topology const&, Mode, std::string const&, bool, bool); /// \return Coordinates of center if wrapping molecules into truncated oct. shape. Vec3 SetupTruncoct( Frame const&, AtomMask*, bool, bool); From 68989e209ad5906f9619269f457832d7dd834d37 Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Sat, 12 Sep 2020 13:38:07 -0400 Subject: [PATCH 32/65] Add function to manually add unit --- src/Image_List_Unit.cpp | 4 ++++ src/Image_List_Unit.h | 2 ++ 2 files changed, 6 insertions(+) diff --git a/src/Image_List_Unit.cpp b/src/Image_List_Unit.cpp index b1fbc02e19..9e61267bec 100644 --- a/src/Image_List_Unit.cpp +++ b/src/Image_List_Unit.cpp @@ -16,3 +16,7 @@ int Image::List_Unit::SetupList(Topology const& Parm, std::string const& maskExp } return 0; } + +void Image::List_Unit::AddUnit(Unit const& unitIn) { + units_.push_back( unitIn ); +} diff --git a/src/Image_List_Unit.h b/src/Image_List_Unit.h index 48ac2f89b0..263e89c727 100644 --- a/src/Image_List_Unit.h +++ b/src/Image_List_Unit.h @@ -18,6 +18,8 @@ class List_Unit : public List { void CopyFrame(Frame& refIn, unsigned int idx, Frame const& tgtIn) const { refIn.CopyFrom(tgtIn, units_[idx]); } + + void AddUnit(Unit const&); protected: typedef std::vector Uarray; Uarray units_; From 2029b255aa94359b6e055a7b72da218ef30fea1c Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Sat, 12 Sep 2020 13:54:19 -0400 Subject: [PATCH 33/65] Add some functions for working with Image_List_Unit directly --- src/Image_List_Unit.h | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/src/Image_List_Unit.h b/src/Image_List_Unit.h index 263e89c727..d57ea8b2e6 100644 --- a/src/Image_List_Unit.h +++ b/src/Image_List_Unit.h @@ -7,6 +7,7 @@ class Unit; namespace Image { /// List with entities defined by Units class List_Unit : public List { + typedef std::vector Uarray; public: List_Unit() {} virtual ~List_Unit() {} @@ -20,8 +21,11 @@ class List_Unit : public List { } void AddUnit(Unit const&); + typedef Uarray::const_iterator const_iterator; + const_iterator begin() const { return units_.begin(); } + const_iterator end() const { return units_.end(); } + bool empty() const { return units_.empty(); } protected: - typedef std::vector Uarray; Uarray units_; }; } From 6f11e30ac37c65fbcecc82f5f07a9613c5f67f94 Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Sat, 12 Sep 2020 13:58:00 -0400 Subject: [PATCH 34/65] Update autoimage to use the new routines. --- src/Action_AutoImage.cpp | 110 +++++++++++++++++---------------------- src/Action_AutoImage.h | 13 ++--- src/cpptrajdepend | 5 +- src/cpptrajfiles | 3 ++ 4 files changed, 63 insertions(+), 68 deletions(-) diff --git a/src/Action_AutoImage.cpp b/src/Action_AutoImage.cpp index f83f9f4196..321668bd95 100644 --- a/src/Action_AutoImage.cpp +++ b/src/Action_AutoImage.cpp @@ -4,7 +4,7 @@ #include "DistRoutines.h" #include "ImageRoutines.h" #include "CharMask.h" -#include "Unit.h" +#include "Image_List_Unit.h" // CONSTRUCTOR Action_AutoImage::Action_AutoImage() : @@ -15,9 +15,17 @@ Action_AutoImage::Action_AutoImage() : truncoct_(false), useMass_(false), movingAnchor_(false), - triclinic_(OFF) + triclinic_(OFF), + fixedList_(0), + mobileList_(0) {} +/** DESTRUCTOR */ +Action_AutoImage::~Action_AutoImage() { + if (fixedList_ != 0) delete fixedList_; + if (mobileList_ != 0) delete mobileList_; +} + void Action_AutoImage::Help() const { mprintf("\t[ | anchor [fixed ] [mobile ]]\n" "\t[origin] [firstatom] [familiar | triclinic] [moveanchor]\n" @@ -75,30 +83,6 @@ Action::RetType Action_AutoImage::Init(ArgList& actionArgs, ActionInit& init, in return Action::OK; } -// Action_AutoImage::SetupAtomRanges() -/** Based on the given atom mask expression determine what molecules are - * selected by the mask. If a mask selects any part of a molecule the - * entire molecule will be selected. - * \return A list of Units for each selected molecule. - */ -Action_AutoImage::Uarray - Action_AutoImage::SetupAtomRanges(Topology const& currentParm, std::string const& maskexpr) -{ - Uarray imageList; - CharMask Mask1( maskexpr.c_str() ); - - if (currentParm.SetupCharMask( Mask1 )) return imageList; - if (Mask1.None()) return imageList; - for (Topology::mol_iterator mol = currentParm.MolStart(); mol != currentParm.MolEnd(); mol++) - { - // Check that any atom in the range is in Mask1 - if (Mask1.AtomsInCharMask(mol->MolUnit())) - imageList.push_back( mol->MolUnit() ); - } - mprintf("\tMask [%s] corresponds to %zu molecules\n", Mask1.MaskString(), imageList.size()); - return imageList; -} - // Action_AutoImage::Setup() Action::RetType Action_AutoImage::Setup(ActionSetup& setup) { bool fixedauto = false; @@ -151,19 +135,34 @@ Action::RetType Action_AutoImage::Setup(ActionSetup& setup) { anchorMask_.AddUnit( setup.Top().Mol(0).MolUnit() ); } + if (fixedList_ != 0) delete fixedList_; + if (mobileList_ != 0) delete mobileList_; // Set up fixed region - if (!fixed_.empty()) - fixedList_ = SetupAtomRanges( setup.Top(), fixed_ ); + // NOTE: Always use molecule center when imaging fixed list + if (!fixed_.empty()) + fixedList_ = (Image::List_Unit*) + Image::CreateImageList(setup.Top(), Image::BYMOL, fixed_, useMass_, true); else { fixedauto = true; - fixedList_.clear(); + fixedList_ = (Image::List_Unit*) + Image::CreateImageList(Image::BYMOL, useMass_, true); + } + if (fixedList_ == 0) { + mprinterr("Internal Error: Could not allocate fixed list.\n"); + return Action::ERR; } // Set up mobile region if (!mobile_.empty()) - mobileList_ = SetupAtomRanges( setup.Top(), mobile_ ); + mobileList_ = (Image::List_Unit*) + Image::CreateImageList(setup.Top(), Image::BYMOL, mobile_, useMass_, usecom_); else { mobileauto = true; - mobileList_.clear(); + mobileList_ = (Image::List_Unit*) + Image::CreateImageList(Image::BYMOL, useMass_, usecom_); + } + if (mobileList_ == 0) { + mprinterr("Internal Error: Could not allocate mobile list.\n"); + return Action::ERR; } // Automatic search through molecules for fixed/mobile if (fixedauto || mobileauto) { @@ -177,11 +176,11 @@ Action::RetType Action_AutoImage::Setup(ActionSetup& setup) { // everything else into fixed list. if ( mol->IsSolvent() || mol->NumAtoms() == 1 ) { if (mobileauto) { - mobileList_.push_back( mol->MolUnit() ); + mobileList_->AddUnit( mol->MolUnit() ); } } else { if (fixedauto) { - fixedList_.push_back( mol->MolUnit() ); + fixedList_->AddUnit( mol->MolUnit() ); } } } @@ -189,18 +188,18 @@ Action::RetType Action_AutoImage::Setup(ActionSetup& setup) { } } // Print fixed and mobile lists - if (!fixedList_.empty()) { - mprintf("\t%zu molecules are fixed to anchor:", fixedList_.size()); - for (Uarray::const_iterator it = fixedList_.begin(); - it != fixedList_.end(); ++it) + if (!fixedList_->empty()) { + mprintf("\t%u molecules are fixed to anchor:", fixedList_->nEntities()); + for (Image::List_Unit::const_iterator it = fixedList_->begin(); + it != fixedList_->end(); ++it) mprintf(" %i", setup.Top()[ it->Front() ].MolNum()+1 ); mprintf("\n"); } - mprintf("\t%zu molecules are mobile.\n", mobileList_.size() ); + mprintf("\t%u molecules are mobile.\n", mobileList_->nEntities() ); if (debug_ > 1) { mprintf("\tThe following molecules are mobile:\n"); - for (Uarray::const_iterator it = mobileList_.begin(); - it != mobileList_.end(); ++it) + for (Image::List_Unit::const_iterator it = mobileList_->begin(); + it != mobileList_->end(); ++it) mprintf(" %i\n", setup.Top()[ it->Front() ].MolNum()+1 ); mprintf("\n"); } @@ -250,12 +249,12 @@ Action::RetType Action_AutoImage::DoAction(int frameNum, ActionFrame& frm) { // TODO: Return OK for now so next frame is tried; eventually indicate SKIP? return Action::OK; // FIXME return MODIFY_COORDS instead? } - Image::Ortho(frm.ModifyFrm(), bp, bm, offset, usecom_, useMass_, mobileList_); + Image::Ortho(frm.ModifyFrm(), bp, bm, offset, *mobileList_); } else { if (truncoct_) fcom = Image::SetupTruncoct( frm.Frm(), 0, useMass_, origin_ ); Image::Nonortho(frm.ModifyFrm(), origin_, fcom, offset, ucell, recip, truncoct_, - usecom_, useMass_, mobileList_); + *mobileList_); } if (movingAnchor_) { @@ -263,15 +262,9 @@ Action::RetType Action_AutoImage::DoAction(int frameNum, ActionFrame& frm) { // more efficient than the !movingAnchor_ case but more testing is // needed. // Loop over fixed molecules - for (pairList::const_iterator atom1 = fixedList_.begin(); - atom1 != fixedList_.end(); atom1 += 2) + for (unsigned int idx = 0; idx != fixedList_->nEntities(); ++idx) { - int firstAtom = *atom1; - int lastAtom = *(atom1+1); - if (useMass_) - framecenter = frm.Frm().VCenterOfMass(firstAtom, lastAtom); - else - framecenter = frm.Frm().VGeometricCenter(firstAtom, lastAtom); + framecenter = fixedList_->GetCoord(idx, frm.Frm()); // Determine distance in terms of box lengths if (ortho_) { @@ -286,7 +279,7 @@ Action::RetType Action_AutoImage::DoAction(int frameNum, ActionFrame& frm) { // frameNum, (atom1-fixedList_.begin())/2, firstAtom+1, lastAtom, // minTrans[0], minTrans[1], minTrans[2]); // Move atoms closer to anchor. Update coords in currentFrame. - frm.ModifyFrm().Translate(minTrans, firstAtom, lastAtom); + fixedList_->DoTranslation(frm.ModifyFrm(), idx, minTrans); // New anchor is previous fixed mol anchorcenter = minImage; } else { @@ -303,7 +296,7 @@ Action::RetType Action_AutoImage::DoAction(int frameNum, ActionFrame& frm) { // Trans[0], Trans[1], Trans[2], sqrt(framedist2), sqrt(imageddist2)); if (imageddist2 < framedist2) { // Imaging these atoms moved them closer to anchor. Update coords in currentFrame. - frm.ModifyFrm().Translate(Trans, firstAtom, lastAtom); + fixedList_->DoTranslation(frm.ModifyFrm(), idx, Trans); newAnchor = imagedcenter; } } @@ -314,15 +307,10 @@ Action::RetType Action_AutoImage::DoAction(int frameNum, ActionFrame& frm) { // For each molecule defined by atom pairs in fixedList, determine if the // imaged position is closer to anchor center than the current position. // Always use molecule center when imaging fixedList. - for (pairList::const_iterator atom1 = fixedList_.begin(); - atom1 != fixedList_.end(); atom1 += 2) + for (unsigned int idx = 0; idx != fixedList_->nEntities(); ++idx) { - int firstAtom = *atom1; - int lastAtom = *(atom1+1); - if (useMass_) - framecenter = frm.Frm().VCenterOfMass(firstAtom, lastAtom); - else - framecenter = frm.Frm().VGeometricCenter(firstAtom, lastAtom); + framecenter = fixedList_->GetCoord(idx, frm.Frm()); + // Determine if molecule would be imaged. if (ortho_) Trans = Image::Ortho(framecenter, bp, bm, box); @@ -338,7 +326,7 @@ Action::RetType Action_AutoImage::DoAction(int frameNum, ActionFrame& frm) { // Trans[0], Trans[1], Trans[2], sqrt(framedist2), sqrt(imageddist2)); if (imageddist2 < framedist2) { // Imaging these atoms moved them closer to anchor. Update coords in currentFrame. - frm.ModifyFrm().Translate(Trans, firstAtom, lastAtom); + fixedList_->DoTranslation(frm.ModifyFrm(), idx, Trans); } } } diff --git a/src/Action_AutoImage.h b/src/Action_AutoImage.h index 109fa3bea9..3332eaab99 100644 --- a/src/Action_AutoImage.h +++ b/src/Action_AutoImage.h @@ -2,9 +2,14 @@ #define INC_ACTION_AUTOIMAGE_H #include "Action.h" class Unit; +namespace Image { + class List_Unit; +} +/// Perform imaging, attempting to keep solute in 1 configuration class Action_AutoImage : public Action { public: Action_AutoImage(); + ~Action_AutoImage(); DispatchObject* Alloc() const { return (DispatchObject*)new Action_AutoImage(); } void Help() const; private: @@ -13,10 +18,6 @@ class Action_AutoImage : public Action { Action::RetType DoAction(int, ActionFrame&); void Print() {} - typedef std::vector Uarray; - - static Uarray SetupAtomRanges(Topology const&, std::string const&); - AtomMask anchorMask_; ///< Used to center anchor region. std::string anchor_; ///< Mask expression for anchor region. std::string fixed_; ///< Mask expression for fixed region. @@ -31,7 +32,7 @@ class Action_AutoImage : public Action { enum TriclinicArg {OFF, FORCE, FAMILIAR}; TriclinicArg triclinic_; ///< Determine whether triclinic code should be used. - Uarray fixedList_; ///< Contain atom indices for fixed elements - Uarray mobileList_; ///< Contain atom indices for mobile elements. + Image::List_Unit* fixedList_; ///< Contain atom indices for fixed elements + Image::List_Unit* mobileList_; ///< Contain atom indices for mobile elements. }; #endif diff --git a/src/cpptrajdepend b/src/cpptrajdepend index d7d549feda..5e109a8f5a 100644 --- a/src/cpptrajdepend +++ b/src/cpptrajdepend @@ -8,7 +8,7 @@ Action_AreaPerMol.o : Action_AreaPerMol.cpp Action.h ActionState.h Action_AreaPe Action_AtomMap.o : Action_AtomMap.cpp Action.h ActionState.h Action_AtomMap.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h StructureMapper.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h Action_AtomicCorr.o : Action_AtomicCorr.cpp Action.h ActionState.h Action_AtomicCorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h Action_AtomicFluct.o : Action_AtomicFluct.cpp Action.h ActionFrameCounter.h ActionState.h Action_AtomicFluct.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h -Action_AutoImage.o : Action_AutoImage.cpp Action.h ActionState.h Action_AutoImage.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageRoutines.h ImageTypes.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_AutoImage.o : Action_AutoImage.cpp Action.h ActionState.h Action_AutoImage.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageRoutines.h ImageTypes.h Image_List.h Image_List_Unit.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h Action_Average.o : Action_Average.cpp Action.h ActionFrameCounter.h ActionState.h Action_Average.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h Action_Bounds.o : Action_Bounds.cpp Action.h ActionState.h Action_Bounds.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h Action_Box.o : Action_Box.cpp Action.h ActionState.h Action_Box.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h @@ -310,6 +310,9 @@ GridAction.o : GridAction.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h HistBin.o : HistBin.cpp Constants.h CpptrajStdio.h Dimension.h HistBin.h Hungarian.o : Hungarian.cpp ArrayIterator.h Constants.h CpptrajStdio.h Hungarian.h Matrix.h ImageRoutines.o : ImageRoutines.cpp Atom.h AtomMask.h Box.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h Frame.h ImageRoutines.h ImageTypes.h Image_List.h Image_List_Mask.h Image_List_Pair.h Image_List_Pair_CoM.h Image_List_Pair_First.h Image_List_Pair_Geom.h Image_List_Unit.h Image_List_Unit_CoM.h Image_List_Unit_First.h Image_List_Unit_Geom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Unit.h Vec3.h +Image_List_Mask.o : Image_List_Mask.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h FileName.h Frame.h Image_List.h Image_List_Mask.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Image_List_Pair.o : Image_List_Pair.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h FileName.h Frame.h Image_List.h Image_List_Pair.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Image_List_Unit.o : Image_List_Unit.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h FileName.h Frame.h Image_List.h Image_List_Unit.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h InputTrajCommon.o : InputTrajCommon.cpp CpptrajStdio.h FileName.h InputTrajCommon.h TrajFrameCounter.h KDE.o : KDE.cpp AssociatedData.h Constants.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_double.h Dimension.h FileIO.h FileName.h HistBin.h KDE.h MetaData.h Parallel.h Range.h TextFormat.h MapAtom.o : MapAtom.cpp Atom.h MapAtom.h NameType.h SymbolExporting.h diff --git a/src/cpptrajfiles b/src/cpptrajfiles index 9128409fde..159268f8a2 100644 --- a/src/cpptrajfiles +++ b/src/cpptrajfiles @@ -310,6 +310,9 @@ COMMON_SOURCES= \ HistBin.cpp \ Hungarian.cpp \ ImageRoutines.cpp \ + Image_List_Mask.cpp \ + Image_List_Pair.cpp \ + Image_List_Unit.cpp \ InputTrajCommon.cpp \ KDE.cpp \ MapAtom.cpp \ From 306864eccb85a229ba8aeb60c24fd99d71f92cfb Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Sat, 12 Sep 2020 18:52:22 -0400 Subject: [PATCH 35/65] Remove unneeded include --- src/ImageTypes.h | 1 - 1 file changed, 1 deletion(-) diff --git a/src/ImageTypes.h b/src/ImageTypes.h index cbe2ffca66..57f70ad3bd 100644 --- a/src/ImageTypes.h +++ b/src/ImageTypes.h @@ -3,7 +3,6 @@ /*! \file ImageTypes.h \brief Data types and enumerations used by imaging routines. */ -#include namespace Image { enum Mode { BYMOL = 0, BYRES, BYATOM }; inline const char* ModeString(Mode m) { From 1fcb157ba6b6d7ab8ed28dff33ca46cdcb1ea0af Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Sat, 12 Sep 2020 19:00:35 -0400 Subject: [PATCH 36/65] Update Closest --- src/Action_Closest.cpp | 26 ++++++++++++++------------ 1 file changed, 14 insertions(+), 12 deletions(-) diff --git a/src/Action_Closest.cpp b/src/Action_Closest.cpp index 7a1da500b7..320aca60c2 100644 --- a/src/Action_Closest.cpp +++ b/src/Action_Closest.cpp @@ -160,7 +160,7 @@ Action::RetType Action_Closest::Setup(ActionSetup& setup) { for (Topology::mol_iterator Mol = setup.Top().MolStart(); Mol != setup.Top().MolEnd(); ++Mol) { - if ( solventMask_.AtomsInCharMask(Mol->BeginAtom(), Mol->EndAtom()) ) { + if ( solventMask_.AtomsInCharMask(Mol->MolUnit()) ) { IsSolventMol.push_back( true ); nSolvent++; } else @@ -214,44 +214,46 @@ Action::RetType Action_Closest::Setup(ActionSetup& setup) { int molnum = 1; int newnatom = 0; int nclosest = 0; - int NsolventAtoms = -1; + unsigned int NsolventAtoms = 0; keptWaterAtomNum_.resize(closestWaters_); for (Topology::mol_iterator Mol = setup.Top().MolStart(); Mol != setup.Top().MolEnd(); ++Mol, ++isSolvent) { if ( !(*isSolvent) ) { // Not solvent, add to solute mask. - stripMask_.AddAtomRange( Mol->BeginAtom(), Mol->EndAtom() ); + stripMask_.AddUnit( Mol->MolUnit() ); newnatom += Mol->NumAtoms(); } else { // Solvent, check for same # of atoms. - if (NsolventAtoms == -1) + if (NsolventAtoms == 0) NsolventAtoms = Mol->NumAtoms(); else if ( NsolventAtoms != Mol->NumAtoms() ) { mprinterr("Error: Solvent molecules in '%s' are not of uniform size.\n" - "Error: First solvent mol = %i atoms, solvent mol %i = %i atoms.\n", - setup.Top().c_str(), NsolventAtoms, molnum, (*Mol).NumAtoms()); + "Error: First solvent mol = %u atoms, solvent mol %i = %u atoms.\n", + setup.Top().c_str(), NsolventAtoms, molnum, Mol->NumAtoms()); return Action::ERR; } // mol here is the output molecule number which is why it starts from 1. mdist->mol = molnum; // Entire solvent molecule mask - mdist->mask.AddAtomRange( Mol->BeginAtom(), Mol->EndAtom() ); + mdist->mask.AddUnit( Mol->MolUnit() ); // Atoms in the solvent molecule to actually calculate distances to. if (firstAtom_) { - mdist->solventAtoms.assign(1, Mol->BeginAtom() ); + mdist->solventAtoms.assign(1, Mol->MolUnit().Front() ); } else { mdist->solventAtoms.clear(); mdist->solventAtoms.reserve( Mol->NumAtoms() ); - for (int svatom = Mol->BeginAtom(); svatom < Mol->EndAtom(); svatom++) - if (solventMask_.AtomInCharMask(svatom)) - mdist->solventAtoms.push_back( svatom ); + for (Unit::const_iterator seg = Mol->MolUnit().segBegin(); + seg != Mol->MolUnit().segEnd(); ++seg) + for (int svatom = seg->Begin(); svatom < seg->End(); svatom++) + if (solventMask_.AtomInCharMask(svatom)) + mdist->solventAtoms.push_back( svatom ); } // For solvent molecules that will be kept, record what the atom number // will be in the new stripped parm. if (nclosest < closestWaters_) { keptWaterAtomNum_[nclosest] = newnatom; - stripMask_.AddAtomRange( Mol->BeginAtom(), Mol->EndAtom() ); + stripMask_.AddUnit( Mol->MolUnit() ); newnatom += Mol->NumAtoms(); ++nclosest; } From d586653e97c11948ccffd0c82c39350139858bef Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Mon, 14 Sep 2020 09:28:52 -0400 Subject: [PATCH 37/65] Update gist and dipole for mol unit --- src/Action_Dipole.cpp | 46 +++++++++++++++++++++++-------------------- src/Action_GIST.cpp | 27 ++++++++++++++----------- 2 files changed, 41 insertions(+), 32 deletions(-) diff --git a/src/Action_Dipole.cpp b/src/Action_Dipole.cpp index 73fb319c35..83e43965fd 100644 --- a/src/Action_Dipole.cpp +++ b/src/Action_Dipole.cpp @@ -73,7 +73,7 @@ Action::RetType Action_Dipole::Setup(ActionSetup& setup) { // Traverse over solvent molecules to find out the // "largest" solvent molecule; allocate space for this // many coordinates. - int NsolventAtoms = 0; + unsigned int NsolventAtoms = 0; for (Topology::mol_iterator Mol = setup.Top().MolStart(); Mol != setup.Top().MolEnd(); ++Mol) { @@ -83,7 +83,7 @@ Action::RetType Action_Dipole::Setup(ActionSetup& setup) { } } //sol_.resize( NsolventAtoms ); - mprintf("\tLargest solvent mol is %i atoms.\n", NsolventAtoms); + mprintf("\tLargest solvent mol is %u atoms.\n", NsolventAtoms); // Setup grid, checks box info. if (GridSetup( setup.Top(), setup.CoordInfo() )) return Action::ERR; @@ -123,26 +123,30 @@ Action::RetType Action_Dipole::DoAction(int frameNum, ActionFrame& frm) { COM.Zero(); double total_mass = 0; // Loop over solvent atoms - for (int satom = (*solvmol).BeginAtom(); satom < (*solvmol).EndAtom(); ++satom) + for (Unit::const_iterator seg = solvmol->MolUnit().segBegin(); + seg != solvmol->MolUnit().segEnd(); ++seg) { - if ( mask_.AtomInCharMask(satom) ) { - // Get coordinates and shift to origin and then to appropriate spacing - // NOTE: Do not shift into grid coords until the very end. - const double* sol = frm.Frm().XYZ( satom ); - // Calculate dipole vector. The center of mass of the solvent is used - // as the "origin" for the vector. - // NOTE: the total charge on the solvent should be neutral for this - // to have any meaning. - double mass = (*CurrentParm_)[satom].Mass(); - total_mass += mass; - COM[0] += (mass * sol[0]); - COM[1] += (mass * sol[1]); - COM[2] += (mass * sol[2]); - - double charge = (*CurrentParm_)[satom].Charge(); - dipolar_vector[0] += (charge * sol[0]); - dipolar_vector[1] += (charge * sol[1]); - dipolar_vector[2] += (charge * sol[2]); + for (int satom = seg->Begin(); satom != seg->End(); ++satom) + { + if ( mask_.AtomInCharMask(satom) ) { + // Get coordinates and shift to origin and then to appropriate spacing + // NOTE: Do not shift into grid coords until the very end. + const double* sol = frm.Frm().XYZ( satom ); + // Calculate dipole vector. The center of mass of the solvent is used + // as the "origin" for the vector. + // NOTE: the total charge on the solvent should be neutral for this + // to have any meaning. + double mass = (*CurrentParm_)[satom].Mass(); + total_mass += mass; + COM[0] += (mass * sol[0]); + COM[1] += (mass * sol[1]); + COM[2] += (mass * sol[2]); + + double charge = (*CurrentParm_)[satom].Charge(); + dipolar_vector[0] += (charge * sol[0]); + dipolar_vector[1] += (charge * sol[1]); + dipolar_vector[2] += (charge * sol[2]); + } } } // If no atoms selected for this solvent molecule, skip. diff --git a/src/Action_GIST.cpp b/src/Action_GIST.cpp index 7b521d3135..4f3745b73b 100644 --- a/src/Action_GIST.cpp +++ b/src/Action_GIST.cpp @@ -383,7 +383,8 @@ Action::RetType Action_GIST::Setup(ActionSetup& setup) { mol != setup.Top().MolEnd(); ++mol, ++midx) { if (mol->IsSolvent()) { - int o_idx = mol->BeginAtom(); + // NOTE: We assume the oxygen is the first atom! + int o_idx = mol->MolUnit().Front(); #ifdef CUDA this->headAtomType_ = setup.Top()[o_idx].TypeIndex(); #endif @@ -456,16 +457,20 @@ Action::RetType Action_GIST::Setup(ActionSetup& setup) { // This is a non-solvent molecule. Save atom indices. May want to exclude // if only 1 atom (probably ion). if (mol->NumAtoms() > 1 || includeIons_) { - for (int u_idx = mol->BeginAtom(); u_idx != mol->EndAtom(); ++u_idx) { - A_idxs_.push_back( u_idx ); - atom_voxel_.push_back( SOLUTE_ ); - NsoluteAtoms++; - #ifdef CUDA - this->molecule_.push_back( setup.Top()[ u_idx ].MolNum() ); - this->charges_.push_back( setup.Top()[ u_idx ].Charge() ); - this->atomTypes_.push_back( setup.Top()[ u_idx ].TypeIndex() ); - this->solvent_[ u_idx ] = false; - #endif + for (Unit::const_iterator seg = mol->MolUnit().segBegin(); + seg != mol->MolUnit().segEnd(); ++seg) + { + for (int u_idx = seg->Begin(); u_idx != seg->End(); ++u_idx) { + A_idxs_.push_back( u_idx ); + atom_voxel_.push_back( SOLUTE_ ); + NsoluteAtoms++; + #ifdef CUDA + this->molecule_.push_back( setup.Top()[ u_idx ].MolNum() ); + this->charges_.push_back( setup.Top()[ u_idx ].Charge() ); + this->atomTypes_.push_back( setup.Top()[ u_idx ].TypeIndex() ); + this->solvent_[ u_idx ] = false; + #endif + } } } } From a710885d1b860636b931f644553b53ce94f9014f Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Mon, 14 Sep 2020 09:59:57 -0400 Subject: [PATCH 38/65] Start updating the image action --- src/Action_AutoImage.h | 1 - src/Action_Image.cpp | 43 +++++++++++++++++++++++++----------------- src/Action_Image.h | 20 ++++++++++++-------- 3 files changed, 38 insertions(+), 26 deletions(-) diff --git a/src/Action_AutoImage.h b/src/Action_AutoImage.h index 3332eaab99..5b124f5560 100644 --- a/src/Action_AutoImage.h +++ b/src/Action_AutoImage.h @@ -1,7 +1,6 @@ #ifndef INC_ACTION_AUTOIMAGE_H #define INC_ACTION_AUTOIMAGE_H #include "Action.h" -class Unit; namespace Image { class List_Unit; } diff --git a/src/Action_Image.cpp b/src/Action_Image.cpp index 7d8f30bd7a..b57fc1619e 100644 --- a/src/Action_Image.cpp +++ b/src/Action_Image.cpp @@ -2,6 +2,7 @@ #include "Action_Image.h" #include "CpptrajStdio.h" #include "ImageRoutines.h" +#include "Image_List.h" // CONSTRUCTOR Action_Image::Action_Image() : @@ -14,8 +15,15 @@ Action_Image::Action_Image() : useMass_(true), truncoct_(false), triclinic_(OFF), - debug_(0) -{ } + debug_(0), + imageList_(0) +{ } + +/** DESTRUCTOR */ +Action_Image::~Action_Image() { + if (imageList_ != 0) delete imageList_; + if (ComMask_!=0) delete ComMask_; +} void Action_Image::Help() const { mprintf("\t[origin] [center] [triclinic | familiar [com ]] \n" @@ -30,11 +38,6 @@ void Action_Image::Help() const { " : Only image atoms in . If no mask given all atoms are imaged.\n"); } -// DESTRUCTOR -Action_Image::~Action_Image() { - if (ComMask_!=0) delete ComMask_; -} - // Action_Image::Init() Action::RetType Action_Image::Init(ArgList& actionArgs, ActionInit& init, int debugIn) { @@ -112,19 +115,25 @@ Action::RetType Action_Image::Setup(ActionSetup& setup) { if (setup.CoordInfo().TrajBox().Type()==Box::ORTHO && triclinic_==OFF) ortho_ = true; // Setup atom pairs to be unwrapped. - imageList_ = Image::CreateAtomPairList(setup.Top(), imageMode_, maskExpression_); - if (imageList_.empty()) { - mprintf("Warning: No atoms selected for topology '%s'.\n", setup.Top().c_str()); + if (imageList_ != 0) delete imageList_; + imageList_ = Image::CreateImageList(setup.Top(), imageMode_, maskExpression_, + useMass_, center_); + if (imageList_ == 0) { + mprinterr("Internal Error: Could not allocate image list.\n"); + return Action::ERR; + } + if (imageList_->nEntities() < 1) { + mprintf("Warning: Nothing selected to image for topology '%s'.\n", setup.Top().c_str()); return Action::SKIP; } - mprintf("\tNumber of %ss to be imaged is %zu\n", - Image::ModeString(imageMode_), imageList_.size()/2); - // DEBUG: Print all pairs - if (debug_>0) { + mprintf("\tNumber of %ss to be imaged is %u\n", + Image::ModeString(imageMode_), imageList_->nEntities()); + // DEBUG: Print all pairs TODO fix this + /*if (debug_>0) { for (std::vector::const_iterator ap = imageList_.begin(); ap != imageList_.end(); ap+=2) mprintf("\t\tFirst-Last atom#: %i - %i\n", (*ap)+1, *(ap+1) ); - } + }*/ // Setup for truncated octahedron if (triclinic_ == FAMILIAR) { if (ComMask_!=0) { @@ -157,13 +166,13 @@ Action::RetType Action_Image::DoAction(int frameNum, ActionFrame& frm) { // TODO: Return OK for now so next frame is tried; eventually indicate SKIP? return Action::OK; } - Image::Ortho(frm.ModifyFrm(), bp, bm, offset_, center_, useMass_, imageList_); + Image::Ortho(frm.ModifyFrm(), bp, bm, offset_, *imageList_); } else { frm.Frm().BoxCrd().ToRecip( ucell, recip ); if (truncoct_) fcom = Image::SetupTruncoct( frm.Frm(), ComMask_, useMass_, origin_ ); Image::Nonortho( frm.ModifyFrm(), origin_, fcom, offset_, ucell, recip, truncoct_, - center_, useMass_, imageList_); + *imageList_); } return Action::MODIFY_COORDS; } diff --git a/src/Action_Image.h b/src/Action_Image.h index 7140f75e87..54f1b42a8e 100644 --- a/src/Action_Image.h +++ b/src/Action_Image.h @@ -2,14 +2,23 @@ #define INC_ACTION_IMAGE_H /// Action to wrap coordinates back into primary box #include "Action.h" -#include "ImageTypes.h" +#include "ImageTypes.h" // Image::Mode +namespace Image { + class List; +} +/// Perform basic imaging. class Action_Image: public Action { public: Action_Image(); + ~Action_Image(); DispatchObject* Alloc() const { return (DispatchObject*)new Action_Image(); } void Help() const; - ~Action_Image(); private: + Action::RetType Init(ArgList&, ActionInit&, int); + Action::RetType Setup(ActionSetup&); + Action::RetType DoAction(int, ActionFrame&); + void Print() {} + Image::Mode imageMode_; /// Mask expression selecting atoms to image. std::string maskExpression_; @@ -29,11 +38,6 @@ class Action_Image: public Action { TriclinicArg triclinic_; int debug_; /// Vector containing atom ranges to be imaged (first to last) - Image::PairType imageList_; - - Action::RetType Init(ArgList&, ActionInit&, int); - Action::RetType Setup(ActionSetup&); - Action::RetType DoAction(int, ActionFrame&); - void Print() {} + Image::List* imageList_; }; #endif From 6b208e4daef0d846e290b598981a3596d5c043ff Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Mon, 14 Sep 2020 10:20:39 -0400 Subject: [PATCH 39/65] When unwrapping, instead of invoking a copy each time an entity is updated, do it at the end with a Unit. This will take advantage of any contiguous regions and potentially reduce the number of copy calls required. --- src/ImageRoutines.cpp | 16 +++++++++------- src/ImageRoutines.h | 13 ++++++++++--- src/Image_List.h | 5 +++-- src/Image_List_Mask.cpp | 9 +++++++++ src/Image_List_Mask.h | 4 +--- src/Image_List_Pair.cpp | 10 ++++++++++ src/Image_List_Pair.h | 4 +--- src/Image_List_Unit.cpp | 12 ++++++++++++ src/Image_List_Unit.h | 4 +--- 9 files changed, 56 insertions(+), 21 deletions(-) diff --git a/src/ImageRoutines.cpp b/src/ImageRoutines.cpp index 7f19f9fef6..13a0fd9200 100644 --- a/src/ImageRoutines.cpp +++ b/src/ImageRoutines.cpp @@ -244,8 +244,9 @@ Vec3 Image::Ortho(Vec3 const& Coord, Vec3 const& bp, Vec3 const& bm, Box const& // ----------------------------------------------------------------------------- // Image::UnwrapNonortho() -void Image::UnwrapNonortho( Frame& tgtIn, Frame& refIn, List const& AtomPairs, - Matrix_3x3 const& ucell, Matrix_3x3 const& recip) +void Image::UnwrapNonortho(Frame& tgtIn, Frame& refIn, List const& AtomPairs, + Unit const& allEntities, + Matrix_3x3 const& ucell, Matrix_3x3 const& recip) { Vec3 vtgt, vref, boxTrans; // Loop over atom pairs @@ -287,13 +288,14 @@ void Image::UnwrapNonortho( Frame& tgtIn, Frame& refIn, List const& AtomPairs, // Translate tgt atoms boxTrans.Neg(); AtomPairs.DoTranslation( tgtIn, idx, boxTrans ); - // Save new ref positions - AtomPairs.CopyFrame(refIn, idx, tgtIn); } // END loop over atom pairs + // Save new ref positions + refIn.CopyFrom(tgtIn, allEntities); } // Image::UnwrapOrtho() -void Image::UnwrapOrtho( Frame& tgtIn, Frame& refIn, List const& AtomPairs) +void Image::UnwrapOrtho(Frame& tgtIn, Frame& refIn, List const& AtomPairs, + Unit const& allEntities) { Vec3 vtgt, vref, boxTrans; Vec3 boxVec = tgtIn.BoxCrd().Lengths(); @@ -309,9 +311,9 @@ void Image::UnwrapOrtho( Frame& tgtIn, Frame& refIn, List const& AtomPairs) boxTrans[2] = -floor( dxyz[2] / boxVec[2] + 0.5 ) * boxVec[2]; // Translate atoms from first to last AtomPairs.DoTranslation( tgtIn, idx, boxTrans ); - // Save new ref positions - AtomPairs.CopyFrame(refIn, idx, tgtIn); } // END loop over atom pairs + // Save new ref positions + refIn.CopyFrom(tgtIn, allEntities); } // ----------------------------------------------------------------------------- diff --git a/src/ImageRoutines.h b/src/ImageRoutines.h index baeaf14bbb..78e9115401 100644 --- a/src/ImageRoutines.h +++ b/src/ImageRoutines.h @@ -1,19 +1,23 @@ #ifndef INC_IMAGEROUTINES_H #define INC_IMAGEROUTINES_H #include +#include +#include "ImageTypes.h" class Topology; class Frame; class AtomMask; class Matrix_3x3; class Vec3; class Box; -#include "ImageTypes.h" +class Unit; + namespace Image { class List; /// \return empty image list for given mode, optionally using mass and centering List* CreateImageList(Mode, bool, bool); /// \return an image list for given Top, mode, mask, optionally using mass and centering List* CreateImageList(Topology const&, Mode, std::string const&, bool, bool); + /// \return Coordinates of center if wrapping molecules into truncated oct. shape. Vec3 SetupTruncoct( Frame const&, AtomMask*, bool, bool); /// Perform non-orthogonal imaging on given pair list, optionally into trunc. oct. shape. @@ -22,17 +26,20 @@ namespace Image { /// Perform non-orthogonal imaging on given coordinates, optionally into trunc. oct. shape. Vec3 Nonortho(Vec3 const&, bool, bool, Matrix_3x3 const&, Matrix_3x3 const&, Vec3 const&, double); + /// Setup box boundaries based on centering type. int SetupOrtho(Box const&, Vec3&, Vec3&, bool); /// Perform orthogonal imaging on given pair list using given box boundaries void Ortho(Frame&, Vec3 const&, Vec3 const&, Vec3 const&, List const&); /// Perform orthogonal imaging on given coordinates using given box boundaries Vec3 Ortho(Vec3 const&, Vec3 const&, Vec3 const&, Box const&); + /// Perform unwrap of non-orthogonal cell using given reference. - void UnwrapNonortho( Frame&, Frame&, List const&, + void UnwrapNonortho( Frame&, Frame&, List const&, Unit const&, Matrix_3x3 const&, Matrix_3x3 const& ); /// Perform unwrap of orthogonal cell using given reference. - void UnwrapOrtho( Frame&, Frame&, List const& ); + void UnwrapOrtho( Frame&, Frame&, List const&, Unit const& ); + /// Wrap selected atom coords from given frame into primary cell, store in result. void WrapToCell0(std::vector&, Frame const&, AtomMask const&, Matrix_3x3 const&, Matrix_3x3 const&); diff --git a/src/Image_List.h b/src/Image_List.h index b0697d2dfe..cf3fbd80db 100644 --- a/src/Image_List.h +++ b/src/Image_List.h @@ -4,6 +4,7 @@ class Topology; class Frame; class Vec3; +class Unit; namespace Image { /// Abstract base class for holding entities to be imaged class List { @@ -18,8 +19,8 @@ class List { virtual Vec3 GetCoord(unsigned int, Frame const&) const = 0; /// Do translation of specified entity according to given translation vector. virtual void DoTranslation(Frame&, unsigned int, Vec3 const&) const = 0; - /// Copy specified entity from Frame to another Frame - virtual void CopyFrame(Frame&, unsigned int, Frame const&) const = 0; + /// \return Unit containing all entities in the list + virtual Unit AllEntities() const = 0; }; } #endif diff --git a/src/Image_List_Mask.cpp b/src/Image_List_Mask.cpp index f7a6619b8c..5f96337ba6 100644 --- a/src/Image_List_Mask.cpp +++ b/src/Image_List_Mask.cpp @@ -1,6 +1,7 @@ #include "Image_List_Mask.h" #include "Topology.h" +/** Set up list to include atoms selected by mask expression. */ int Image::List_Mask::SetupList(Topology const& Parm, std::string const& maskExpression) { mask_.ResetMask(); @@ -10,3 +11,11 @@ int Image::List_Mask::SetupList(Topology const& Parm, std::string const& maskExp if (mask_.None()) return -1; return 0; } + +/** \return Unit containing all atoms. */ +Unit Image::List_Mask::AllEntities() const { + Unit unitOut; + for (AtomMask::const_iterator at = mask_.begin(); at != mask_.end(); ++at) + unitOut.AddIndex( *at ); + return unitOut; +} diff --git a/src/Image_List_Mask.h b/src/Image_List_Mask.h index abe62166d1..df9ce5c417 100644 --- a/src/Image_List_Mask.h +++ b/src/Image_List_Mask.h @@ -15,9 +15,7 @@ class List_Mask : public List { void DoTranslation(Frame& frm, unsigned int idx, Vec3 const& boxTrans) const { frm.Translate(boxTrans, mask_[idx]); } - void CopyFrame(Frame& refIn, unsigned int idx, Frame const& tgtIn) const { - refIn.CopyFrom(tgtIn, mask_[idx], mask_[idx]); - } + Unit AllEntities() const; protected: AtomMask mask_; }; diff --git a/src/Image_List_Pair.cpp b/src/Image_List_Pair.cpp index aeb7a57fa2..3f2cce693d 100644 --- a/src/Image_List_Pair.cpp +++ b/src/Image_List_Pair.cpp @@ -2,6 +2,7 @@ #include "AtomMask.h" #include "Topology.h" +/** Set up list to contain all residues selected by mask expression */ int Image::List_Pair::SetupList(Topology const& Parm, std::string const& maskExpression) { AtomMask mask; @@ -17,3 +18,12 @@ int Image::List_Pair::SetupList(Topology const& Parm, std::string const& maskExp } return 0; } + +/** \return Unit containing all residues. */ +Unit Image::List_Pair::AllEntities() const { + Unit unitOut; + for (unsigned int jdx = 0; jdx != begin_.size(); ++jdx) + for (int idx = begin_[jdx]; idx != end_[jdx]; ++idx) + unitOut.AddIndex( idx ); + return unitOut; +} diff --git a/src/Image_List_Pair.h b/src/Image_List_Pair.h index 7c64c59eb1..45bc9de0a7 100644 --- a/src/Image_List_Pair.h +++ b/src/Image_List_Pair.h @@ -14,9 +14,7 @@ class List_Pair : public List { void DoTranslation(Frame& frm, unsigned int idx, Vec3 const& boxTrans) const { frm.Translate(boxTrans, begin_[idx], end_[idx]); } - void CopyFrame(Frame& refIn, unsigned int idx, Frame const& tgtIn) const { - refIn.CopyFrom(tgtIn, begin_[idx], end_[idx]); - } + Unit AllEntities() const; protected: typedef std::vector Iarray; Iarray begin_; diff --git a/src/Image_List_Unit.cpp b/src/Image_List_Unit.cpp index 9e61267bec..7794afc947 100644 --- a/src/Image_List_Unit.cpp +++ b/src/Image_List_Unit.cpp @@ -2,6 +2,7 @@ #include "AtomMask.h" #include "Topology.h" +/** Set up list to contain units selected by the mask expression. */ int Image::List_Unit::SetupList(Topology const& Parm, std::string const& maskExpression) { AtomMask mask; @@ -17,6 +18,17 @@ int Image::List_Unit::SetupList(Topology const& Parm, std::string const& maskExp return 0; } +/** Add given unit to the list. */ void Image::List_Unit::AddUnit(Unit const& unitIn) { units_.push_back( unitIn ); } + +/** \return A Unit containing all units in the list. */ +Unit Image::List_Unit::AllEntities() const { + Unit unitOut; + for (Uarray::const_iterator unit = units_.begin(); unit != units_.end(); ++unit) + for (Unit::const_iterator seg = unit->segBegin(); seg != unit->segEnd(); ++seg) + for (int idx = seg->Begin(); idx != seg->End(); ++idx) + unitOut.AddIndex( idx ); + return unitOut; +} diff --git a/src/Image_List_Unit.h b/src/Image_List_Unit.h index d57ea8b2e6..edfd512103 100644 --- a/src/Image_List_Unit.h +++ b/src/Image_List_Unit.h @@ -16,9 +16,7 @@ class List_Unit : public List { void DoTranslation(Frame& frm, unsigned int idx, Vec3 const& boxTrans) const { frm.Translate(boxTrans, units_[idx]); } - void CopyFrame(Frame& refIn, unsigned int idx, Frame const& tgtIn) const { - refIn.CopyFrom(tgtIn, units_[idx]); - } + Unit AllEntities() const; void AddUnit(Unit const&); typedef Uarray::const_iterator const_iterator; From a5128fefacb8e967d1e38834382d78869f63df00 Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Mon, 14 Sep 2020 10:35:35 -0400 Subject: [PATCH 40/65] Add print function for debugging --- src/Image_List.h | 2 ++ src/Image_List_Mask.cpp | 8 ++++++++ src/Image_List_Mask.h | 1 + src/Image_List_Pair.cpp | 8 ++++++++ src/Image_List_Pair.h | 1 + src/Image_List_Unit.cpp | 13 +++++++++++++ src/Image_List_Unit.h | 1 + 7 files changed, 34 insertions(+) diff --git a/src/Image_List.h b/src/Image_List.h index cf3fbd80db..3340b33a47 100644 --- a/src/Image_List.h +++ b/src/Image_List.h @@ -21,6 +21,8 @@ class List { virtual void DoTranslation(Frame&, unsigned int, Vec3 const&) const = 0; /// \return Unit containing all entities in the list virtual Unit AllEntities() const = 0; + /// Print entities to STDOUT + virtual void PrintEntities() const = 0; }; } #endif diff --git a/src/Image_List_Mask.cpp b/src/Image_List_Mask.cpp index 5f96337ba6..3d7b0855e3 100644 --- a/src/Image_List_Mask.cpp +++ b/src/Image_List_Mask.cpp @@ -1,5 +1,7 @@ #include "Image_List_Mask.h" #include "Topology.h" +#include "StringRoutines.h" +#include "CpptrajStdio.h" /** Set up list to include atoms selected by mask expression. */ int Image::List_Mask::SetupList(Topology const& Parm, std::string const& maskExpression) @@ -19,3 +21,9 @@ Unit Image::List_Mask::AllEntities() const { unitOut.AddIndex( *at ); return unitOut; } + +/** Print atoms to be imaged to STDOUT. */ +void Image::List_Mask::PrintEntities() const { + std::string range = ArrayToRangeExpression( mask_.Selected(), 1 ); + mprintf("\tImaging the following atoms: %s\n", range.c_str()); +} diff --git a/src/Image_List_Mask.h b/src/Image_List_Mask.h index df9ce5c417..cc74f59081 100644 --- a/src/Image_List_Mask.h +++ b/src/Image_List_Mask.h @@ -16,6 +16,7 @@ class List_Mask : public List { frm.Translate(boxTrans, mask_[idx]); } Unit AllEntities() const; + void PrintEntities() const; protected: AtomMask mask_; }; diff --git a/src/Image_List_Pair.cpp b/src/Image_List_Pair.cpp index 3f2cce693d..568ebad197 100644 --- a/src/Image_List_Pair.cpp +++ b/src/Image_List_Pair.cpp @@ -1,6 +1,7 @@ #include "Image_List_Pair.h" #include "AtomMask.h" #include "Topology.h" +#include "CpptrajStdio.h" /** Set up list to contain all residues selected by mask expression */ int Image::List_Pair::SetupList(Topology const& Parm, std::string const& maskExpression) @@ -27,3 +28,10 @@ Unit Image::List_Pair::AllEntities() const { unitOut.AddIndex( idx ); return unitOut; } + +/** Print residues to be imaged to STDOUT. */ +void Image::List_Pair::PrintEntities() const { + mprintf("\tImaging residues defined by atom ranges:\n"); + for (unsigned int jdx = 0; jdx != begin_.size(); ++jdx) + mprintf("\t %10i to %10i\n", begin_[jdx]+1, end_[jdx]); +} diff --git a/src/Image_List_Pair.h b/src/Image_List_Pair.h index 45bc9de0a7..739cfcd769 100644 --- a/src/Image_List_Pair.h +++ b/src/Image_List_Pair.h @@ -15,6 +15,7 @@ class List_Pair : public List { frm.Translate(boxTrans, begin_[idx], end_[idx]); } Unit AllEntities() const; + void PrintEntities() const; protected: typedef std::vector Iarray; Iarray begin_; diff --git a/src/Image_List_Unit.cpp b/src/Image_List_Unit.cpp index 7794afc947..461c6ab84e 100644 --- a/src/Image_List_Unit.cpp +++ b/src/Image_List_Unit.cpp @@ -1,6 +1,7 @@ #include "Image_List_Unit.h" #include "AtomMask.h" #include "Topology.h" +#include "CpptrajStdio.h" /** Set up list to contain units selected by the mask expression. */ int Image::List_Unit::SetupList(Topology const& Parm, std::string const& maskExpression) @@ -32,3 +33,15 @@ Unit Image::List_Unit::AllEntities() const { unitOut.AddIndex( idx ); return unitOut; } + +/** Print molecules to be imaged to STDOUT. */ +void Image::List_Unit::PrintEntities() const { + mprintf("\tImaging molecules defined by atom ranges:\n"); + for (Uarray::const_iterator unit = units_.begin(); unit != units_.end(); ++unit) + { + mprintf("\t "); + for (Unit::const_iterator seg = unit->segBegin(); seg != unit->segEnd(); ++seg) + mprintf(" %i-%i", seg->Begin()+1, seg->End()); + mprintf("\n"); + } +} diff --git a/src/Image_List_Unit.h b/src/Image_List_Unit.h index edfd512103..6c0bfaee77 100644 --- a/src/Image_List_Unit.h +++ b/src/Image_List_Unit.h @@ -17,6 +17,7 @@ class List_Unit : public List { frm.Translate(boxTrans, units_[idx]); } Unit AllEntities() const; + void PrintEntities() const; void AddUnit(Unit const&); typedef Uarray::const_iterator const_iterator; From 3b42ac3183c63fb8b0f271be76dedb4f3dafc9ce Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Mon, 14 Sep 2020 10:36:19 -0400 Subject: [PATCH 41/65] Enable debug print --- src/Action_Image.cpp | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/src/Action_Image.cpp b/src/Action_Image.cpp index b57fc1619e..12358b43b0 100644 --- a/src/Action_Image.cpp +++ b/src/Action_Image.cpp @@ -128,12 +128,9 @@ Action::RetType Action_Image::Setup(ActionSetup& setup) { } mprintf("\tNumber of %ss to be imaged is %u\n", Image::ModeString(imageMode_), imageList_->nEntities()); - // DEBUG: Print all pairs TODO fix this - /*if (debug_>0) { - for (std::vector::const_iterator ap = imageList_.begin(); - ap != imageList_.end(); ap+=2) - mprintf("\t\tFirst-Last atom#: %i - %i\n", (*ap)+1, *(ap+1) ); - }*/ + // DEBUG: Print all entities + if (debug_>0) + imageList_->PrintEntities(); // Setup for truncated octahedron if (triclinic_ == FAMILIAR) { if (ComMask_!=0) { From 9c8a4c73707c5c4b5f215f4443ba2a92f4c46338 Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Mon, 14 Sep 2020 10:37:14 -0400 Subject: [PATCH 42/65] Update dependencies --- src/cpptrajdepend | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/cpptrajdepend b/src/cpptrajdepend index 5e109a8f5a..5de8e9f515 100644 --- a/src/cpptrajdepend +++ b/src/cpptrajdepend @@ -39,7 +39,7 @@ Action_GIST.o : Action_GIST.cpp Action.h ActionState.h Action_GIST.h ArgList.h A Action_Grid.o : Action_Grid.cpp Action.h ActionState.h Action_Grid.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridAction.h GridBin.h MaskArray.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h Action_GridFreeEnergy.o : Action_GridFreeEnergy.cpp Action.h ActionState.h Action_GridFreeEnergy.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridAction.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h Action_HydrogenBond.o : Action_HydrogenBond.cpp Action.h ActionState.h Action_HydrogenBond.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h -Action_Image.o : Action_Image.cpp Action.h ActionState.h Action_Image.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h ImageRoutines.h ImageTypes.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_Image.o : Action_Image.cpp Action.h ActionState.h Action_Image.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h ImageRoutines.h ImageTypes.h Image_List.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h Action_InfraredSpectrum.o : Action_InfraredSpectrum.cpp Action.h ActionState.h Action_InfraredSpectrum.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h Action_Jcoupling.o : Action_Jcoupling.cpp Action.h ActionState.h Action_Jcoupling.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h Action_LESsplit.o : Action_LESsplit.cpp Action.h ActionFrameCounter.h ActionState.h Action_LESsplit.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h @@ -310,9 +310,9 @@ GridAction.o : GridAction.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h HistBin.o : HistBin.cpp Constants.h CpptrajStdio.h Dimension.h HistBin.h Hungarian.o : Hungarian.cpp ArrayIterator.h Constants.h CpptrajStdio.h Hungarian.h Matrix.h ImageRoutines.o : ImageRoutines.cpp Atom.h AtomMask.h Box.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h Frame.h ImageRoutines.h ImageTypes.h Image_List.h Image_List_Mask.h Image_List_Pair.h Image_List_Pair_CoM.h Image_List_Pair_First.h Image_List_Pair_Geom.h Image_List_Unit.h Image_List_Unit_CoM.h Image_List_Unit_First.h Image_List_Unit_Geom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Unit.h Vec3.h -Image_List_Mask.o : Image_List_Mask.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h FileName.h Frame.h Image_List.h Image_List_Mask.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h -Image_List_Pair.o : Image_List_Pair.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h FileName.h Frame.h Image_List.h Image_List_Pair.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h -Image_List_Unit.o : Image_List_Unit.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h FileName.h Frame.h Image_List.h Image_List_Unit.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Image_List_Mask.o : Image_List_Mask.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h Image_List.h Image_List_Mask.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Image_List_Pair.o : Image_List_Pair.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h Image_List.h Image_List_Pair.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Image_List_Unit.o : Image_List_Unit.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h Image_List.h Image_List_Unit.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h InputTrajCommon.o : InputTrajCommon.cpp CpptrajStdio.h FileName.h InputTrajCommon.h TrajFrameCounter.h KDE.o : KDE.cpp AssociatedData.h Constants.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_double.h Dimension.h FileIO.h FileName.h HistBin.h KDE.h MetaData.h Parallel.h Range.h TextFormat.h MapAtom.o : MapAtom.cpp Atom.h MapAtom.h NameType.h SymbolExporting.h From 5b8dbf1beb9015abb49b6c69657ab4f147895ddb Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Mon, 14 Sep 2020 10:50:11 -0400 Subject: [PATCH 43/65] Make Visited array indexed by absolute atom number since molecules no longer need to be contiguous. --- src/Action_LipidOrder.cpp | 176 ++++++++++++++++++++------------------ 1 file changed, 93 insertions(+), 83 deletions(-) diff --git a/src/Action_LipidOrder.cpp b/src/Action_LipidOrder.cpp index 6a5b0afb76..655847ded0 100644 --- a/src/Action_LipidOrder.cpp +++ b/src/Action_LipidOrder.cpp @@ -118,95 +118,105 @@ Action::RetType Action_LipidOrder::Setup(ActionSetup& setup) for (Topology::mol_iterator mol = setup.Top().MolStart(); mol != setup.Top().MolEnd(); ++mol) { - if (!mol->IsSolvent() && mask_.AtomsInCharMask(mol->BeginAtom(), mol->EndAtom())) + if (!mol->IsSolvent() && mask_.AtomsInCharMask(mol->MolUnit())) { if (debug_ > 0) mprintf(" Mol %zu\n", mol - setup.Top().MolStart() + 1); - std::vector Visited(mol->NumAtoms(), false); - int offset = mol->BeginAtom(); - // First mark any atoms not in the mask as visited. - for (int at = mol->BeginAtom(); at != mol->EndAtom(); ++at) - if (!mask_.AtomInCharMask( at )) - Visited[at - offset] = true; + // Array to keep track of visited atoms. Since molecules do not need + // to be contiguous have the array correspond to all atoms. Initially + // set it up so that all atoms are visited. + std::vector Visited(setup.Top().Natom(), true); + // Mark any atoms in the mask as not visited. + for (Unit::const_iterator seg = mol->MolUnit().segBegin(); + seg != mol->MolUnit().segEnd(); ++seg) + { + for (int at = seg->Begin(); at != seg->End(); ++at) + if (mask_.AtomInCharMask( at )) + Visited[at] = false; + } // Search for the start of lipid chains - for (int at = mol->BeginAtom(); at != mol->EndAtom(); ++at) + for (Unit::const_iterator seg = mol->MolUnit().segBegin(); + seg != mol->MolUnit().segEnd(); ++seg) { - if (!Visited[at - offset]) { - Atom const& atom = setup.Top()[at]; - if (atom.Element() == Atom::CARBON) { - // Should be bonded to two oxygens and 1 carbon - int n_O = 0; - int n_C = 0; - int C_idx = 0; - for (Atom::bond_iterator bnd = atom.bondbegin(); - bnd != atom.bondend(); ++bnd) - { - if (setup.Top()[*bnd].Element() == Atom::OXYGEN) - n_O++; - else if (setup.Top()[*bnd].Element() == Atom::CARBON) { - n_C++; - C_idx = *bnd; - } else { - n_O = 0; - n_C = 0; - break; - } - } - if (n_O == 2 && n_C == 1 && mask_.AtomInCharMask(C_idx)) { - nChains++; - Visited[at - offset] = true; - // Determine if this is a new or existing chain type by first - // carbon residue name and carboxyl carbon atom name. - int cresnum = setup.Top()[C_idx].ResNum(); - int chainIdx = FindChain( Npair(setup.Top().Res(cresnum).Name(), atom.Name()) ); - ChainType& Chain = Chains_[chainIdx]; - // Starting at the bonded carbon follow the chain down - if (debug_ > 0) - mprintf("DEBUG: Lipid chain type %i (%zu atoms) starting at" - " (but not including) %s\n", chainIdx, Chains_[chainIdx].size(), - setup.Top().TruncResAtomName(at).c_str()); - int position = 0; - std::stack nextAtom; - nextAtom.push( C_idx ); - while (!nextAtom.empty()) { - int current_at = nextAtom.top(); - nextAtom.pop(); - Visited[current_at - offset] = true; - Atom const& curr_atm = setup.Top()[current_at]; - // Add carbon if it does not yet exist in chain. - if (position >= (int)Chain.size()) - Chain.resize( position+1 ); - CarbonData& Cdata = Chain[position]; - if (!Cdata.Init()) - Cdata.SetName( curr_atm.Name() ); - else if (Cdata.Name() != curr_atm.Name()) - mprintf("Warning: Atom name %s at position %i (#%i) does not match %s\n", - *(curr_atm.Name()), position+1, current_at+1, Cdata.name()); - // Add site - Sites_.push_back( CarbonSite(current_at, chainIdx, position) ); - CarbonSite& site = Sites_.back(); - if (debug_ > 1) - mprintf("\t\t%i %s %s %i %i\n", position, - setup.Top().TruncResAtomNameNum(current_at).c_str(), - Cdata.name(), current_at, chainIdx); - // Loop over atoms bonded to this carbon, add hydrogens to site - for (Atom::bond_iterator bnd = setup.Top()[current_at].bondbegin(); - bnd != setup.Top()[current_at].bondend(); ++bnd) - { - if (setup.Top()[*bnd].Element() == Atom::HYDROGEN) - site.AddHindex( *bnd ); - else if (!Visited[*bnd - offset] && - setup.Top()[*bnd].Element() == Atom::CARBON) - nextAtom.push( *bnd ); + for (int at = seg->Begin(); at != seg->End(); ++at) + { + if (!Visited[at]) { + Atom const& atom = setup.Top()[at]; + if (atom.Element() == Atom::CARBON) { + // Should be bonded to two oxygens and 1 carbon + int n_O = 0; + int n_C = 0; + int C_idx = 0; + for (Atom::bond_iterator bnd = atom.bondbegin(); + bnd != atom.bondend(); ++bnd) + { + if (setup.Top()[*bnd].Element() == Atom::OXYGEN) + n_O++; + else if (setup.Top()[*bnd].Element() == Atom::CARBON) { + n_C++; + C_idx = *bnd; + } else { + n_O = 0; + n_C = 0; + break; } - // Update number of hydrogens in carbon data - Cdata.SetNumH( site.NumH() ); - position++; - } // END loop over atom number stack - } // END carbon is carboxyl - } // END if carbon - } // END if selected - } // END loop over molecule atoms + } + if (n_O == 2 && n_C == 1 && mask_.AtomInCharMask(C_idx)) { + nChains++; + Visited[at] = true; + // Determine if this is a new or existing chain type by first + // carbon residue name and carboxyl carbon atom name. + int cresnum = setup.Top()[C_idx].ResNum(); + int chainIdx = FindChain( Npair(setup.Top().Res(cresnum).Name(), atom.Name()) ); + ChainType& Chain = Chains_[chainIdx]; + // Starting at the bonded carbon follow the chain down + if (debug_ > 0) + mprintf("DEBUG: Lipid chain type %i (%zu atoms) starting at" + " (but not including) %s\n", chainIdx, Chains_[chainIdx].size(), + setup.Top().TruncResAtomName(at).c_str()); + int position = 0; + std::stack nextAtom; + nextAtom.push( C_idx ); + while (!nextAtom.empty()) { + int current_at = nextAtom.top(); + nextAtom.pop(); + Visited[current_at] = true; + Atom const& curr_atm = setup.Top()[current_at]; + // Add carbon if it does not yet exist in chain. + if (position >= (int)Chain.size()) + Chain.resize( position+1 ); + CarbonData& Cdata = Chain[position]; + if (!Cdata.Init()) + Cdata.SetName( curr_atm.Name() ); + else if (Cdata.Name() != curr_atm.Name()) + mprintf("Warning: Atom name %s at position %i (#%i) does not match %s\n", + *(curr_atm.Name()), position+1, current_at+1, Cdata.name()); + // Add site + Sites_.push_back( CarbonSite(current_at, chainIdx, position) ); + CarbonSite& site = Sites_.back(); + if (debug_ > 1) + mprintf("\t\t%i %s %s %i %i\n", position, + setup.Top().TruncResAtomNameNum(current_at).c_str(), + Cdata.name(), current_at, chainIdx); + // Loop over atoms bonded to this carbon, add hydrogens to site + for (Atom::bond_iterator bnd = setup.Top()[current_at].bondbegin(); + bnd != setup.Top()[current_at].bondend(); ++bnd) + { + if (setup.Top()[*bnd].Element() == Atom::HYDROGEN) + site.AddHindex( *bnd ); + else if (!Visited[*bnd] && + setup.Top()[*bnd].Element() == Atom::CARBON) + nextAtom.push( *bnd ); + } + // Update number of hydrogens in carbon data + Cdata.SetNumH( site.NumH() ); + position++; + } // END loop over atom number stack + } // END carbon is carboxyl + } // END if carbon + } // END if selected + } // END loop over molecule segment atoms + } // END loop over molecule segments } // END mol not solvent and some of mol selected } // END loop over molecules From bd5f6498dc3bc0e1f838f9174fa94cc8eeec7d3e Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Mon, 14 Sep 2020 14:30:02 -0400 Subject: [PATCH 44/65] Update for molecule unit --- src/Action_RandomizeIons.cpp | 62 +++++++++++++----------------------- src/Action_RandomizeIons.h | 20 ++++++------ 2 files changed, 32 insertions(+), 50 deletions(-) diff --git a/src/Action_RandomizeIons.cpp b/src/Action_RandomizeIons.cpp index 5a2373be31..30e646e8d3 100644 --- a/src/Action_RandomizeIons.cpp +++ b/src/Action_RandomizeIons.cpp @@ -6,7 +6,6 @@ Action_RandomizeIons::Action_RandomizeIons() : overlap_(0.0), min_(0.0), - n_solvent_(0), debug_(0) {} @@ -60,8 +59,7 @@ Action::RetType Action_RandomizeIons::Init(ArgList& actionArgs, ActionInit& init // Action_RandomizeIons::Setup() Action::RetType Action_RandomizeIons::Setup(ActionSetup& setup) { - n_solvent_ = setup.Top().Nsolvent(); - if (n_solvent_ < 1) { + if (setup.Top().Nsolvent() < 1) { mprinterr("Error: This command only works if solvent information has been specified.\n"); return Action::ERR; } @@ -101,35 +99,19 @@ Action::RetType Action_RandomizeIons::Setup(ActionSetup& setup) { } } - // Check the solvent information to make sure that each solvent listed has the - // same number of atoms in each molecule; otherwise a uniform trajectory is not - // possible and therefore this command will be ignored. - // Also save the start and end atom of each solvent molecule. - int NsolventAtoms = -1; - solventStart_.clear(); - solventEnd_.clear(); - solventStart_.reserve( n_solvent_ ); - solventEnd_.reserve( n_solvent_ ); + // Save each solvent molecule. + solvMols_.clear(); + solvMols_.reserve( setup.Top().Nsolvent() ); for (Topology::mol_iterator Mol = setup.Top().MolStart(); Mol != setup.Top().MolEnd(); ++Mol) { if ( Mol->IsSolvent() ) { - if (NsolventAtoms == -1) - NsolventAtoms = Mol->NumAtoms(); - else if ( NsolventAtoms != Mol->NumAtoms() ) { - mprinterr("Error: Solvent molecules in %s are not of uniform size.\n", - setup.Top().c_str()); - mprinterr("Error: First solvent mol = %i atoms, this solvent mol = %i atoms.\n", - NsolventAtoms, Mol->NumAtoms()); - return Action::ERR; - } - solventStart_.push_back( Mol->BeginAtom() ); - solventEnd_.push_back( Mol->EndAtom() ); + solvMols_.push_back( Mol->MolUnit() ); } } image_.SetupImaging( setup.CoordInfo().TrajBox().Type() ); - // Allocate solvent molecule mask - solvent_.resize( n_solvent_ ); + // Allocate solvent molecule considered for swap mask + solvent_.resize( solvMols_.size() ); return Action::OK; } @@ -142,11 +124,12 @@ Action::RetType Action_RandomizeIons::DoAction(int frameNum, ActionFrame& frm) { frm.Frm().BoxCrd().ToRecip(ucell, recip); // Loop over all solvent molecules and mark those that are too close to the solute int n_active_solvent = 0; - for (int idx = 0; idx != n_solvent_; idx++) { + for (unsigned int idx = 0; idx != solvMols_.size(); idx++) { solvent_[idx] = true; if (around_.MaskStringSet()) { - const double* solventXYZ = frm.Frm().XYZ( solventStart_[idx] ); // Is solvent molecule too close to any atom in the around mask? + // For speed, use only the first solvent atom. + const double* solventXYZ = frm.Frm().XYZ( solvMols_[idx].Front() ); for (AtomMask::const_iterator atom = around_.begin(); atom != around_.end(); ++atom) { double dist = DIST2( solventXYZ, frm.Frm().XYZ(*atom), image_.ImageType(), @@ -169,16 +152,16 @@ Action::RetType Action_RandomizeIons::DoAction(int frameNum, ActionFrame& frm) { // DEBUG - print solvent molecule mask if (debug_ > 2) { - mprintf("RANDOMIZEIONS: The following waters are ACTIVE so far:\n"); - int smoltot = 0; - for (int idx = 0; idx != n_solvent_; idx++) { + mprintf("RANDOMIZEIONS: The following waters (first atoms) are ACTIVE so far:\n"); + unsigned int smoltot = 0; + for (unsigned int idx = 0; idx != solvMols_.size(); idx++) { if (solvent_[idx]) { - mprintf(" %5i ", solventStart_[idx]+1 ); + mprintf(" %6i ", solvMols_[idx].Front()+1 ); ++smoltot; if (smoltot%10 == 0) mprintf("\n"); } } - mprintf("RANDOMIZEIONS: A total of %i waters (out of %zu) are active\n", + mprintf("RANDOMIZEIONS: A total of %u waters (out of %zu) are active\n", smoltot, solvent_.size()); } @@ -187,9 +170,10 @@ Action::RetType Action_RandomizeIons::DoAction(int frameNum, ActionFrame& frm) { { //mprintf("RANDOMIZEIONS: Processing ion atom %i\n", *ion1+1); // Is a potential solvent molecule close to any of the ions (except this one)? - for (int idx = 0; idx != n_solvent_; idx++) { + for (unsigned int idx = 0; idx != solvMols_.size(); idx++) { if (solvent_[idx]) { - const double* solventXYZ = frm.Frm().XYZ( solventStart_[idx] ); + // For speed, use only the first solvent atom. + const double* solventXYZ = frm.Frm().XYZ( solvMols_[idx].Front() ); // This solvent is active; check distance to all other ions for (AtomMask::const_iterator ion2 = ions_.begin(); ion2 != ions_.end(); ++ion2) { @@ -208,13 +192,13 @@ Action::RetType Action_RandomizeIons::DoAction(int frameNum, ActionFrame& frm) { } } // END loop over solvent molecules // The solvent_ array should now be true for all solvent molecules eligible - // to swap with ion. + // to swap with ion. Select an elegible solvent molecule. int loop = 1; int swapMol = 0; while (loop > 0 && loop < 10000) { // Run the random number generator so that the same number is not produced // when the seed was set manually. - swapMol = (int)(RN_.rn_gen() * (double)n_solvent_); + swapMol = (int)(RN_.rn_gen() * (double)solvMols_.size()); if ( solvent_[swapMol] ) loop = -1; else @@ -229,12 +213,12 @@ Action::RetType Action_RandomizeIons::DoAction(int frameNum, ActionFrame& frm) { if (debug_ > 2) mprintf("RANDOMIZEIONS: Swapping solvent mol %i for ion @%i\n", swapMol+1, *ion1+1); const double* ionXYZ = frm.Frm().XYZ( *ion1 ); - int sbegin = solventStart_[ swapMol ]; - const double* watXYZ = frm.Frm().XYZ( sbegin ); + // Use only the first solvent atom + const double* watXYZ = frm.Frm().XYZ( solvMols_[swapMol].Front() ); Vec3 trans( ionXYZ[0] - watXYZ[0], ionXYZ[1] - watXYZ[1], ionXYZ[2] - watXYZ[2]); - frm.ModifyFrm().Translate( trans, sbegin, solventEnd_[ swapMol ] ); + frm.ModifyFrm().Translate( trans, solvMols_[swapMol] ); trans.Neg(); frm.ModifyFrm().Translate( trans, *ion1 ); } diff --git a/src/Action_RandomizeIons.h b/src/Action_RandomizeIons.h index a513289f00..ab6bc51693 100644 --- a/src/Action_RandomizeIons.h +++ b/src/Action_RandomizeIons.h @@ -3,6 +3,7 @@ #include "Action.h" #include "ImagedAction.h" #include "Random.h" +/// Used to randomize ion positions by swapping with solvent molecules. class Action_RandomizeIons : public Action { public: Action_RandomizeIons(); @@ -14,17 +15,14 @@ class Action_RandomizeIons : public Action { Action::RetType DoAction(int, ActionFrame&); void Print() {} - ImagedAction image_; ///< Imaging routines. - Random_Number RN_; ///< Random number generator. - AtomMask ions_; ///< Mask of ions to be moved. - AtomMask around_; ///< The 'around' mask (region of space for ions to avoid) - double overlap_; ///< The minimum allowed distance between ions - double min_; ///< The minimum distance to the 'around' mask - int n_solvent_; ///< Total number of solvent molecules. + ImagedAction image_; ///< Imaging routines. + Random_Number RN_; ///< Random number generator. + AtomMask ions_; ///< Mask of ions to be moved. + AtomMask around_; ///< The 'around' mask (region of space for ions to avoid) + double overlap_; ///< The minimum allowed distance between ions + double min_; ///< The minimum distance to the 'around' mask int debug_; - // TODO: Combine the below 3 into a struct? - std::vector solventStart_; ///< Solvent molecule start atoms. - std::vector solventEnd_; ///< Solvent molecule end atoms. - std::vector solvent_; ///< True if solvent mol being considered for swap. + std::vector solvMols_; ///< Hold all solvent molecules + std::vector solvent_; ///< True if solvent mol being considered for swap. }; #endif From 2ebf6c167fd20510f4695e2873779cbb4efd73ac Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Mon, 14 Sep 2020 14:31:45 -0400 Subject: [PATCH 45/65] Allow checking of all solvent molecules --- src/Action_RandomizeIons.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/Action_RandomizeIons.cpp b/src/Action_RandomizeIons.cpp index 30e646e8d3..7712189a8b 100644 --- a/src/Action_RandomizeIons.cpp +++ b/src/Action_RandomizeIons.cpp @@ -195,7 +195,7 @@ Action::RetType Action_RandomizeIons::DoAction(int frameNum, ActionFrame& frm) { // to swap with ion. Select an elegible solvent molecule. int loop = 1; int swapMol = 0; - while (loop > 0 && loop < 10000) { + while (loop > 0 && loop < (int)solvMols_.size()) { // Run the random number generator so that the same number is not produced // when the seed was set manually. swapMol = (int)(RN_.rn_gen() * (double)solvMols_.size()); From ba009f1c15dcb4191bbf91171f18af8cfec9084e Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Mon, 14 Sep 2020 14:43:22 -0400 Subject: [PATCH 46/65] Update unwrap for mol unit --- src/Action_Unwrap.cpp | 29 ++++++++++++++++++++++------- src/Action_Unwrap.h | 19 ++++++++++++------- 2 files changed, 34 insertions(+), 14 deletions(-) diff --git a/src/Action_Unwrap.cpp b/src/Action_Unwrap.cpp index b1014957b0..d0c626242f 100644 --- a/src/Action_Unwrap.cpp +++ b/src/Action_Unwrap.cpp @@ -1,15 +1,22 @@ #include "Action_Unwrap.h" #include "CpptrajStdio.h" #include "ImageRoutines.h" +#include "Image_List.h" // CONSTRUCTOR Action_Unwrap::Action_Unwrap() : + imageList_(0), imageMode_(Image::BYATOM), RefParm_(0), orthogonal_(false), center_(false) { } +/** DESTRUCTOR */ +Action_Unwrap::~Action_Unwrap() { + if (imageList_ != 0) delete imageList_; +} + void Action_Unwrap::Help() const { mprintf("\t[center] [{bymol | byres | byatom}]\n" "\t[ %s ] []\n", DataSetList::RefArgs); @@ -92,14 +99,22 @@ Action::RetType Action_Unwrap::Setup(ActionSetup& setup) { if (setup.CoordInfo().TrajBox().Type()==Box::ORTHO) orthogonal_ = true; - // Setup atom pairs to be unwrapped. - imageList_ = Image::CreateAtomPairList(setup.Top(), imageMode_, maskExpression_); - if (imageList_.empty()) { + // Setup atom pairs to be unwrapped. Always use CoM TODO why? + if (imageList_ != 0) delete imageList_; + imageList_ = Image::CreateImageList(setup.Top(), imageMode_, maskExpression_, + true, center_); + if (imageList_ == 0) { + mprinterr("Internal Error: Could not allocate unwrap list.\n"); + return Action::ERR; + } + if (imageList_->nEntities() < 1) { mprintf("Warning: Mask selects no atoms for topology '%s'.\n", setup.Top().c_str()); return Action::SKIP; } - mprintf("\tNumber of %ss to be unwrapped is %zu\n", - Image::ModeString(imageMode_), imageList_.size()/2); + mprintf("\tNumber of %ss to be unwrapped is %u\n", + Image::ModeString(imageMode_), imageList_->nEntities()); + // Get entities that need to be updated in reference + allEntities_ = imageList_->AllEntities(); // Use current parm as reference if not already set if (RefParm_ == 0) @@ -117,10 +132,10 @@ Action::RetType Action_Unwrap::DoAction(int frameNum, ActionFrame& frm) { } if (orthogonal_) - Image::UnwrapOrtho( frm.ModifyFrm(), RefFrame_, imageList_, center_, true ); + Image::UnwrapOrtho( frm.ModifyFrm(), RefFrame_, *imageList_, allEntities_ ); else { frm.Frm().BoxCrd().ToRecip( ucell, recip ); - Image::UnwrapNonortho( frm.ModifyFrm(), RefFrame_, imageList_, ucell, recip, center_, true ); + Image::UnwrapNonortho( frm.ModifyFrm(), RefFrame_, *imageList_, allEntities_, ucell, recip ); } return Action::MODIFY_COORDS; diff --git a/src/Action_Unwrap.h b/src/Action_Unwrap.h index bae69360f4..77622810ff 100644 --- a/src/Action_Unwrap.h +++ b/src/Action_Unwrap.h @@ -2,9 +2,13 @@ #define INC_ACTION_UNWRAP_H #include "Action.h" #include "ImageTypes.h" +namespace Image { + class List; +} class Action_Unwrap : public Action { public: Action_Unwrap(); + ~Action_Unwrap(); DispatchObject* Alloc() const { return (DispatchObject*)new Action_Unwrap(); } void Help() const; private: @@ -13,13 +17,14 @@ class Action_Unwrap : public Action { Action::RetType DoAction(int, ActionFrame&); void Print() {} - Image::PairType imageList_; - Image::Mode imageMode_; - std::string maskExpression_; - Frame RefFrame_; - Topology* RefParm_; - bool orthogonal_; - bool center_; + Image::List* imageList_; ///< List of entities to unwrap + Image::Mode imageMode_; ///< Specifiy unwrapping by atom, res, or mol + std::string maskExpression_; ///< Expression selecting entities to unwrap + Frame RefFrame_; ///< Reference frame, updated each DoAction + Topology* RefParm_; ///< Reference topology + bool orthogonal_; ///< If true, cell is orthogonal + bool center_; ///< If true, determine distances to centers + Unit allEntities_; ///< Hold atoms to copy from target to reference # ifdef MPI Parallel::Comm trajComm_; # endif From 5087efd5b49cf0b2cc38cb4f4f4c66c64c2e676c Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Mon, 14 Sep 2020 14:45:43 -0400 Subject: [PATCH 47/65] Update for mol unit --- src/Action_Watershell.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/Action_Watershell.cpp b/src/Action_Watershell.cpp index 8f3756c4f3..47edc248d4 100644 --- a/src/Action_Watershell.cpp +++ b/src/Action_Watershell.cpp @@ -133,7 +133,7 @@ Action::RetType Action_Watershell::Setup(ActionSetup& setup) { for (Topology::mol_iterator mol = setup.Top().MolStart(); mol != setup.Top().MolEnd(); ++mol) if ( mol->IsSolvent() ) - solventMask_.AddAtomRange( mol->BeginAtom(), mol->EndAtom() ); + solventMask_.AddUnit( mol->MolUnit() ); mprintf("\tSelecting all solvent atoms (%i total)\n", solventMask_.Nselected()); } if ( solventMask_.None() ) { From f667c83455dc81cfb255f6aa299068ed77faed0c Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Mon, 14 Sep 2020 15:01:33 -0400 Subject: [PATCH 48/65] Update xtalsymm for mol unit --- src/Action_XtalSymm.cpp | 54 ++++++++++++++++++++++++----------------- src/Action_XtalSymm.h | 2 +- src/Frame.h | 7 ++++++ 3 files changed, 40 insertions(+), 23 deletions(-) diff --git a/src/Action_XtalSymm.cpp b/src/Action_XtalSymm.cpp index 1ca245e940..93de822c1f 100644 --- a/src/Action_XtalSymm.cpp +++ b/src/Action_XtalSymm.cpp @@ -526,20 +526,27 @@ Action::RetType Action_XtalSymm::Setup(ActionSetup& setup) // separately and remove them from the list of individual atoms to remove. nMolecule_ = setup.Top().Nmol(); molLimits_.clear(); - molLimits_.reserve(2 * nMolecule_); + molLimits_.reserve(nMolecule_); molInSolvent_.assign(nMolecule_, true); for (i = 0; i < nMolecule_; i++) { - molLimits_.push_back( setup.Top().Mol(i).BeginAtom() ); - molLimits_.push_back( setup.Top().Mol(i).EndAtom() ); - for (j = molLimits_[2*i]; j < molLimits_[2*i + 1]; j++) { - if (LoneAtoms[j] == 0) { - molInSolvent_[i] = false; + molLimits_.push_back( setup.Top().Mol(i).MolUnit() ); + for (Unit::const_iterator seg = molLimits_.back().segBegin(); + seg != molLimits_.back().segEnd(); ++seg) + { + for (j = seg->Begin(); j < seg->End(); j++) { + if (LoneAtoms[j] == 0) { + molInSolvent_[i] = false; + } } } if (molInSolvent_[i]) { - for (j = molLimits_[2*i]; j < molLimits_[2*i + 1]; j++) { - LoneAtoms[j] = 0; - MoleAtoms[j] = 1; + for (Unit::const_iterator seg = molLimits_.back().segBegin(); + seg != molLimits_.back().segEnd(); ++seg) + { + for (j = seg->Begin(); j < seg->End(); j++) { + LoneAtoms[j] = 0; + MoleAtoms[j] = 1; + } } } } @@ -865,7 +872,8 @@ Action::RetType Action_XtalSymm::DoAction(int frameNum, ActionFrame& frm) if (molInSolvent_[i]) { // Re-image the entire molecule - double x = 0.0; + Vec3 xyz = frm.Frm().VGeometricCenter( molLimits_[i] ); + /*double x = 0.0; double y = 0.0; double z = 0.0; for (j = molLimits_[2*i]; j < molLimits_[2*i + 1]; j++) { @@ -876,24 +884,26 @@ Action::RetType Action_XtalSymm::DoAction(int frameNum, ActionFrame& frm) double dfac = 1.0 / (double)(molLimits_[2*i + 1] - molLimits_[2*i]); x *= dfac; y *= dfac; - z *= dfac; - frm.ModifyFrm().Translate(Vec3(0.5 - round(x), 0.5 - round(y), 0.5 - round(z)), - molLimits_[2*i], molLimits_[2*i + 1]); - x += 0.5 - round(x); - y += 0.5 - round(y); - z += 0.5 - round(z); + z *= dfac;*/ + frm.ModifyFrm().Translate(Vec3(0.5 - round(xyz[0]), + 0.5 - round(xyz[1]), + 0.5 - round(xyz[2])), + molLimits_[i]); + xyz[0] += 0.5 - round(xyz[0]); + xyz[1] += 0.5 - round(xyz[1]); + xyz[2] += 0.5 - round(xyz[2]); // Use the grid to determine the asymmetric unit (if the grid says "operation -1", // an intensive search will be done to find the correct ASU) - int gidx = (int)(x * DASU_GRID_BINS_); - int gidy = (int)(y * DASU_GRID_BINS_); - int gidz = (int)(z * DASU_GRID_BINS_); + int gidx = (int)(xyz[0] * DASU_GRID_BINS_); + int gidy = (int)(xyz[1] * DASU_GRID_BINS_); + int gidz = (int)(xyz[2] * DASU_GRID_BINS_); gidx = (gidx*IASU_GRID_BINS_ + gidy)*IASU_GRID_BINS_ + gidz; - TransOp Vm = (AsuGrid_[gidx].opID_ == -1) ? DetectAsuResidence(x, y, z) : + TransOp Vm = (AsuGrid_[gidx].opID_ == -1) ? DetectAsuResidence(xyz[0], xyz[1], xyz[2]) : AsuGrid_[gidx]; frm.ModifyFrm().Translate(Vec3(Vm.tr_x_, Vm.tr_y_, Vm.tr_z_) - T_[Vm.opID_], - molLimits_[2*i], molLimits_[2*i + 1]); - frm.ModifyFrm().Rotate(Rinv_[Vm.opID_], molLimits_[2*i], molLimits_[2*i + 1]); + molLimits_[i]); + frm.ModifyFrm().Rotate(Rinv_[Vm.opID_], molLimits_[i]); } } frm.ModifyFrm().Rotate(U, SolventMolecules_); diff --git a/src/Action_XtalSymm.h b/src/Action_XtalSymm.h index e0b1f05c91..ddfac049f0 100644 --- a/src/Action_XtalSymm.h +++ b/src/Action_XtalSymm.h @@ -68,7 +68,7 @@ class Action_XtalSymm : public Action { /** Start and end points for each molecule (all molecules are assumed to be contiguous within the topology, but it is not assumed that molecule i+1 starts where molecule i ends). */ - std::vector molLimits_; + std::vector molLimits_; /**< Flags to indicate whether each molecule is part of the non-ASU, free-floating "solvent" component. */ std::vector molInSolvent_; diff --git a/src/Frame.h b/src/Frame.h index e27c1a7e24..2080f8b405 100644 --- a/src/Frame.h +++ b/src/Frame.h @@ -231,6 +231,8 @@ class Frame { inline void Rotate(Matrix_3x3 const&); /// Rotate all atoms in range by matrix inline void Rotate(Matrix_3x3 const&, int, int); + /// Rotate all atoms in unit by matrix + inline void Rotate(Matrix_3x3 const&, Unit const&); /// Rotate all atoms in mask by matrix inline void Rotate(Matrix_3x3 const&, AtomMask const&); /// Apply inverse of rotation defined by matrix to all atoms in mask @@ -466,6 +468,11 @@ void Frame::Rotate(Matrix_3x3 const& T, int firstAtom, int lastAtom) { } } +void Frame::Rotate(Matrix_3x3 const& T, Unit const& unit) { + for (Unit::const_iterator seg = unit.segBegin(); seg != unit.segEnd(); ++seg) + Rotate(T, seg->Begin(), seg->End()); +} + void Frame::Rotate(Matrix_3x3 const& RotMatrix, AtomMask const& mask) { for (AtomMask::const_iterator atom = mask.begin(); atom != mask.end(); ++atom) { double* XYZ = X_ + (*atom * 3) ; From 20e8c8eead427b3c769e20a41ba8901dfdc80c5c Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Mon, 14 Sep 2020 15:02:20 -0400 Subject: [PATCH 49/65] Fix code comment --- src/Action_XtalSymm.h | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/src/Action_XtalSymm.h b/src/Action_XtalSymm.h index ddfac049f0..b8daf913e1 100644 --- a/src/Action_XtalSymm.h +++ b/src/Action_XtalSymm.h @@ -65,9 +65,7 @@ class Action_XtalSymm : public Action { unit re-imaged to the primary ASU volume. */ bool molCentToASU_; /**< Flag to use molecule centroids, not individual atoms, in the above re-imaging. */ - /** Start and end points for each molecule (all molecules are assumed - to be contiguous within the topology, but it is not assumed - that molecule i+1 starts where molecule i ends). */ + /// Hold definitions for each molecule std::vector molLimits_; /**< Flags to indicate whether each molecule is part of the non-ASU, free-floating "solvent" component. */ From 6f65ed4f18dbedd9f5b2d7b151dd95e78dbff5b6 Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Mon, 14 Sep 2020 15:16:18 -0400 Subject: [PATCH 50/65] Use Front() --- src/BondSearch.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/BondSearch.cpp b/src/BondSearch.cpp index 35254e6964..b3256969e1 100644 --- a/src/BondSearch.cpp +++ b/src/BondSearch.cpp @@ -289,7 +289,7 @@ int BondSearch_ByResidue( Topology& top, Frame const& frameIn, double offset, in // this residue >= first atom of next molecule, which indicates this // residue and the previous residue are in different molecules. if ( (nextmol != top.MolEnd()) && - (res->FirstAtom() >= nextmol->BeginAtom()) ) + (res->FirstAtom() >= nextmol->MolUnit().Front()) ) { ++nextmol; continue; From b0235f35acf27868d19f03b6a7a3227957d41643 Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Mon, 14 Sep 2020 15:16:25 -0400 Subject: [PATCH 51/65] Add function to determine # residues in a molecule unit --- src/Topology.cpp | 9 +++++++++ src/Topology.h | 2 ++ 2 files changed, 11 insertions(+) diff --git a/src/Topology.cpp b/src/Topology.cpp index f8ba27ce9f..9cd349d4e2 100644 --- a/src/Topology.cpp +++ b/src/Topology.cpp @@ -987,6 +987,15 @@ void Topology::ClearMolecules() { atom->SetMol( -1 ); } +/** \return Number of residues in specified molecule. */ +int Topology::NresInMol(int idx) const { + int nres = 0; + for (Unit::const_iterator seg = molecules_[idx].MolUnit().segBegin(); + seg != molecules_[idx].MolUnit().segEnd(); ++seg) + nres += atoms_[seg->End()-1].ResNum() - atoms_[seg->Begin()].ResNum() + 1; + return nres; +} + // Topology::DetermineMolecules() /** Determine individual molecules using bond information. Performs a * recursive search over the bonds of each atom. diff --git a/src/Topology.h b/src/Topology.h index a7b5c67116..345e003b74 100644 --- a/src/Topology.h +++ b/src/Topology.h @@ -64,6 +64,8 @@ class Topology { inline mol_iterator MolStart() const { return molecules_.begin(); } inline mol_iterator MolEnd() const { return molecules_.end(); } const Molecule& Mol(int idx) const { return molecules_[idx]; } + /// \return number of residues in the specified molecule. + int NresInMol(int) const; /// Determine molecules based on bond information int DetermineMolecules(); // ----- Bond-specific routines -------------- From 32ea154ba6c35ffd8bddb1187944abf35a2b3d73 Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Mon, 14 Sep 2020 17:17:13 -0400 Subject: [PATCH 52/65] Fix splitcoords --- src/AtomMask.cpp | 10 ++++++++-- src/AtomMask.h | 2 ++ src/Exec_SplitCoords.cpp | 10 +++++----- 3 files changed, 15 insertions(+), 7 deletions(-) diff --git a/src/AtomMask.cpp b/src/AtomMask.cpp index 6e32acdea1..ebc6a2dd8d 100644 --- a/src/AtomMask.cpp +++ b/src/AtomMask.cpp @@ -3,13 +3,19 @@ #include "CpptrajStdio.h" #include "Unit.h" -// CONSTRUCTOR +/** CONSTRUCTOR - atom range */ AtomMask::AtomMask(int beginAtom, int endAtom) : Natom_(0), maskChar_(SelectedChar_) { AddAtomRange(beginAtom, endAtom); } -// CONSTRUCTOR +/** CONSTRUCTOR - unit */ +AtomMask::AtomMask(Unit const& unit) : Natom_(0), maskChar_(SelectedChar_) +{ + AddUnit( unit ); +} + +/** CONSTRUCTOR - single atom */ AtomMask::AtomMask(int atomNum) : Selected_(1, atomNum), Natom_(1), maskChar_(SelectedChar_) {} // AtomMask::ResetMask() diff --git a/src/AtomMask.h b/src/AtomMask.h index fc648e68e3..c1840f317f 100644 --- a/src/AtomMask.h +++ b/src/AtomMask.h @@ -24,6 +24,8 @@ class AtomMask : public MaskTokenArray { maskChar_(SelectedChar_) {} /// Create mask selecting atoms from begin up to (not including) end. AtomMask(int,int); + /// Create mask selecting atoms in unit + AtomMask(Unit const&); /// Create mask with single atom selected. AtomMask(int); /// \return Internal selected atom array. diff --git a/src/Exec_SplitCoords.cpp b/src/Exec_SplitCoords.cpp index b4c207bbb4..34489cc21e 100644 --- a/src/Exec_SplitCoords.cpp +++ b/src/Exec_SplitCoords.cpp @@ -43,16 +43,16 @@ Exec::RetType Exec_SplitCoords::Execute(CpptrajState& State, ArgList& argIn) mprinterr("Error: Topology for '%s' has less than 2 molecules.\n", CRD->legend()); return CpptrajState::ERR; } - int molNatoms = -1; + unsigned int molNatoms = 0; int molNres = -1; for (Topology::mol_iterator mol = topIn.MolStart(); mol != topIn.MolEnd(); ++mol) { - int nres = topIn[mol->BeginAtom()].ResNum() - topIn[mol->EndAtom()-1].ResNum() + 1; - if (molNatoms == -1) { + int nres = topIn.NresInMol(mol-topIn.MolStart()); + if (molNatoms == 0) { molNatoms = mol->NumAtoms(); molNres = nres; } else if (molNatoms != mol->NumAtoms()) { - mprinterr("Error: Molecule %li has different number of atoms (%i) than first molecule (%i)\n", + mprinterr("Error: Molecule %li has different number of atoms (%u) than first molecule (%u)\n", mol - topIn.MolStart() + 1, mol->NumAtoms(), molNatoms); return CpptrajState::ERR; } else if (molNres != nres) { @@ -67,7 +67,7 @@ Exec::RetType Exec_SplitCoords::Execute(CpptrajState& State, ArgList& argIn) Topology* topOut = 0; for (Topology::mol_iterator mol = topIn.MolStart(); mol != topIn.MolEnd(); ++mol) { - Masks.push_back( AtomMask(mol->BeginAtom(), mol->EndAtom()) ); + Masks.push_back( AtomMask(mol->MolUnit()) ); // Set total number of atoms Masks.back().SetNatoms( topIn.Natom() ); // First time around set up the output topology. From f0ad644a659db247f3c3bd3ad68df19e542e3b8e Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Tue, 15 Sep 2020 11:16:59 -0400 Subject: [PATCH 53/65] More updates for unit --- src/ForLoop_mask.cpp | 4 +-- src/MaskToken.cpp | 79 +++++++++++++++++++++++++++----------------- src/Mol.cpp | 59 +++++++++++++++++++-------------- src/Unit.h | 1 + 4 files changed, 86 insertions(+), 57 deletions(-) diff --git a/src/ForLoop_mask.cpp b/src/ForLoop_mask.cpp index b7e2756a5f..200ca62cac 100644 --- a/src/ForLoop_mask.cpp +++ b/src/ForLoop_mask.cpp @@ -70,9 +70,9 @@ int ForLoop_mask::SetupFor(CpptrajState& State, ArgList& argIn) { else { int res; if (mtype_ == MOLFIRSTRES) - res = (*currentTop)[ currentTop->Mol( mol ).BeginAtom() ].ResNum(); + res = (*currentTop)[ currentTop->Mol( mol ).MolUnit().Front() ].ResNum(); else // MOLLASTRES - res = (*currentTop)[ currentTop->Mol( mol ).EndAtom()-1 ].ResNum(); + res = (*currentTop)[ currentTop->Mol( mol ).MolUnit().Back()-1 ].ResNum(); Idxs_.push_back( res ); } curMol = mol; diff --git a/src/MaskToken.cpp b/src/MaskToken.cpp index 587e6cb14f..499a4fff8c 100644 --- a/src/MaskToken.cpp +++ b/src/MaskToken.cpp @@ -852,25 +852,32 @@ int MaskTokenArray::SelectDistance(const double* REF, char *mask, for (moli = 0; moli < n_of_mol; moli++) { // Initial state char schar = char0; - int atomi = molecules[moli].BeginAtom(); - const double* i_crd = REF + (atomi * 3); - // Loop over molecule atoms - for (; atomi != molecules[moli].EndAtom(); atomi++, i_crd += 3) { - // Loop over initially selected atoms - for (Uarray::const_iterator idx = Idx.begin(); idx != Idx.end(); ++idx) { - double d2 = DIST2_NoImage(i_crd, REF + *idx); - if (d2 < dcut2) { - // State changes - schar = char1; - break; - } - } // END loop over initially selected atoms - if (schar == char1) break; - } // END loop over molecule atoms + // Loop over molecule segments + for (Unit::const_iterator seg = molecules[moli].MolUnit().segBegin(); + seg != molecules[moli].MolUnit().segEnd(); ++seg) + { + int atomi = seg->Begin(); + const double* i_crd = REF + (atomi * 3); + // Loop over segment atoms + for (; atomi != seg->End(); atomi++, i_crd += 3) + { + // Loop over initially selected atoms + for (Uarray::const_iterator idx = Idx.begin(); idx != Idx.end(); ++idx) { + double d2 = DIST2_NoImage(i_crd, REF + *idx); + if (d2 < dcut2) { + // State changes + schar = char1; + break; + } + } // END loop over initially selected atoms + if (schar == char1) break; + } // END loop over segment atoms + } // END loop over molecule segments // Set molecule selection status - for (atomi = molecules[moli].BeginAtom(); - atomi != molecules[moli].EndAtom(); atomi++) - mask[atomi] = schar; + for (Unit::const_iterator seg = molecules[moli].MolUnit().segBegin(); + seg != molecules[moli].MolUnit().segEnd(); ++seg) + for (int atomi = seg->Begin(); atomi != seg->End(); atomi++) + mask[atomi] = schar; } // END loop over all molecules # ifdef _OPENMP } // END pragma omp parallel @@ -968,7 +975,12 @@ void MaskTokenArray::SelectChainID(ResArrayT const& residues, NameType const& na std::fill(mask + res->FirstAtom(), mask + res->LastAtom(), SelectedChar_); } -/** Select by molecule number. */ +/** Select by molecule number. + * \param molecules The array of molecules + * \param mol1 Start molecule arg (from 1) + * \param mol2 End molecule arg (from 1) + * \param mask The output mask + */ void MaskTokenArray::SelectMolNum(MolArrayT const& molecules, int mol1, int mol2, char* mask) const { @@ -976,20 +988,25 @@ void MaskTokenArray::SelectMolNum(MolArrayT const& molecules, int mol1, int mol2 mprintf("Warning: No molecule information, cannot select by molecule.\n"); return; } - int endatom; - int nmol = (int)molecules.size(); - // Mask args expected to start from 1 - if (mol1 > nmol) { - mprintf("Warning: Select molecules: mol 1 out of range (%i > %i)\n", mol1, nmol); + // Check start molecule arg. + unsigned int molStart = mol1 - 1; + if (molStart >= molecules.size()) { + mprintf("Warning: Select molecules: molecule start arg %i out of range (1-%zu)\n", + mol1, molecules.size()); return; } - // If last mol > nmol, make it nmol - if ( mol2 >= nmol ) - endatom = molecules.back().EndAtom(); - else - endatom = molecules[mol2-1].EndAtom(); - // Select atoms - std::fill(mask + molecules[mol1-1].BeginAtom(), mask + endatom, SelectedChar_); + // Check end molecule arg. If beyond last molecule, make it the last molecule + unsigned int molEnd = mol2; + if (molEnd > molecules.size()) + molEnd = molecules.size(); + // Loop over molecules + for (unsigned int midx = molStart; midx < molEnd; midx++) + { + // Loop over segments + for (Unit::const_iterator seg = molecules[midx].MolUnit().segBegin(); + seg != molecules[midx].MolUnit().segEnd(); ++seg) + std::fill(mask + seg->Begin(), mask + seg->End(), SelectedChar_); + } } /** Select by atomic element. */ diff --git a/src/Mol.cpp b/src/Mol.cpp index e023c632d6..8db8490b84 100644 --- a/src/Mol.cpp +++ b/src/Mol.cpp @@ -7,44 +7,55 @@ Mol::Marray Mol::UniqueCount(Topology const& top, std::vector const& molNums) { Marray mols; - // Hold begin residue for each molecule type - Iarray Res0; - // Hold end residue for each molecule type - Iarray Res1; + // Loop over all molecule numbers for (std::vector::const_iterator mnum = molNums.begin(); mnum != molNums.end(); ++mnum) { Molecule const& CurMol = top.Mol(*mnum); - // Has this molecule been seen before? + // Has this molecule been seen before? Check # atoms and residues. int natom = CurMol.NumAtoms(); - int res0 = top[ CurMol.BeginAtom() ].ResNum(); // CurMol first residue - int res1 = top[ CurMol.EndAtom()-1 ].ResNum(); // CurMol last residue - int nres = res1 - res0 + 1; + int nres = top.NresInMol(*mnum); + std::string curName = top.Res(top[ CurMol.MolUnit().Front() ].ResNum()).Name().Truncated(); int matchIdx = -1; for (int idx = 0; idx != (int)mols.size(); idx++) { - // First check number of atoms, then number residues, then residue names. + // First check number of atoms, then number residues. if ( mols[idx].natom_ == natom ) { if ( mols[idx].nres_ == nres ) { - matchIdx = idx; - int cridx = res0; // current molecule residue index - for (int rridx = Res0[idx]; rridx <= Res1[idx]; rridx++, cridx++) - { - if ( top.Res(rridx).Name() != top.Res(cridx).Name() ) { - // Residue name mismatch. - matchIdx = -1; - break; - } - } // END loop over all residues - } - } + Molecule const& PrevMol = top.Mol( mols[idx].idxs_.front() ); + // Check that # segments match + if ( CurMol.MolUnit().nSegments() == PrevMol.MolUnit().nSegments() ) { + matchIdx = idx; + // Now check that residue names in CurMol match those in PrevMol + for (unsigned int iseg = 0; iseg != CurMol.MolUnit().nSegments(); iseg++) + { + int curRes0 = top[ CurMol.MolUnit()[iseg].Begin() ].ResNum(); + int curRes1 = top[ CurMol.MolUnit()[iseg].End()-1 ].ResNum(); + int prevRes0 = top[ PrevMol.MolUnit()[iseg].Begin() ].ResNum(); + int prevRes1 = top[ PrevMol.MolUnit()[iseg].End()-1 ].ResNum(); + if (curRes1 - curRes0 != prevRes1 - prevRes0) { + matchIdx = -1; + break; + } + while (curRes0 <= curRes1) { + if (top.Res(curRes0).Name() != top.Res(prevRes0).Name()) { + // Residue name mismatch. + matchIdx = -1; + iseg = CurMol.MolUnit().nSegments(); + break; + } + curRes0++; + prevRes0++; + } + } // END loop over segments + } // END # segments match + } // END # residues match + } // END # atoms match if (matchIdx != -1) break; } // END loop over found molecule types if (matchIdx == -1) { // New molecule - mols.push_back( Type(*mnum, natom, nres, top.Res(res0).Name().Truncated()) ); - Res0.push_back( res0 ); - Res1.push_back( res1 ); + mols.push_back( Type(*mnum, natom, nres, curName) ); } else { // Existing molecule. Update count. mols[matchIdx].UpdateCount(*mnum); diff --git a/src/Unit.h b/src/Unit.h index 403460f60f..749323a66a 100644 --- a/src/Unit.h +++ b/src/Unit.h @@ -16,6 +16,7 @@ class Unit { const_iterator segBegin() const { return segArray_.begin(); } const_iterator segEnd() const { return segArray_.end(); } unsigned int nSegments() const { return segArray_.size(); } + Segment const& operator[](int idx) const { return segArray_[idx]; } /// \return Total unit size unsigned int Size() const { From 78676a5b8a0479d9cc4e1b02d88217fb3c834c78 Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Tue, 15 Sep 2020 13:13:06 -0400 Subject: [PATCH 54/65] Try to handle non-contiguous molecules in amber topology --- src/Parm_Amber.cpp | 123 ++++++++++++++++++++++++++++++++++----------- 1 file changed, 93 insertions(+), 30 deletions(-) diff --git a/src/Parm_Amber.cpp b/src/Parm_Amber.cpp index 2eec0d1c4c..2c693ac629 100644 --- a/src/Parm_Amber.cpp +++ b/src/Parm_Amber.cpp @@ -2032,39 +2032,102 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) { // Write solvent info if IFBOX > 0 if (ifbox > 0) { - // Determine first solvent molecule - int firstSolventMol = -1; - for (Topology::mol_iterator mol = TopOut.MolStart(); mol != TopOut.MolEnd(); ++mol) { - if ( mol->IsSolvent() ) { - firstSolventMol = (int)(mol - TopOut.MolStart()); + // Need to check if molecules are contiguous or not via + // how many segments they have. + bool molsAreContiguous = true; + for (Topology::mol_iterator mol = TopOut.MolStart(); mol != TopOut.MolEnd(); ++mol) + if (mol->MolUnit().nSegments() > 1) { + molsAreContiguous = false; break; } + if (molsAreContiguous) { + // ----- Contiguous molecules -------------- + // Determine first solvent molecule + int firstSolventMol = -1; + for (Topology::mol_iterator mol = TopOut.MolStart(); mol != TopOut.MolEnd(); ++mol) { + if ( mol->IsSolvent() ) { + firstSolventMol = (int)(mol - TopOut.MolStart()); + break; + } + } + // Determine final solute residue based on first solvent molecule. + int finalSoluteRes = 0; + if (firstSolventMol == -1) + finalSoluteRes = TopOut.Nres(); // No solvent Molecules + else if (firstSolventMol > 0) { + int finalSoluteAtom = TopOut.Mol(firstSolventMol).MolUnit().Front() - 1; + finalSoluteRes = TopOut[finalSoluteAtom].ResNum() + 1; + } + // If no solvent, just set to 1 beyond # of molecules + if (firstSolventMol == -1) + firstSolventMol = TopOut.Nmol(); + // SOLVENT POINTERS + if (BufferAlloc(F_SOLVENT_POINTER, 3)) return 1; + file_.IntToBuffer( finalSoluteRes ); // Already +1 + file_.IntToBuffer( TopOut.Nmol() ); + file_.IntToBuffer( firstSolventMol + 1 ); + file_.FlushBuffer(); + // ATOMS PER MOLECULE + if (BufferAlloc(F_ATOMSPERMOL, TopOut.Nmol())) return 1; + for (Topology::mol_iterator mol = TopOut.MolStart(); mol != TopOut.MolEnd(); mol++) + file_.IntToBuffer( mol->NumAtoms() ); + file_.FlushBuffer(); + } else { + // ----- Non-contiguous molecules ---------- + // Molecules are not contiguous. In order to ensure that #s in the + // ATOMS_PER_MOLECULE section match up, do segments instead. + mprintf("Warning: Topology has non-contiguous molecules.\n" + "Warning: Setting up SOLVENT_POINTERS and ATOMS_PER_MOLECULE\n" + "Warning: based on contiguous segments. The resulting Topology\n" + "Warning: will not strictly correspond to Amber specifications\n" + "Warning: and should be used with caution.\n" + "Warning: The 'fixatomorder' command can be used to reorder\n" + "Warning: molecules into contiguous segments.\n"); + // Map segment to solvent status + typedef std::pair SegPair; + typedef std::vector SegArray; + SegArray segments; + for (Topology::mol_iterator mol = TopOut.MolStart(); mol != TopOut.MolEnd(); ++mol) { + for (Unit::const_iterator seg = mol->MolUnit().segBegin(); + seg != mol->MolUnit().segEnd(); ++seg) + segments.push_back( SegPair(*seg, mol->IsSolvent()) ); + } + std::sort(segments.begin(), segments.end()); + mprintf("\t%zu segments.\n", segments.size()); + // Determine first solvent molecule + SegArray::const_iterator firstSolventSeg = segments.end(); + int firstSolventMol = -1; + for (SegArray::const_iterator it = segments.begin(); it != segments.end(); ++it) { + // it->second is true if segment was part of solvent molecule + if ( it->second ) { + firstSolventSeg = it; + firstSolventMol = it - segments.begin(); + break; + } + } + // Determine final solute residue based on first solvent molecule. + int finalSoluteRes = 0; + if (firstSolventSeg == segments.end()) + finalSoluteRes = TopOut.Nres(); // No solvent Molecules + else if (firstSolventSeg != segments.begin()) { + int finalSoluteAtom = firstSolventSeg->first.Begin() - 1; + finalSoluteRes = TopOut[finalSoluteAtom].ResNum() + 1; + } + // If no solvent, just set to 1 beyond # of segments + if (firstSolventMol == -1) + firstSolventMol = segments.size(); + // SOLVENT POINTERS + if (BufferAlloc(F_SOLVENT_POINTER, 3)) return 1; + file_.IntToBuffer( finalSoluteRes ); // Already +1 + file_.IntToBuffer( segments.size() ); + file_.IntToBuffer( firstSolventMol + 1 ); + file_.FlushBuffer(); + // ATOMS PER MOLECULE + if (BufferAlloc(F_ATOMSPERMOL, segments.size())) return 1; + for (SegArray::const_iterator it = segments.begin(); it != segments.end(); ++it) + file_.IntToBuffer( it->first.Size() ); + file_.FlushBuffer(); } - // Determine final solute residue based on first solvent molecule. - int finalSoluteRes = 0; - if (firstSolventMol == -1) - finalSoluteRes = TopOut.Nres(); // No solvent Molecules - else if (firstSolventMol > 0) { - int finalSoluteAtom = TopOut.Mol(firstSolventMol).BeginAtom() - 1; - finalSoluteRes = TopOut[finalSoluteAtom].ResNum() + 1; - } - // If no solvent, just set to 1 beyond # of molecules - if (firstSolventMol == -1) - firstSolventMol = TopOut.Nmol(); - - // SOLVENT POINTERS - if (BufferAlloc(F_SOLVENT_POINTER, 3)) return 1; - file_.IntToBuffer( finalSoluteRes ); // Already +1 - file_.IntToBuffer( TopOut.Nmol() ); - file_.IntToBuffer( firstSolventMol + 1 ); - file_.FlushBuffer(); - - // ATOMS PER MOLECULE - if (BufferAlloc(F_ATOMSPERMOL, TopOut.Nmol())) return 1; - for (Topology::mol_iterator mol = TopOut.MolStart(); mol != TopOut.MolEnd(); mol++) - file_.IntToBuffer( mol->NumAtoms() ); - file_.FlushBuffer(); - // BOX DIMENSIONS if (BufferAlloc(F_PARMBOX, 4)) return 1; file_.DblToBuffer( TopOut.ParmBox().Beta() ); From ce92af74ed49cd9db827f4f3012fa5b541ec7bf4 Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Wed, 16 Sep 2020 11:24:20 -0400 Subject: [PATCH 55/65] More updates for mol unit --- src/TopInfo.cpp | 27 ++++++++++++++++----------- src/Traj_PDBfile.cpp | 2 +- 2 files changed, 17 insertions(+), 12 deletions(-) diff --git a/src/TopInfo.cpp b/src/TopInfo.cpp index 051de06a26..1eac24028c 100644 --- a/src/TopInfo.cpp +++ b/src/TopInfo.cpp @@ -248,7 +248,7 @@ int TopInfo::maxMolNameWidth(std::vector const& molNums) const { int nWidth = 4; for (std::vector::const_iterator mnum = molNums.begin(); mnum != molNums.end(); ++mnum) { - int molAtom0 = parm_->Mol( *mnum ).BeginAtom(); + int molAtom0 = parm_->Mol( *mnum ).MolUnit().Front(); int firstres = (*parm_)[ molAtom0 ].ResNum(); int mn_size = parm_->Res(firstres).Name().len(); if (mn_size > nWidth) @@ -269,6 +269,7 @@ int TopInfo::PrintMoleculeInfo(std::string const& maskString) const { else { std::vector molNums = parm_->MolnumsSelectedBy( mask ); mprintf("%zu molecules.\n", molNums.size()); + // TODO determine max segments int mn_width = maxMolNameWidth( molNums ); int awidth = std::max(5, DigitWidth(parm_->Natom())); int rwidth = std::max(5, DigitWidth(parm_->Nres())); @@ -285,16 +286,20 @@ int TopInfo::PrintMoleculeInfo(std::string const& maskString) const { mnum != molNums.end(); ++mnum) { Molecule const& Mol = parm_->Mol(*mnum); - int firstres = (*parm_)[ Mol.BeginAtom() ].ResNum(); - int lastres = (*parm_)[ Mol.EndAtom()-1 ].ResNum(); - outfile_->Printf("%*u %*i %*i %*i %*i %-*s %c", - mwidth, *mnum+1, - awidth, Mol.NumAtoms(), - rwidth, lastres-firstres+1, - rwidth, firstres+1, - rwidth, lastres+1, - mn_width, parm_->Res(firstres).c_str(), - parm_->Res(firstres).ChainId()); + outfile_->Printf("%*u %*i", mwidth, *mnum+1, awidth, Mol.NumAtoms()); + // Loop over segments + for (Unit::const_iterator seg = Mol.MolUnit().segBegin(); + seg != Mol.MolUnit().segEnd(); ++seg) + { + int firstres = (*parm_)[ seg->Begin() ].ResNum(); + int lastres = (*parm_)[ seg->End()-1 ].ResNum(); + outfile_->Printf(" %*i %*i %*i %-*s %c", + rwidth, lastres-firstres+1, + rwidth, firstres+1, + rwidth, lastres+1, + mn_width, parm_->Res(firstres).c_str(), + parm_->Res(firstres).ChainId()); + } // END loop over segments if ( Mol.IsSolvent() ) outfile_->Printf(" SOLVENT"); outfile_->Printf("\n"); } diff --git a/src/Traj_PDBfile.cpp b/src/Traj_PDBfile.cpp index a93b132bba..0bec5726d4 100644 --- a/src/Traj_PDBfile.cpp +++ b/src/Traj_PDBfile.cpp @@ -703,7 +703,7 @@ int Traj_PDBfile::setupTrajout(FileName const& fname, Topology* trajParm, if ( trajParm->Nmol() > 0 ) { for (Topology::mol_iterator mol = trajParm->MolStart(); mol != trajParm->MolEnd(); ++mol) - TER_idxs_.push_back( mol->EndAtom() - 1 ); + TER_idxs_.push_back( mol->MolUnit().Back() - 1 ); } } TER_idxs_.push_back( -1 ); // Indicates that final TER has been written. From df705f5ed3e5cf8801c5aa7d09a72929eea29528 Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Wed, 16 Sep 2020 11:54:23 -0400 Subject: [PATCH 56/65] Hide some debug info --- src/Topology.cpp | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/src/Topology.cpp b/src/Topology.cpp index 9cd349d4e2..be978bf548 100644 --- a/src/Topology.cpp +++ b/src/Topology.cpp @@ -1043,17 +1043,19 @@ int Topology::DetermineMolecules() { Atom const& atom = atoms_[atomIdx]; molecules_[atom.MolNum()].ModifyUnit().AddIndex( atomIdx ); } - mprintf("Molecule information:\n"); + if (debug_ > 0) mprintf("DEBUG: Molecule segment information:\n"); std::vector< std::vector::const_iterator > nonContiguousMols; for (std::vector::const_iterator mol = molecules_.begin(); mol != molecules_.end(); ++mol) { if (mol->MolUnit().nSegments() > 1) nonContiguousMols.push_back( mol ); - mprintf("\t%8li %8u segments:", mol - molecules_.begin(), mol->MolUnit().nSegments()); - for (Unit::const_iterator seg = mol->MolUnit().segBegin(); - seg != mol->MolUnit().segEnd(); ++seg) - mprintf(" %i-%i (%i) ", seg->Begin(), seg->End(), seg->Size()); - mprintf("\n"); + if (debug_ > 0) { + mprintf("DEBUG:\t%8li %8u segments:", mol - molecules_.begin() + 1, mol->MolUnit().nSegments()); + for (Unit::const_iterator seg = mol->MolUnit().segBegin(); + seg != mol->MolUnit().segEnd(); ++seg) + mprintf(" %i-%i (%i) ", seg->Begin()+1, seg->End(), seg->Size()); + mprintf("\n"); + } } if (!nonContiguousMols.empty()) { mprintf("Warning: %zu molecules have non-contiguous segments of atoms.\n", nonContiguousMols.size()); From 21f811f42993e75306424f78bb894327f7bd6795 Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Wed, 16 Sep 2020 13:27:09 -0400 Subject: [PATCH 57/65] Remove break --- src/Topology.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/Topology.cpp b/src/Topology.cpp index be978bf548..50f14c78d3 100644 --- a/src/Topology.cpp +++ b/src/Topology.cpp @@ -1186,6 +1186,7 @@ int Topology::SetSolvent(std::string const& maskexpr) { // Setup mask CharMask mask( maskexpr ); SetupCharMask( mask ); + mask.MaskInfo(); if (mask.None()) { mprinterr("Error: SetSolvent [%s]: Mask %s selects no atoms.\n", c_str(), maskexpr.c_str()); return 1; @@ -1204,7 +1205,6 @@ int Topology::SetSolvent(std::string const& maskexpr) { mol->SetSolvent(); ++NsolventMolecules_; numSolvAtoms += mol->NumAtoms(); - break; } } From ebf831ee5abeab8014e198e71d98210d411372dd Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Wed, 16 Sep 2020 13:30:10 -0400 Subject: [PATCH 58/65] Remove unneeded check --- src/Action_FixAtomOrder.cpp | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/src/Action_FixAtomOrder.cpp b/src/Action_FixAtomOrder.cpp index 30c7f6adc2..89fa47dfed 100644 --- a/src/Action_FixAtomOrder.cpp +++ b/src/Action_FixAtomOrder.cpp @@ -136,12 +136,12 @@ Action::RetType Action_FixAtomOrder::PdbOrder(ActionSetup& setup) { /** Fix molecules that are not contiguous. */ Action::RetType Action_FixAtomOrder::FixMolecules(ActionSetup& setup) { // If topology already has molecule info assume no need to reorder. - if (setup.Top().Nmol() > 0) { - mprintf("Warning: %s already has molecule information. No reordering will occur.\n" - "Warning: This indicates that there is no need to fix atom ordering in this topology.\n", - setup.Top().c_str()); - return Action::SKIP; - } + //if (setup.Top().Nmol() > 0) { + // mprintf("Warning: %s already has molecule information. No reordering will occur.\n" + // "Warning: This indicates that there is no need to fix atom ordering in this topology.\n", + // setup.Top().c_str()); + // return Action::SKIP; + // } molNums_.resize( setup.Top().Natom(), -1 ); // Perform recursive search along bonds of each atom. int Nmol = 0; From aa7fa70c4dadb195f52e10944b74c61f268e04a4 Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Wed, 16 Sep 2020 13:41:34 -0400 Subject: [PATCH 59/65] Move debug info back into Setup() --- src/Action_FixAtomOrder.cpp | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/src/Action_FixAtomOrder.cpp b/src/Action_FixAtomOrder.cpp index 89fa47dfed..c6de048681 100644 --- a/src/Action_FixAtomOrder.cpp +++ b/src/Action_FixAtomOrder.cpp @@ -82,6 +82,13 @@ Action::RetType Action_FixAtomOrder::Setup(ActionSetup& setup) { if (ret != Action::OK) return ret; + if (debug_ > 0) { + mprintf("\tNew atom mapping:\n"); + for (MapType::const_iterator atom = atomMap_.begin(); + atom != atomMap_.end(); ++atom) + mprintf("\t\tNew atom %8li => old atom %8i\n", atom - atomMap_.begin() + 1, *atom + 1); + } + // Create new topology based on map if (newParm_ != 0) delete newParm_; newParm_ = setup.Top().ModifyByMap( atomMap_ ); @@ -172,14 +179,7 @@ Action::RetType Action_FixAtomOrder::FixMolecules(ActionSetup& setup) { mol != molecules.end(); ++mol) for (MapType::const_iterator atom = mol->begin(); atom != mol->end(); ++atom) atomMap_.push_back( *atom ); - if (debug_ > 0) { - mprintf("\tNew atom mapping:\n"); - for (MapType::const_iterator atom = atomMap_.begin(); - atom != atomMap_.end(); ++atom) - mprintf("\t\tNew atom %8li => old atom %8i\n", atom - atomMap_.begin() + 1, *atom + 1); - } - - return Action::OK; + return Action::OK; } // Action_FixAtomOrder::action() From cc97163d61e29146f2cce41a40108ad026f84113 Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Wed, 16 Sep 2020 13:54:04 -0400 Subject: [PATCH 60/65] Use molecule segments to re-order Topology --- src/Action_FixAtomOrder.cpp | 64 ++++++++----------------------------- src/Action_FixAtomOrder.h | 5 ++- 2 files changed, 15 insertions(+), 54 deletions(-) diff --git a/src/Action_FixAtomOrder.cpp b/src/Action_FixAtomOrder.cpp index c6de048681..b6a1a3f11f 100644 --- a/src/Action_FixAtomOrder.cpp +++ b/src/Action_FixAtomOrder.cpp @@ -18,7 +18,7 @@ Action_FixAtomOrder::~Action_FixAtomOrder() { // void Action_FixAtomOrder::Help() void Action_FixAtomOrder::Help() const { mprintf("%s", ActionTopWriter::Keywords()); - mprintf("\t[pdborder [hetatm ]] (EXPERIMENTAL)\n"); + mprintf("\t[pdborder [hetatm ] (EXPERIMENTAL)]\n"); mprintf(" Fix atom ordering so that all atoms in molecules are sequential.\n" " If 'pdborder' is specified, attempt to organize atoms by PDB\n" " information (i.e. Chain ID, original residue numbering, and\n" @@ -44,10 +44,9 @@ Action::RetType Action_FixAtomOrder::Init(ArgList& actionArgs, ActionInit& init, } if (mode_ == FIX_MOLECULES) - mprintf(" FIXATOMORDER: Will attempt to fix atom ordering when atom numbering\n" - " in molecules is non-sequential.\n"); + mprintf(" FIXATOMORDER: Re-ordering atoms so molecules are contiguous.\n"); else { - mprintf(" FIXATOMORDER: Will attempt to re-order according to PDB info.\n"); + mprintf(" FIXATOMORDER: Re-ordering atoms according to PDB info.\n"); if (hetatm_.MaskStringSet()) mprintf("\tAtoms selected by %s will be considered HETATM.\n", hetatm_.MaskString()); } @@ -56,18 +55,6 @@ Action::RetType Action_FixAtomOrder::Init(ArgList& actionArgs, ActionInit& init, return Action::OK; } -/** Mark atom as visited, visit all bonded atoms and mark them as well. */ -void Action_FixAtomOrder::VisitAtom(int atomnum, int mol, Topology const& Parm) { - // Return if this atom already has a molecule number - if (molNums_[atomnum]!=-1) return; - // Mark this atom as visited - molNums_[atomnum] = mol; - // Visit each atom bonded to this atom - for (Atom::bond_iterator bondedatom = Parm[atomnum].bondbegin(); - bondedatom != Parm[atomnum].bondend(); bondedatom++) - VisitAtom(*bondedatom, mol, Parm); -} - // Action_FixAtomOrder::setup() Action::RetType Action_FixAtomOrder::Setup(ActionSetup& setup) { Action::RetType ret; @@ -142,44 +129,19 @@ Action::RetType Action_FixAtomOrder::PdbOrder(ActionSetup& setup) { /** Fix molecules that are not contiguous. */ Action::RetType Action_FixAtomOrder::FixMolecules(ActionSetup& setup) { - // If topology already has molecule info assume no need to reorder. - //if (setup.Top().Nmol() > 0) { - // mprintf("Warning: %s already has molecule information. No reordering will occur.\n" - // "Warning: This indicates that there is no need to fix atom ordering in this topology.\n", - // setup.Top().c_str()); - // return Action::SKIP; - // } - molNums_.resize( setup.Top().Natom(), -1 ); - // Perform recursive search along bonds of each atom. - int Nmol = 0; - for (int atomnum = 0; atomnum < setup.Top().Natom(); ++atomnum) + atomMap_.clear(); + atomMap_.reserve( setup.Top().Natom() ); + for (Topology::mol_iterator mol = setup.Top().MolStart(); + mol != setup.Top().MolEnd(); ++mol) { - if (molNums_[atomnum] == -1) { - VisitAtom( atomnum, Nmol, setup.Top() ); - ++Nmol; + for (Unit::const_iterator seg = mol->MolUnit().segBegin(); + seg != mol->MolUnit().segEnd(); ++seg) + { + for (int idx = seg->Begin(); idx != seg->End(); ++idx) + atomMap_.push_back( idx ); } } - mprintf("\tDetected %i molecules.\n", Nmol); - if (Nmol < 1) { - mprinterr("Error: No molecules detected in %s\n", setup.Top().c_str()); - return Action::ERR; - } - if (debug_ > 0) { - for (MapType::const_iterator mnum = molNums_.begin(); mnum != molNums_.end(); ++mnum) - mprintf("\t\tAtom %li assigned to molecule %i\n", mnum - molNums_.begin() + 1, *mnum + 1); - } - // Figure out which atoms should go in which molecules - std::vector molecules(Nmol); - for (int atomnum = 0; atomnum < setup.Top().Natom(); ++atomnum) - molecules[molNums_[atomnum]].push_back( atomnum ); - atomMap_.clear(); - atomMap_.reserve( setup.Top().Natom() ); - // Place all atoms in molecule 0 first, molecule 1 next and so on - for (std::vector::const_iterator mol = molecules.begin(); - mol != molecules.end(); ++mol) - for (MapType::const_iterator atom = mol->begin(); atom != mol->end(); ++atom) - atomMap_.push_back( *atom ); - return Action::OK; + return Action::OK; } // Action_FixAtomOrder::action() diff --git a/src/Action_FixAtomOrder.h b/src/Action_FixAtomOrder.h index 6a82b976d6..926ed668a1 100644 --- a/src/Action_FixAtomOrder.h +++ b/src/Action_FixAtomOrder.h @@ -26,11 +26,10 @@ class Action_FixAtomOrder: public Action { int debug_; typedef std::vector MapType; MapType atomMap_; ///< Map original atoms to new atoms. - MapType molNums_; ///< Hold molecule number for each atom. Topology* newParm_; ///< Re-ordered topology Frame newFrame_; ///< Re-ordered frame ActionTopWriter topWriter_; ///< Use to write re-ordered Topology - ModeType mode_; - CharMask hetatm_; + ModeType mode_; ///< How atoms should be reordered + CharMask hetatm_; ///< If PDB reorder, atoms that should be HETATM }; #endif From da6d671ef8d8eafa31ddb071c9845cb4888a51ee Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Wed, 16 Sep 2020 15:56:41 -0400 Subject: [PATCH 61/65] Test will no longer print error messages --- src/Parm_PDB.cpp | 4 ++-- test/Test_FixAtomOrder/RunTest.sh | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/Parm_PDB.cpp b/src/Parm_PDB.cpp index da0d24160c..d96caf2b5c 100644 --- a/src/Parm_PDB.cpp +++ b/src/Parm_PDB.cpp @@ -157,10 +157,10 @@ int Parm_PDB::ReadParm(FileName const& fname, Topology &TopIn) { } else if ( !missingResidues && infile.RecType() == PDBfile::MISSING_RES ) { missingResidues = true; mprintf("Warning: PDB file has MISSING RESIDUES section.\n"); - if (readConect) + /*if (readConect) mprintf("Warning: If molecule determination fails try specifying 'noconect' instead.\n"); if (readLink) - mprintf("Warning: If molecule determination fails try not specifying 'link' instead.\n"); + mprintf("Warning: If molecule determination fails try not specifying 'link' instead.\n");*/ } } // END loop over PDB records if (nAltLocSkipped > 0) diff --git a/test/Test_FixAtomOrder/RunTest.sh b/test/Test_FixAtomOrder/RunTest.sh index b83319dd76..c192c8715d 100755 --- a/test/Test_FixAtomOrder/RunTest.sh +++ b/test/Test_FixAtomOrder/RunTest.sh @@ -18,7 +18,7 @@ trajin min1.crd 1 10 fixatomorder outprefix reorder parmopts nopdbinfo trajout reorder.mdcrd EOF -RunCpptraj "$TESTNAME (will print error messages)" +RunCpptraj "$TESTNAME" DoTest reorder.outoforder.parm7.save reorder.outoforder.parm7 -I %VERSION DoTest reorder.mdcrd.save reorder.mdcrd From fec0fa42beb7b9362b67f1ca1899bdce3a26ba82 Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Wed, 16 Sep 2020 16:02:04 -0400 Subject: [PATCH 62/65] Hide debug info --- src/ImageRoutines.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/ImageRoutines.cpp b/src/ImageRoutines.cpp index 13a0fd9200..aea9494c44 100644 --- a/src/ImageRoutines.cpp +++ b/src/ImageRoutines.cpp @@ -57,8 +57,8 @@ Image::List* Image::CreateImageList(Topology const& Parm, Mode modeIn, delete listOut; return 0; } - mprintf("DEBUG: Image list for '%s' over %u %ss.\n", - maskExpression.c_str(), listOut->nEntities(), ModeString(modeIn)); + //mprintf("DEBUG: Image list for '%s' over %u %ss.\n", + // maskExpression.c_str(), listOut->nEntities(), ModeString(modeIn)); } return listOut; } From a98062853d3c1ebcb7ad2e570a9a7651a7b48f35 Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Wed, 16 Sep 2020 16:05:45 -0400 Subject: [PATCH 63/65] Minor version bump for handling non-contiguous molecules. --- src/Version.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/Version.h b/src/Version.h index 8ff6924ab9..0e9bd46cf3 100644 --- a/src/Version.h +++ b/src/Version.h @@ -12,7 +12,7 @@ * Whenever a number that precedes is incremented, all subsequent * numbers should be reset to 0. */ -#define CPPTRAJ_INTERNAL_VERSION "V4.29.9" +#define CPPTRAJ_INTERNAL_VERSION "V4.30.0" /// PYTRAJ relies on this #define CPPTRAJ_VERSION_STRING CPPTRAJ_INTERNAL_VERSION #endif From 084e0d6c3d09189b9201b5325797ed08e8006914 Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Thu, 17 Sep 2020 13:15:37 -0400 Subject: [PATCH 64/65] Update dependencies --- src/cpptrajdepend | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/cpptrajdepend b/src/cpptrajdepend index 5de8e9f515..4d0c7dd1ca 100644 --- a/src/cpptrajdepend +++ b/src/cpptrajdepend @@ -81,7 +81,7 @@ Action_Temperature.o : Action_Temperature.cpp Action.h ActionState.h Action_Temp Action_Time.o : Action_Time.cpp Action.h ActionState.h Action_Time.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h Action_Translate.o : Action_Translate.cpp Action.h ActionState.h Action_Translate.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h Action_Unstrip.o : Action_Unstrip.cpp Action.h ActionState.h Action_Unstrip.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h -Action_Unwrap.o : Action_Unwrap.cpp Action.h ActionState.h Action_Unwrap.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h ImageRoutines.h ImageTypes.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h +Action_Unwrap.o : Action_Unwrap.cpp Action.h ActionState.h Action_Unwrap.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h ImageRoutines.h ImageTypes.h Image_List.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h Action_Vector.o : Action_Vector.cpp Action.h ActionState.h Action_Vector.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h Action_VelocityAutoCorr.o : Action_VelocityAutoCorr.cpp Action.h ActionState.h Action_VelocityAutoCorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h Action_Volmap.o : Action_Volmap.cpp Action.h ActionState.h Action_Volmap.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridDbl.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h From c00534c70415e2768f01ed62ad97eb360e475d7a Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Thu, 17 Sep 2020 18:02:06 -0400 Subject: [PATCH 65/65] Fix cuda build --- src/Action_Watershell.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/Action_Watershell.cpp b/src/Action_Watershell.cpp index 47edc248d4..0938a802eb 100644 --- a/src/Action_Watershell.cpp +++ b/src/Action_Watershell.cpp @@ -159,7 +159,7 @@ Action::RetType Action_Watershell::Setup(ActionSetup& setup) { NsolventMolecules_ = 0; CharMask cMask( solventMask_.ConvertToCharMask(), solventMask_.Nselected() ); for (Topology::mol_iterator mol = setup.Top().MolStart(); mol != setup.Top().MolEnd(); ++mol) - if ( cMask.AtomsInCharMask( mol->BeginAtom(), mol->EndAtom() ) ) + if ( cMask.AtomsInCharMask( mol->MolUnit() ) ) NsolventMolecules_++; // Sanity check if ( (NsolventMolecules_ * NAtoms_) != solventMask_.Nselected() ) {