diff --git a/doc/CpptrajManual.pdf b/doc/CpptrajManual.pdf index 2a27bcbcc2..907e1b7826 100644 Binary files a/doc/CpptrajManual.pdf and b/doc/CpptrajManual.pdf differ diff --git a/doc/cpptraj.lyx b/doc/cpptraj.lyx index 3738a89f3d..52f18bb580 100644 --- a/doc/cpptraj.lyx +++ b/doc/cpptraj.lyx @@ -13929,15 +13929,27 @@ Options for pdb format: \end_layout \begin_layout LyX-Code - [model | multi] [dumpq | parse | vdw] [chainid ] + [dumpq | parse | vdw] [pdbres] [pdbatom] \end_layout \begin_layout LyX-Code - [pdbres] [pdbatom] [pdbv3] [teradvance] [usecol21] -\begin_inset Separator latexpar -\end_inset + [pdbv3] [teradvance] [terbyres | pdbter | noter] +\end_layout + +\begin_layout LyX-Code + [model | multi] [chainid ] [sg ] +\end_layout +\begin_layout LyX-Code + [include_ep] [conect] [keepext] [usecol21] +\end_layout + +\begin_layout LyX-Code + [bfacdata ] [occdata ] [bfacbyres] [occbyres] +\end_layout +\begin_layout LyX-Code + [bfacscale] [occscale] [bfacmax ] [occmax ] \end_layout \begin_deeper @@ -14026,6 +14038,56 @@ keepext Keep filename extension; write '..' instead (implies usecol21 Use column 21 for 4-letter residue names. \end_layout +\begin_layout Description +bfacdata +\begin_inset space ~ +\end_inset + + Use data in for B-factor column. +\end_layout + +\begin_layout Description +occdata +\begin_inset space ~ +\end_inset + + Use data in for occupancy column. +\end_layout + +\begin_layout Description +bfacbyres If specified assume X values in B-factor data set are residue + numbers. +\end_layout + +\begin_layout Description +occbyres If specified assume X values in occupancy data set are residue + numbers. +\end_layout + +\begin_layout Description +bfacscale If specified scale values in B-factor column between 0 and . +\end_layout + +\begin_layout Description +occscale If specified scale values in occupancy column between 0 and . +\end_layout + +\begin_layout Description +bfacmax +\begin_inset space ~ +\end_inset + + Max value for bfacscale. +\end_layout + +\begin_layout Description +occmax +\begin_inset space ~ +\end_inset + + Max value for occscale. +\end_layout + \end_deeper \begin_layout Subsubsection diff --git a/src/Action_Average.cpp b/src/Action_Average.cpp index 430e53293e..86b0eb789f 100644 --- a/src/Action_Average.cpp +++ b/src/Action_Average.cpp @@ -59,6 +59,7 @@ Action::RetType Action_Average::Init(ArgList& actionArgs, ActionInit& init, int if (crdset_ == 0) { outtraj_.SetDebug( debug_ ); if (outtraj_.InitEnsembleTrajWrite(avgfilename, actionArgs.RemainingArgs(), + init.DSL(), TrajectoryFile::UNKNOWN_TRAJ, init.DSL().EnsembleNum())) return Action::ERR; } diff --git a/src/Action_LESsplit.cpp b/src/Action_LESsplit.cpp index 268c2e7ad8..01211f1e8b 100644 --- a/src/Action_LESsplit.cpp +++ b/src/Action_LESsplit.cpp @@ -41,12 +41,13 @@ Action::RetType Action_LESsplit::Init(ArgList& actionArgs, ActionInit& init, int // NOTE: Cannot yet init split traj since we dont know how many. if (lesAverage_) { avgTraj_.SetDebug( debugIn ); - if (avgTraj_.InitTrajWrite( avgfilename, trajArgs_, TrajectoryFile::UNKNOWN_TRAJ )) + if (avgTraj_.InitTrajWrite( avgfilename, trajArgs_, init.DSL(), TrajectoryFile::UNKNOWN_TRAJ )) return Action::ERR; # ifdef MPI avgTraj_.SetTrajComm( trajComm_ ); # endif } + masterDSL_ = init.DslPtr(); mprintf(" LESSPLIT:\n"); if (lesSplit_) mprintf("\tSplit output to '%s.X'\n", splitfilename_.c_str()); @@ -93,7 +94,7 @@ Action::RetType Action_LESsplit::Setup(ActionSetup& setup) { for (unsigned int idx = 0; idx != lesMasks_.size(); idx++) { // FIXME this will have to be changed if lessplit every enabled for ensemble lesTraj_.push_back( new Trajout_Single() ); - if (lesTraj_.back()->InitEnsembleTrajWrite( splitfilename_, trajArgs_, + if (lesTraj_.back()->InitEnsembleTrajWrite( splitfilename_, trajArgs_, *masterDSL_, TrajectoryFile::UNKNOWN_TRAJ, idx )) return Action::ERR; # ifdef MPI diff --git a/src/Action_LESsplit.h b/src/Action_LESsplit.h index ea55af29be..5c1f3606c2 100644 --- a/src/Action_LESsplit.h +++ b/src/Action_LESsplit.h @@ -27,6 +27,7 @@ class Action_LESsplit : public Action { Frame lesFrame_; ///< Frame for LES split Frame avgFrame_; ///< Frame for LES average Topology* lesParm_; ///< Topology for LES split/average + DataSetList* masterDSL_; # ifdef MPI Parallel::Comm trajComm_; # endif diff --git a/src/Action_Mask.cpp b/src/Action_Mask.cpp index 6da508439c..d76ef51272 100644 --- a/src/Action_Mask.cpp +++ b/src/Action_Mask.cpp @@ -62,7 +62,7 @@ Action::RetType Action_Mask::Init(ArgList& actionArgs, ActionInit& init, int deb trajFmt = TrajectoryFile::MOL2FILE; trajArgs = ArgList("multi nobox"); } - if (outtraj_.InitEnsembleTrajWrite(maskpdb, trajArgs, trajFmt, init.DSL().EnsembleNum())) + if (outtraj_.InitEnsembleTrajWrite(maskpdb, trajArgs, init.DSL(), trajFmt, init.DSL().EnsembleNum())) return Action::ERR; writeTraj_ = true; } else diff --git a/src/Action_Outtraj.cpp b/src/Action_Outtraj.cpp index 6b1e646b7d..d0c8ab2f4c 100644 --- a/src/Action_Outtraj.cpp +++ b/src/Action_Outtraj.cpp @@ -78,7 +78,7 @@ Action::RetType Action_Outtraj::Init(ArgList& actionArgs, ActionInit& init, int // Initialize output trajectory with remaining arguments if (isActive_) { outtraj_.SetDebug(debugIn); - if ( outtraj_.InitEnsembleTrajWrite(trajfilename, actionArgs.RemainingArgs(), + if ( outtraj_.InitEnsembleTrajWrite(trajfilename, actionArgs.RemainingArgs(), init.DSL(), TrajectoryFile::UNKNOWN_TRAJ, init.DSL().EnsembleNum()) ) return Action::ERR; } diff --git a/src/Action_Pairwise.cpp b/src/Action_Pairwise.cpp index 21140e1f94..4fc030aac1 100644 --- a/src/Action_Pairwise.cpp +++ b/src/Action_Pairwise.cpp @@ -428,7 +428,8 @@ int Action_Pairwise::WriteCutFrame(int frameNum, Topology const& Parm, AtomMask CutParm->SetAtom(i).SetCharge( CutCharges[i] ); int err = 0; Trajout_Single tout; - if (tout.PrepareTrajWrite(outfilename, "multi", CutParm, CoordinateInfo(), 1, + // NOTE: Since no user-specified arguments, pass in blank data set list. + if (tout.PrepareTrajWrite(outfilename, "multi", DataSetList(), CutParm, CoordinateInfo(), 1, TrajectoryFile::MOL2FILE)) { mprinterr("Error: Could not set up cut mol2 file %s\n", outfilename.c_str()); diff --git a/src/Action_ReplicateCell.cpp b/src/Action_ReplicateCell.cpp index f8e53f7877..bcb54c066c 100644 --- a/src/Action_ReplicateCell.cpp +++ b/src/Action_ReplicateCell.cpp @@ -98,7 +98,7 @@ Action::RetType Action_ReplicateCell::Init(ArgList& actionArgs, ActionInit& init // Initialize output trajectory with remaining arguments if (!trajfilename.empty()) { outtraj_.SetDebug( debugIn ); - if ( outtraj_.InitEnsembleTrajWrite(trajfilename, actionArgs.RemainingArgs(), + if ( outtraj_.InitEnsembleTrajWrite(trajfilename, actionArgs.RemainingArgs(), init.DSL(), TrajectoryFile::UNKNOWN_TRAJ, init.DSL().EnsembleNum()) ) return Action::ERR; writeTraj_ = true; diff --git a/src/Analysis_Clustering.cpp b/src/Analysis_Clustering.cpp index 1b75a934da..e6d5480fc8 100644 --- a/src/Analysis_Clustering.cpp +++ b/src/Analysis_Clustering.cpp @@ -1005,7 +1005,7 @@ void Analysis_Clustering::WriteClusterTraj( ClusterList const& CList ) { std::string cfilename = clusterfile_ + ".c" + integerToString( cnum ); // Set up trajectory file Trajout_Single clusterout; - if (clusterout.PrepareTrajWrite(cfilename, ArgList(), clusterparm, + if (clusterout.PrepareTrajWrite(cfilename, ArgList(), DataSetList(), clusterparm, coords_->CoordsInfo(), C->Nframes(), clusterfmt_)) { @@ -1041,7 +1041,7 @@ void Analysis_Clustering::WriteAvgStruct( ClusterList const& CList ) { std::string cfilename = avgfile_ + ".c" + integerToString( cnum ) + tmpExt; // Set up trajectory file Trajout_Single clusterout; // FIXME CoordinateInfo OK for just coords? - if (clusterout.PrepareTrajWrite(cfilename, ArgList(), &avgparm, + if (clusterout.PrepareTrajWrite(cfilename, ArgList(), DataSetList(), &avgparm, CoordinateInfo(), 1, avgfmt_)) { mprinterr("Error: Could not set up cluster average file %s for write.\n", @@ -1075,7 +1075,7 @@ void Analysis_Clustering::WriteSingleRepTraj( ClusterList const& CList ) { Trajout_Single clusterout; // Set up trajectory file. Use parm from COORDS DataSet. Topology *clusterparm = coords_->TopPtr(); - if (clusterout.PrepareTrajWrite(singlerepfile_, ArgList(), clusterparm, + if (clusterout.PrepareTrajWrite(singlerepfile_, ArgList(), DataSetList(), clusterparm, coords_->CoordsInfo(), CList.Nclusters() * nRepsToSave_, singlerepfmt_)) { @@ -1127,7 +1127,7 @@ void Analysis_Clustering::WriteRepTraj( ClusterList const& CList ) { std::string cfilename = reptrajfile_ + ".c" + integerToString(C->Num()) + ("." + integerToString(framenum+1)) + tmpExt; // Set up trajectory file. - if (clusterout.PrepareTrajWrite(cfilename, ArgList(), clusterparm, + if (clusterout.PrepareTrajWrite(cfilename, ArgList(), DataSetList(), clusterparm, coords_->CoordsInfo(), 1, reptrajfmt_)) { mprinterr("Error: Could not set up representative trajectory file %s for write.\n", @@ -1146,7 +1146,7 @@ void Analysis_Clustering::WriteRepTraj( ClusterList const& CList ) { // Create filename based on cluster number std::string cfilename = reptrajfile_ + ".c" + integerToString(C->Num()) + tmpExt; // Set up trajectory file. - if (clusterout.PrepareTrajWrite(cfilename, ArgList(), clusterparm, + if (clusterout.PrepareTrajWrite(cfilename, ArgList(), DataSetList(), clusterparm, coords_->CoordsInfo(), nRepsToSave_, reptrajfmt_)) { mprinterr("Error: Could not set up representative trajectory file %s for write.\n", diff --git a/src/Analysis_Hist.cpp b/src/Analysis_Hist.cpp index b58de27478..c2b36f6294 100644 --- a/src/Analysis_Hist.cpp +++ b/src/Analysis_Hist.cpp @@ -483,7 +483,7 @@ Analysis::RetType Analysis_Hist::Analyze() { mprinterr("Error: Could not write pseudo topology to '%s'\n", parmoutName_.c_str()); } Trajout_Single out; - if (out.PrepareTrajWrite(traj3dName_, ArgList(), &pseudo, CoordinateInfo(), + if (out.PrepareTrajWrite(traj3dName_, ArgList(), DataSetList(), &pseudo, CoordinateInfo(), Ndata, traj3dFmt_) == 0) { Frame outFrame(1); diff --git a/src/Analysis_Modes.cpp b/src/Analysis_Modes.cpp index 035e3d80c2..6c0e31f30e 100644 --- a/src/Analysis_Modes.cpp +++ b/src/Analysis_Modes.cpp @@ -155,7 +155,7 @@ Analysis::RetType Analysis_Modes::Setup(ArgList& analyzeArgs, AnalysisSetup& set return Analysis::ERR; } // Setup output traj - if (trajout_.InitTrajWrite( tOutName, ArgList(), tOutFmt ) != 0) { + if (trajout_.InitTrajWrite( tOutName, ArgList(), DataSetList(), tOutFmt ) != 0) { mprinterr("Error: Could not init output trajectory.\n"); return Analysis::ERR; } diff --git a/src/Analysis_Wavelet.cpp b/src/Analysis_Wavelet.cpp index d45e32bbd8..4c3507ab17 100644 --- a/src/Analysis_Wavelet.cpp +++ b/src/Analysis_Wavelet.cpp @@ -520,7 +520,7 @@ int Analysis_Wavelet::WAFEX(DataSet_MatrixFlt const& matrix) { // Set up trajectory file int nframes = CL->MaxCol() - CL->MinCol() + 1; Trajout_Single clusterout; - if (clusterout.PrepareTrajWrite(cfilename, ArgList(), regionTop, + if (clusterout.PrepareTrajWrite(cfilename, ArgList(), DataSetList(), regionTop, CoordinateInfo(), nframes, TrajectoryFile::PDBFILE)) return Analysis::ERR; // Setup frame for region @@ -564,6 +564,7 @@ int Analysis_Wavelet::WAFEX(DataSet_MatrixFlt const& matrix) { int nframes = (int)coords_->Size(); Trajout_Single overlay; if (overlay.PrepareTrajWrite(overlayName_, "title 'Wavelet trajectory'", + DataSetList(), maskTop, CoordinateInfo(), nframes, TrajectoryFile::UNKNOWN_TRAJ)) return Analysis::ERR; diff --git a/src/Box.h b/src/Box.h index d18f117232..abe351a51f 100644 --- a/src/Box.h +++ b/src/Box.h @@ -1,6 +1,7 @@ #ifndef INC_BOX_H #define INC_BOX_H #include "Matrix_3x3.h" +#include "Vec3.h" #ifdef MPI # include "Parallel.h" #endif diff --git a/src/CoordinateInfo.h b/src/CoordinateInfo.h index 7ca69c8183..eb489c112b 100644 --- a/src/CoordinateInfo.h +++ b/src/CoordinateInfo.h @@ -3,9 +3,6 @@ #include #include "ReplicaDimArray.h" #include "Box.h" -#ifdef MPI -# include "Parallel.h" -#endif /// All metadata associated with a Frame. class CoordinateInfo { public: diff --git a/src/Cpptraj.cpp b/src/Cpptraj.cpp index 122df21ac9..b7839bc2bb 100644 --- a/src/Cpptraj.cpp +++ b/src/Cpptraj.cpp @@ -14,6 +14,7 @@ #include "TopInfo.h" // ProcessMask #include "Timer.h" #include "StringRoutines.h" // TimeString +#include "TrajectoryFile.h" // for autodetect #ifdef CUDA # include #endif diff --git a/src/CpptrajState.cpp b/src/CpptrajState.cpp index a530609e67..bd040c45d8 100644 --- a/src/CpptrajState.cpp +++ b/src/CpptrajState.cpp @@ -3,6 +3,7 @@ #include "Action_CreateCrd.h" // in case default COORDS need to be created #include "DataSet_Coords_REF.h" // AddReference #include "DataSet_Topology.h" // AddTopology +#include "FrameArray.h" // RunEnsemble #include "ProgressBar.h" #ifdef MPI # include "Parallel.h" @@ -127,9 +128,9 @@ int CpptrajState::AddOutputTrajectory( ArgList& argIn ) { Topology* top = DSL_.GetTopology( argIn ); int err = 1; if (mode_ == NORMAL) - err = trajoutList_.AddTrajout( fname, argIn, top ); + err = trajoutList_.AddTrajout( fname, argIn, DSL_, top ); else if (mode_ == ENSEMBLE) - err = ensembleOut_.AddEnsembleOut( fname, argIn, top, trajinList_.EnsembleSize() ); + err = ensembleOut_.AddEnsembleOut( fname, argIn, DSL_, top, trajinList_.EnsembleSize() ); return err; } diff --git a/src/DataIO_VecTraj.cpp b/src/DataIO_VecTraj.cpp index fd9b2417ee..3d06bfedb8 100644 --- a/src/DataIO_VecTraj.cpp +++ b/src/DataIO_VecTraj.cpp @@ -84,7 +84,7 @@ int DataIO_VecTraj::WriteData(FileName const& fname, DataSetList const& SetList) } // Write out vectors Trajout_Single out; - if (out.PrepareTrajWrite(fname, ArgList(), &pseudo, CoordinateInfo(), + if (out.PrepareTrajWrite(fname, ArgList(), DataSetList(), &pseudo, CoordinateInfo(), vec_size, trajoutFmt_) == 0) { Frame outFrame(pseudo.Natom()); diff --git a/src/DataSetList.h b/src/DataSetList.h index 572088ebf8..e1569609fb 100644 --- a/src/DataSetList.h +++ b/src/DataSetList.h @@ -1,12 +1,13 @@ #ifndef INC_DATASETLIST_H #define INC_DATASETLIST_H #include -#include "DataSet.h" -#include "ArgList.h" // GetReferenceFrame, GetTopology #include "ReferenceFrame.h" // GetReferenceFrame #ifdef TIMER # include "Timer.h" #endif +// Forward declarations +class DataSet; +class ArgList; /// Hold list of DataSets. /** Main class for handling DataSets. All DataSet types can be allocated * by DataSetList. There is a master DataSetList in CpptrajState that will diff --git a/src/DataSet_Coords_REF.h b/src/DataSet_Coords_REF.h index f9cdf2f7e1..e392eb1778 100644 --- a/src/DataSet_Coords_REF.h +++ b/src/DataSet_Coords_REF.h @@ -1,7 +1,8 @@ #ifndef INC_DATASET_COORDS_REF_H #define INC_DATASET_COORDS_REF_H #include "DataSet_Coords.h" -#include "ArgList.h" +// Forward declarations +class ArgList; /// Store a single reference frame in double precision. class DataSet_Coords_REF : public DataSet_Coords { public: diff --git a/src/EnsembleIn.h b/src/EnsembleIn.h index 536392f5a0..7cca6da76a 100644 --- a/src/EnsembleIn.h +++ b/src/EnsembleIn.h @@ -1,15 +1,19 @@ #ifndef INC_ENSEMBLEIN_H #define INC_ENSEMBLEIN_H #include "InputTrajCommon.h" -#include "FrameArray.h" +// Not forward-declared because is just a typedef #include "FramePtrArray.h" #include "ReplicaInfo.h" +#include "Frame.h" // For RemdIdxType TODO put RemdIdxType in ReplicaInfo #ifdef MPI # include "Parallel.h" # ifdef TIMER # include "Timer.h" # endif #endif +// Forward declarations +class FrameArray; +class CoordinateInfo; /// Read in an array of frames at a time. class EnsembleIn { public: diff --git a/src/EnsembleIn_Multi.cpp b/src/EnsembleIn_Multi.cpp index 7c1dc13cb9..e0e4c9c4f1 100644 --- a/src/EnsembleIn_Multi.cpp +++ b/src/EnsembleIn_Multi.cpp @@ -1,4 +1,5 @@ #include "EnsembleIn_Multi.h" +#include "FrameArray.h" #include "CpptrajStdio.h" #include "DataFile.h" // TODO remove #include "StringRoutines.h" // integerToString TODO remove diff --git a/src/EnsembleIn_Single.cpp b/src/EnsembleIn_Single.cpp index cb73d6ef7d..08e3aa947d 100644 --- a/src/EnsembleIn_Single.cpp +++ b/src/EnsembleIn_Single.cpp @@ -1,5 +1,8 @@ #ifdef ENABLE_SINGLE_ENSEMBLE #include "EnsembleIn_Single.h" +#include "TrajectoryIO.h" +#include "Topology.h" +#include "FrameArray.h" #include "TrajectoryFile.h" #include "CpptrajStdio.h" diff --git a/src/EnsembleIn_Single.h b/src/EnsembleIn_Single.h index 6d9e53559c..f36e9fe8ed 100644 --- a/src/EnsembleIn_Single.h +++ b/src/EnsembleIn_Single.h @@ -2,7 +2,8 @@ #define INC_ENSEMBLEIN_SINGLE_H #ifdef ENABLE_SINGLE_ENSEMBLE #include "EnsembleIn.h" -#include "TrajectoryIO.h" +// Forward declarations +class TrajectoryIO; /// Read in an array of frames at a time from a single file. class EnsembleIn_Single : public EnsembleIn { public: diff --git a/src/EnsembleOut.h b/src/EnsembleOut.h index 9067237489..16edc7325f 100644 --- a/src/EnsembleOut.h +++ b/src/EnsembleOut.h @@ -1,6 +1,9 @@ #ifndef INC_ENSEMBLEOUT_H #define INC_ENSEMBLEOUT_H #include "OutputTrajCommon.h" +#include "FramePtrArray.h" +// Forward Declarations +class DataSetList; /// Write out an array of frames at a time. class EnsembleOut { public: @@ -9,7 +12,7 @@ class EnsembleOut { void SetDebug(int d) { debug_ = d; } // ----- Inherited Functions ----------------- /// Prepare ensemble for writing given format, no Topology setup. - virtual int InitEnsembleWrite(std::string const&, ArgList const&, + virtual int InitEnsembleWrite(std::string const&, ArgList const&, DataSetList const&, int, TrajectoryFile::TrajFormatType) = 0; /// Perform Topology-related setup for ensemble and open. TODO const& virtual int SetupEnsembleWrite(Topology*, CoordinateInfo const&, int) = 0; diff --git a/src/EnsembleOutList.cpp b/src/EnsembleOutList.cpp index 369b4cb13b..d3699b2c1f 100644 --- a/src/EnsembleOutList.cpp +++ b/src/EnsembleOutList.cpp @@ -1,8 +1,19 @@ #include "EnsembleOutList.h" +#include "Topology.h" #include "CpptrajStdio.h" #include "EnsembleOut_Single.h" #include "EnsembleOut_Multi.h" +/// CONSTRUCTOR +EnsembleOutList::EnsembleOutList() : debug_(0) {} + +/// DESTRUCTOR +EnsembleOutList::~EnsembleOutList() { Clear(); } + +/** Set the list debug level. Will apply to new output ensembles. */ +void EnsembleOutList::SetDebug(int d) { debug_ = d; } + +/** Clear the output ensemble list and free memory. */ void EnsembleOutList::Clear() { for (EnsArray::const_iterator ens = ensout_.begin(); ens != ensout_.end(); ++ens) delete *ens; @@ -14,6 +25,7 @@ void EnsembleOutList::Clear() { // TODO Pass in more ensemble information, maps etc? int EnsembleOutList::AddEnsembleOut(std::string const& fname, ArgList const& args, + DataSetList const& DSLin, Topology* eParm, int ensembleSize) { if (eParm == 0) { @@ -44,7 +56,7 @@ int EnsembleOutList::AddEnsembleOut(std::string const& fname, ArgList const& arg // Create new multi output trajectory ens = new EnsembleOut_Multi(); if (ens == 0) return 1; - if (ens->InitEnsembleWrite(fname, argIn, ensembleSize, TrajectoryFile::UNKNOWN_TRAJ)) { + if (ens->InitEnsembleWrite(fname, argIn, DSLin, ensembleSize, TrajectoryFile::UNKNOWN_TRAJ)) { delete ens; return 1; } diff --git a/src/EnsembleOutList.h b/src/EnsembleOutList.h index 3c50786934..dcafea62eb 100644 --- a/src/EnsembleOutList.h +++ b/src/EnsembleOutList.h @@ -1,15 +1,27 @@ #ifndef INC_ENSEMBLEOUTLIST_H #define INC_ENSEMBLEOUTLIST_H -#include "EnsembleOut.h" +#include +#include +// Not forward-declared since its only a typedef +#include "FramePtrArray.h" +#ifdef MPI +# include "Parallel.h" +#endif +// Forward declarations +class EnsembleOut; +class ArgList; +class DataSetList; +class Topology; +class CoordinateInfo; /// Hold output ensembles. class EnsembleOutList { public: - EnsembleOutList() : debug_(0) {} - ~EnsembleOutList() { Clear(); } - void SetDebug(int d) { debug_ = d; } + EnsembleOutList(); + ~EnsembleOutList(); + void SetDebug(int); void Clear(); /// Add output ensemble of given size to the list and associate with given Topology - int AddEnsembleOut(std::string const&, ArgList const&, Topology*, int); + int AddEnsembleOut(std::string const&, ArgList const&, DataSetList const&, Topology*, int); /// Set up ensembles for given topology. int SetupEnsembleOut(Topology*, CoordinateInfo const&, int); //TODO const Topology? /// Write array of Frames to ensemble diff --git a/src/EnsembleOut_Multi.cpp b/src/EnsembleOut_Multi.cpp index ec1089fa0f..8411305285 100644 --- a/src/EnsembleOut_Multi.cpp +++ b/src/EnsembleOut_Multi.cpp @@ -1,4 +1,6 @@ #include "EnsembleOut_Multi.h" +#include "TrajectoryIO.h" +#include "Topology.h" #include "CpptrajStdio.h" #include "StringRoutines.h" // AppendNumber #ifdef MPI @@ -25,7 +27,8 @@ void EnsembleOut_Multi::Clear() { * and process arguments. */ int EnsembleOut_Multi::InitEnsembleWrite(std::string const& tnameIn, - ArgList const& argIn, int ensembleSizeIn, + ArgList const& argIn, DataSetList const& DSLin, + int ensembleSizeIn, TrajectoryFile::TrajFormatType writeFormatIn) { // Require a base filename @@ -104,7 +107,7 @@ int EnsembleOut_Multi::InitEnsembleWrite(std::string const& tnameIn, // Process any write arguments specific to certain formats not related // to parm file. Options related to parm file are handled in SetupTrajWrite ArgList rep_args = trajout_args; - if (ioarray_.back()->processWriteArgs( rep_args )) { + if (ioarray_.back()->processWriteArgs( rep_args, DSLin )) { mprinterr("Error: trajout %s: Could not process arguments.\n",fileNames_[m].c_str()); return 1; } diff --git a/src/EnsembleOut_Multi.h b/src/EnsembleOut_Multi.h index a3caf12450..151fd93598 100644 --- a/src/EnsembleOut_Multi.h +++ b/src/EnsembleOut_Multi.h @@ -7,7 +7,7 @@ class EnsembleOut_Multi : public EnsembleOut { EnsembleOut_Multi(); ~EnsembleOut_Multi(); // ----- Inherited Functions ----------------- - int InitEnsembleWrite(std::string const&, ArgList const&, int, TrajectoryFile::TrajFormatType); + int InitEnsembleWrite(std::string const&, ArgList const&, DataSetList const&, int, TrajectoryFile::TrajFormatType); int SetupEnsembleWrite(Topology*, CoordinateInfo const&, int); void EndEnsemble(); int WriteEnsemble(int, FramePtrArray const&); diff --git a/src/EnsembleOut_Single.cpp b/src/EnsembleOut_Single.cpp index d601eb326e..f467fd97df 100644 --- a/src/EnsembleOut_Single.cpp +++ b/src/EnsembleOut_Single.cpp @@ -1,5 +1,7 @@ #ifdef ENABLE_SINGLE_ENSEMBLE #include "EnsembleOut_Single.h" +#include "TrajectoryIO.h" +#include "Topology.h" #include "CpptrajStdio.h" // CONSTRUCTOR @@ -13,7 +15,8 @@ EnsembleOut_Single::~EnsembleOut_Single() { // EnsembleOut_Single::InitEnsembleWrite() int EnsembleOut_Single::InitEnsembleWrite(std::string const& tnameIn, - ArgList const& argIn, int ensembleSizeIn, + ArgList const& argIn, DataSetList const& DSLin, + int ensembleSizeIn, TrajectoryFile::TrajFormatType writeFormatIn) { // Require a base filename @@ -60,7 +63,7 @@ int EnsembleOut_Single::InitEnsembleWrite(std::string const& tnameIn, eio_->SetTitle( Traj().Title() ); // Process any write arguments specific to certain formats not related // to parm file. Options related to parm file are handled in SetupTrajWrite - if (eio_->processWriteArgs(trajout_args)) { + if (eio_->processWriteArgs(trajout_args, DSLin)) { mprinterr("Error: trajout %s: Could not process arguments.\n",Traj().Filename().full()); return 1; } diff --git a/src/EnsembleOut_Single.h b/src/EnsembleOut_Single.h index e64de3308c..90be4146e3 100644 --- a/src/EnsembleOut_Single.h +++ b/src/EnsembleOut_Single.h @@ -8,7 +8,7 @@ class EnsembleOut_Single : public EnsembleOut { EnsembleOut_Single(); ~EnsembleOut_Single(); // ----- Inherited Functions ----------------- - int InitEnsembleWrite(std::string const&, ArgList const&, int, TrajectoryFile::TrajFormatType); + int InitEnsembleWrite(std::string const&, ArgList const&, DataSetList const&, int, TrajectoryFile::TrajFormatType); int SetupEnsembleWrite(Topology*, CoordinateInfo const&, int); void EndEnsemble(); int WriteEnsemble(int, FramePtrArray const&); diff --git a/src/Exec_CrdOut.cpp b/src/Exec_CrdOut.cpp index 965ec407c5..803bc8576f 100644 --- a/src/Exec_CrdOut.cpp +++ b/src/Exec_CrdOut.cpp @@ -1,4 +1,5 @@ #include "Exec_CrdOut.h" +#include "Trajout_Single.h" #include "CpptrajStdio.h" #include "ProgressBar.h" @@ -52,7 +53,7 @@ Exec::RetType Exec_CrdOut::WriteCrd(CpptrajState& State, ArgList& argIn) { if (frameCount.CheckFrameArgs( CRD->Size(), crdarg )) return CpptrajState::ERR; frameCount.PrintInfoLine( CRD->legend() ); Trajout_Single outtraj; - if (outtraj.PrepareTrajWrite( setname, argIn, CRD->TopPtr(), CRD->CoordsInfo(), + if (outtraj.PrepareTrajWrite( setname, argIn, State.DSL(), CRD->TopPtr(), CRD->CoordsInfo(), CRD->Size(), TrajectoryFile::UNKNOWN_TRAJ)) { mprinterr("Error: crdout: Could not set up output trajectory.\n"); diff --git a/src/Exec_Help.cpp b/src/Exec_Help.cpp index ee613aa861..e79674f3b4 100644 --- a/src/Exec_Help.cpp +++ b/src/Exec_Help.cpp @@ -2,6 +2,7 @@ #include "CpptrajStdio.h" #include "Command.h" #include "ParmFile.h" +#include "TrajectoryFile.h" void Exec_Help::Help() const { mprintf("\t[ { All |\n" diff --git a/src/Exec_PermuteDihedrals.cpp b/src/Exec_PermuteDihedrals.cpp index 55930efa92..5e1eeaf0d6 100644 --- a/src/Exec_PermuteDihedrals.cpp +++ b/src/Exec_PermuteDihedrals.cpp @@ -94,7 +94,7 @@ Exec::RetType Exec_PermuteDihedrals::Execute(CpptrajState& State, ArgList& argIn return CpptrajState::ERR; } // Setup output trajectory FIXME: Correct frames for # of rotations - if (outtraj_.PrepareTrajWrite(outfilename, argIn, CRD->TopPtr(), CRD->CoordsInfo(), + if (outtraj_.PrepareTrajWrite(outfilename, argIn, State.DSL(), CRD->TopPtr(), CRD->CoordsInfo(), CRD->Size(), TrajectoryFile::UNKNOWN_TRAJ)) return CpptrajState::ERR; } diff --git a/src/Exec_SequenceAlign.cpp b/src/Exec_SequenceAlign.cpp index 6e23d2dac0..f1580fdb05 100644 --- a/src/Exec_SequenceAlign.cpp +++ b/src/Exec_SequenceAlign.cpp @@ -229,7 +229,7 @@ Exec::RetType Exec_SequenceAlign::Execute(CpptrajState& State, ArgList& argIn) { //Frame sFrame(qref.Coord(), sMask); // Write output traj Trajout_Single trajout; - if (trajout.PrepareTrajWrite(outfilename, argIn, &sTop, CoordinateInfo(), 1, fmt)) + if (trajout.PrepareTrajWrite(outfilename, argIn, State.DSL(), &sTop, CoordinateInfo(), 1, fmt)) return CpptrajState::ERR; if (trajout.WriteSingle(0, sFrame)) return CpptrajState::ERR; trajout.EndTraj(); diff --git a/src/Exec_Traj.cpp b/src/Exec_Traj.cpp index 21f9153da7..e3459231a0 100644 --- a/src/Exec_Traj.cpp +++ b/src/Exec_Traj.cpp @@ -1,5 +1,6 @@ #include "Exec_Traj.h" #include "CpptrajStdio.h" +#include "ActionFrameCounter.h" void Exec_Trajin::Help() const { mprintf("\t {[] [ | last] []} | lastframe\n" diff --git a/src/FileTypes.cpp b/src/FileTypes.cpp index 710d4b0f19..1c63573f93 100644 --- a/src/FileTypes.cpp +++ b/src/FileTypes.cpp @@ -125,9 +125,11 @@ void FileTypes::Options(KeyPtr begin, AllocPtr allocArray, FileFormatType UNK, mprintf(" %s options for %s: %s\n", Ustr[otype],allocArray[i].Description, fmtstr.c_str()); switch (otype) { case READOPT: - if (allocArray[i].ReadHelp != 0) allocArray[i].ReadHelp(); break; + if (allocArray[i].ReadHelp != 0) allocArray[i].ReadHelp(); + break; case WRITEOPT: - if (allocArray[i].WriteHelp != 0) allocArray[i].WriteHelp(); break; + if (allocArray[i].WriteHelp != 0) allocArray[i].WriteHelp(); + break; } } } diff --git a/src/Frame.h b/src/Frame.h index 50f222a33e..c149057a5a 100644 --- a/src/Frame.h +++ b/src/Frame.h @@ -1,8 +1,11 @@ #ifndef INC_FRAME_H #define INC_FRAME_H -#include "Atom.h" +#include #include "AtomMask.h" +#include "Box.h" #include "CoordinateInfo.h" +// Forward declarations +class Atom; /// Hold coordinates, perform various operations/transformations on them. /** Intended to hold coordinates e.g. from a trajectory or reference frame, * along with box coordinates (used in imaging calculations), mass information, @@ -43,7 +46,7 @@ class Frame { Frame(int, double*); Frame(const Frame&); Frame& operator=(Frame); - typedef std::vector RemdIdxType; ///< For dealing with replica indices + typedef std::vector RemdIdxType; ///< For dealing with replica indices TODO put in ReplicaInfo typedef std::vector RemdValType; /// < For reading replica values // ------------------------------------------- /// This type interfaces with DataSet_Coords_CRD diff --git a/src/FramePtrArray.h b/src/FramePtrArray.h index 5a0205ff08..acf89f62e3 100644 --- a/src/FramePtrArray.h +++ b/src/FramePtrArray.h @@ -1,6 +1,7 @@ #ifndef INC_FRAMEPTRARRAY_H #define INC_FRAMEPTRARRAY_H -#include "Frame.h" +// Forward declares +class Frame; /// Store frame addresses in ensemble for sorting. typedef std::vector FramePtrArray; #endif diff --git a/src/InputTrajCommon.h b/src/InputTrajCommon.h index 69b778597a..cd059b1fe8 100644 --- a/src/InputTrajCommon.h +++ b/src/InputTrajCommon.h @@ -1,7 +1,9 @@ #ifndef INC_INPUTTRAJCOMMON_H #define INC_INPUTTRAJCOMMON_H -#include "Topology.h" #include "TrajFrameCounter.h" +#include "FileName.h" +// Forward declarations +class Topology; /// Input trajectory/ensemble common functionality. class InputTrajCommon { public: diff --git a/src/OutputTrajCommon.cpp b/src/OutputTrajCommon.cpp index dc6d14b6a4..9d6afe8f7b 100644 --- a/src/OutputTrajCommon.cpp +++ b/src/OutputTrajCommon.cpp @@ -1,4 +1,6 @@ #include "OutputTrajCommon.h" +#include "TrajectoryIO.h" +#include "Topology.h" #include "CpptrajStdio.h" #include "StringRoutines.h" // fileExists diff --git a/src/OutputTrajCommon.h b/src/OutputTrajCommon.h index 2195b05265..a1aaa84451 100644 --- a/src/OutputTrajCommon.h +++ b/src/OutputTrajCommon.h @@ -3,6 +3,9 @@ #include "TrajectoryFile.h" #include "Range.h" #include "ActionFrameCounter.h" +#include "CoordinateInfo.h" +// Forward declarations +class Topology; /// Output trajectory/ensemble common functionality. class OutputTrajCommon { public: diff --git a/src/ReferenceFrame.h b/src/ReferenceFrame.h index d2a6bf638a..63f69e418e 100644 --- a/src/ReferenceFrame.h +++ b/src/ReferenceFrame.h @@ -1,6 +1,7 @@ #ifndef INC_REFERENCEFRAME_H #define INC_REFERENCEFRAME_H #include "DataSet_Coords_REF.h" +// Forward declarations /// Wrapper around DataSet_Coords_REF DataSet. /** Intended as a non-modifiable holder for the DataSet_Coords_REF DataSet * that also can hold an error status. diff --git a/src/ReplicaInfo.h b/src/ReplicaInfo.h index bd970c645a..80b615f529 100644 --- a/src/ReplicaInfo.h +++ b/src/ReplicaInfo.h @@ -1,6 +1,7 @@ #ifndef INC_REPLICAINFO_H #define INC_REPLICAINFO_H #include +#include /// Hold types/classes/functions having to do with processing ensemble/replica data. namespace ReplicaInfo { // TODO just Replica /// Replica sort target type diff --git a/src/TrajFrameCounter.cpp b/src/TrajFrameCounter.cpp index 9f0aeff7a9..ad8c7d7e36 100644 --- a/src/TrajFrameCounter.cpp +++ b/src/TrajFrameCounter.cpp @@ -1,4 +1,5 @@ #include "TrajFrameCounter.h" +#include "ArgList.h" #include "CpptrajStdio.h" TrajFrameCounter::TrajFrameCounter() : diff --git a/src/TrajFrameCounter.h b/src/TrajFrameCounter.h index eb4533d0cb..32cee72124 100644 --- a/src/TrajFrameCounter.h +++ b/src/TrajFrameCounter.h @@ -1,6 +1,7 @@ #ifndef INC_TRAJFRAMECOUNTER_H #define INC_TRAJFRAMECOUNTER_H -#include "ArgList.h" +// Forward declarations +class ArgList; /// Used to keep track of frame # during traj read. class TrajFrameCounter { public: diff --git a/src/TrajIOarray.cpp b/src/TrajIOarray.cpp index 5566e25ecf..ffb079d208 100644 --- a/src/TrajIOarray.cpp +++ b/src/TrajIOarray.cpp @@ -1,4 +1,5 @@ #include "TrajIOarray.h" +#include "Topology.h" #include "StringRoutines.h" // integerToString, validInteger #include "CpptrajStdio.h" #include "TrajectoryFile.h" diff --git a/src/TrajIOarray.h b/src/TrajIOarray.h index 99fd59d1fa..02265c8128 100644 --- a/src/TrajIOarray.h +++ b/src/TrajIOarray.h @@ -2,6 +2,7 @@ #define INC_TRAJIOARRAY_H #include "TrajectoryIO.h" #include "TrajFrameCounter.h" +#include "FileName.h" /// Hold an array of TrajectoryIO classes. class TrajIOarray { public: diff --git a/src/Traj_AmberCoord.cpp b/src/Traj_AmberCoord.cpp index dda9fbb58d..dc0082efeb 100644 --- a/src/Traj_AmberCoord.cpp +++ b/src/Traj_AmberCoord.cpp @@ -1,6 +1,9 @@ // Traj_AmberCoord #include // sscanf #include "Traj_AmberCoord.h" +#include "Frame.h" +#include "Topology.h" +#include "ArgList.h" #include "CpptrajStdio.h" /// Size of REMD header @@ -326,7 +329,7 @@ void Traj_AmberCoord::WriteHelp() { } // Traj_AmberCoord::processWriteArgs() -int Traj_AmberCoord::processWriteArgs(ArgList& argIn) { +int Traj_AmberCoord::processWriteArgs(ArgList& argIn, DataSetList const& DSLin) { outputTemp_ = argIn.hasKey("remdtraj"); if (argIn.hasKey("highprecision")) { outfmt_ = "%8.6f"; diff --git a/src/Traj_AmberCoord.h b/src/Traj_AmberCoord.h index d59ede35f9..8ca64e4496 100644 --- a/src/Traj_AmberCoord.h +++ b/src/Traj_AmberCoord.h @@ -19,7 +19,7 @@ class Traj_AmberCoord: public TrajectoryIO { int readFrame(int,Frame&); int writeFrame(int,Frame const&); void Info(); - int processWriteArgs(ArgList&); + int processWriteArgs(ArgList&, DataSetList const&); int readVelocity(int, Frame&); int readForce(int, Frame&); int processReadArgs(ArgList&) { return 0; } diff --git a/src/Traj_AmberNetcdf.cpp b/src/Traj_AmberNetcdf.cpp index 1afda77f6c..9f65b1b384 100644 --- a/src/Traj_AmberNetcdf.cpp +++ b/src/Traj_AmberNetcdf.cpp @@ -3,8 +3,12 @@ // netcdf trajectory files used with amber. // Dan Roe 10-2008 // Original implementation of netcdf in Amber by John Mongan. -#include "Traj_AmberNetcdf.h" #include +#include "Traj_AmberNetcdf.h" +#include "CpptrajFile.h" +#include "ArgList.h" +#include "Topology.h" +#include "Frame.h" #include "CpptrajStdio.h" #include "NC_Routines.h" #ifdef MPI @@ -97,7 +101,7 @@ void Traj_AmberNetcdf::WriteHelp() { } // Traj_AmberNetcdf::processWriteArgs() -int Traj_AmberNetcdf::processWriteArgs(ArgList& argIn) { +int Traj_AmberNetcdf::processWriteArgs(ArgList& argIn, DataSetList const& DSLin) { outputTemp_ = argIn.hasKey("remdtraj"); write_mdcrd_ = argIn.hasKey("mdcrd"); if (argIn.hasKey("velocity")) diff --git a/src/Traj_AmberNetcdf.h b/src/Traj_AmberNetcdf.h index 1e2cfc38b4..cf586072c1 100644 --- a/src/Traj_AmberNetcdf.h +++ b/src/Traj_AmberNetcdf.h @@ -3,6 +3,7 @@ #ifdef BINTRAJ #include "TrajectoryIO.h" #include "NetcdfFile.h" +#include "FileName.h" /// Reads and writes Amber Netcdf format trajectories. class Traj_AmberNetcdf : public TrajectoryIO, private NetcdfFile { public: @@ -22,7 +23,7 @@ class Traj_AmberNetcdf : public TrajectoryIO, private NetcdfFile { int readForce(int, Frame&); int writeFrame(int,Frame const&); void Info(); - int processWriteArgs(ArgList&); + int processWriteArgs(ArgList&, DataSetList const&); int processReadArgs(ArgList&); # ifdef MPI // Parallel functions diff --git a/src/Traj_AmberRestart.cpp b/src/Traj_AmberRestart.cpp index b914b38cbf..db13815d51 100644 --- a/src/Traj_AmberRestart.cpp +++ b/src/Traj_AmberRestart.cpp @@ -1,6 +1,10 @@ // Traj_AmberRestart #include // sscanf #include "Traj_AmberRestart.h" +#include "Topology.h" +#include "ArgList.h" +#include "Frame.h" +#include "CpptrajFile.h" #include "CpptrajStdio.h" #include "StringRoutines.h" // NoTrailingWhitespace @@ -63,7 +67,7 @@ void Traj_AmberRestart::WriteHelp() { } // Traj_AmberRestart::processWriteArgs() -int Traj_AmberRestart::processWriteArgs(ArgList& argIn) { +int Traj_AmberRestart::processWriteArgs(ArgList& argIn, DataSetList const& DSLin) { outputTemp_ = argIn.hasKey("remdtraj"); time0_ = argIn.getKeyDouble("time0", -1.0); dt_ = argIn.getKeyDouble("dt",1.0); diff --git a/src/Traj_AmberRestart.h b/src/Traj_AmberRestart.h index 84369cd06b..9236a750cc 100644 --- a/src/Traj_AmberRestart.h +++ b/src/Traj_AmberRestart.h @@ -23,7 +23,7 @@ class Traj_AmberRestart : public TrajectoryIO { int readVelocity(int, Frame&); int readForce(int, Frame&) { return 1; } int writeFrame(int,Frame const&); - int processWriteArgs(ArgList&); + int processWriteArgs(ArgList&, DataSetList const&); void Info(); # ifdef MPI // Parallel functions diff --git a/src/Traj_AmberRestartNC.cpp b/src/Traj_AmberRestartNC.cpp index 0613062f44..5fc3c6b6be 100644 --- a/src/Traj_AmberRestartNC.cpp +++ b/src/Traj_AmberRestartNC.cpp @@ -2,8 +2,12 @@ // This file contains a collection of routines designed for reading // (and writing?) netcdf restart files used with amber. // Dan Roe 2011-01-07 -#include "Traj_AmberRestartNC.h" #include +#include "Traj_AmberRestartNC.h" +#include "Topology.h" +#include "ArgList.h" +#include "Frame.h" +#include "CpptrajFile.h" #include "NC_Routines.h" #include "CpptrajStdio.h" #include "StringRoutines.h" // integerToString @@ -88,7 +92,7 @@ void Traj_AmberRestartNC::WriteHelp() { } // Traj_AmberRestartNC::processWriteArgs() -int Traj_AmberRestartNC::processWriteArgs(ArgList& argIn) { +int Traj_AmberRestartNC::processWriteArgs(ArgList& argIn, DataSetList const& DSLin) { outputTemp_ = argIn.hasKey("remdtraj"); prependExt_ = argIn.hasKey("keepext"); time0_ = argIn.getKeyDouble("time0", -1.0); diff --git a/src/Traj_AmberRestartNC.h b/src/Traj_AmberRestartNC.h index 000aaa7aa6..2916f597aa 100644 --- a/src/Traj_AmberRestartNC.h +++ b/src/Traj_AmberRestartNC.h @@ -3,6 +3,7 @@ #ifdef BINTRAJ #include "TrajectoryIO.h" #include "NetcdfFile.h" +#include "FileName.h" // Class: Traj_AmberRestartNC /// TrajectoryIO class for reading and writing Amber Netcdf Restarts class Traj_AmberRestartNC : public TrajectoryIO, private NetcdfFile { @@ -22,7 +23,7 @@ class Traj_AmberRestartNC : public TrajectoryIO, private NetcdfFile { int readVelocity(int, Frame&); int readForce(int, Frame&); int writeFrame(int,Frame const&); - int processWriteArgs(ArgList&); + int processWriteArgs(ArgList&, DataSetList const&); int processReadArgs(ArgList&); void Info(); # ifdef MPI diff --git a/src/Traj_Binpos.cpp b/src/Traj_Binpos.cpp index 1ec4ad4e5f..89a2249535 100644 --- a/src/Traj_Binpos.cpp +++ b/src/Traj_Binpos.cpp @@ -1,4 +1,6 @@ #include "Traj_Binpos.h" +#include "Topology.h" +#include "Frame.h" #include "CpptrajStdio.h" // CONSTRUCTOR diff --git a/src/Traj_Binpos.h b/src/Traj_Binpos.h index 11b3317167..ce21d5a6f0 100644 --- a/src/Traj_Binpos.h +++ b/src/Traj_Binpos.h @@ -1,7 +1,7 @@ #ifndef INC_TRAJ_BINPOS #define INC_TRAJ_BINPOS #include "TrajectoryIO.h" -// Class: Traj_Binpos +#include "CpptrajFile.h" /// Read and write SCRIPPS BINPOS format class Traj_Binpos : public TrajectoryIO { public: @@ -18,7 +18,7 @@ class Traj_Binpos : public TrajectoryIO { int readFrame(int,Frame&); int writeFrame(int,Frame const&); void Info(); - int processWriteArgs(ArgList&) { return 0; } + int processWriteArgs(ArgList&, DataSetList const&) { return 0; } int bpnatom_; int bpnatom3_; diff --git a/src/Traj_CIF.cpp b/src/Traj_CIF.cpp index 5f4a242582..f3035358d1 100644 --- a/src/Traj_CIF.cpp +++ b/src/Traj_CIF.cpp @@ -1,5 +1,7 @@ // Traj_CIF #include "Traj_CIF.h" +#include "Topology.h" +#include "Frame.h" #include "CpptrajStdio.h" #include "StringRoutines.h" // convertToInteger, convertToDouble diff --git a/src/Traj_CIF.h b/src/Traj_CIF.h index 34c21ecdbb..d078342530 100644 --- a/src/Traj_CIF.h +++ b/src/Traj_CIF.h @@ -17,7 +17,7 @@ class Traj_CIF : public TrajectoryIO { int readFrame(int,Frame&); void Info(); void closeTraj() {} - int processWriteArgs(ArgList&) { return 0; } + int processWriteArgs(ArgList&, DataSetList const&) { return 0; } int readVelocity(int, Frame&) { return 1; } int readForce(int, Frame&) { return 1; } int processReadArgs(ArgList&) { return 0; } diff --git a/src/Traj_CharmmCor.cpp b/src/Traj_CharmmCor.cpp index c714a0f108..c378d90a0b 100644 --- a/src/Traj_CharmmCor.cpp +++ b/src/Traj_CharmmCor.cpp @@ -1,5 +1,9 @@ #include // sscanf #include "Traj_CharmmCor.h" +#include "Topology.h" +#include "ArgList.h" +#include "Frame.h" +#include "CpptrajFile.h" #include "StringRoutines.h" #include "CpptrajStdio.h" diff --git a/src/Traj_CharmmCor.h b/src/Traj_CharmmCor.h index 7b45146772..bb8d936d5c 100644 --- a/src/Traj_CharmmCor.h +++ b/src/Traj_CharmmCor.h @@ -18,7 +18,7 @@ class Traj_CharmmCor : public TrajectoryIO { int setupTrajout(FileName const&, Topology*, CoordinateInfo const&,int, bool); int writeFrame(int,Frame const&); void Info(); - int processWriteArgs(ArgList&) { return 0; } + int processWriteArgs(ArgList&, DataSetList const&) { return 0; } int readVelocity(int, Frame&) { return 1; } int readForce(int, Frame&) { return 1; } int processReadArgs(ArgList&) { return 0; } diff --git a/src/Traj_CharmmDcd.cpp b/src/Traj_CharmmDcd.cpp index 72dbb2c4a0..7a608ef72a 100644 --- a/src/Traj_CharmmDcd.cpp +++ b/src/Traj_CharmmDcd.cpp @@ -2,6 +2,9 @@ #include // for cos, acos #include // memset #include "Traj_CharmmDcd.h" +#include "Topology.h" +#include "ArgList.h" +#include "Frame.h" #include "Constants.h" #include "CpptrajStdio.h" #include "ByteRoutines.h" @@ -615,7 +618,7 @@ void Traj_CharmmDcd::WriteHelp() { } // Traj_CharmmDcd::processWriteArgs() -int Traj_CharmmDcd::processWriteArgs(ArgList& argIn) { +int Traj_CharmmDcd::processWriteArgs(ArgList& argIn, DataSetList const& DSLin) { // Default is to write 32 bit is64bit_ = argIn.hasKey("x64"); if (is64bit_) diff --git a/src/Traj_CharmmDcd.h b/src/Traj_CharmmDcd.h index a9cdab4ef2..9bc46c587e 100644 --- a/src/Traj_CharmmDcd.h +++ b/src/Traj_CharmmDcd.h @@ -1,7 +1,7 @@ #ifndef INC_TRAJ_CHARMMDCD_H #define INC_TRAJ_CHARMMDCD_H #include "TrajectoryIO.h" -// Class: Traj_CharmmDcd +#include "CpptrajFile.h" /// TrajectoryIO class for reading coordinates from charmm dcd files. class Traj_CharmmDcd : public TrajectoryIO { public : @@ -55,7 +55,7 @@ class Traj_CharmmDcd : public TrajectoryIO { int writeFrame(int,Frame const&); void Info(); int processReadArgs(ArgList&); - int processWriteArgs(ArgList&); + int processWriteArgs(ArgList&, DataSetList const&); int readForce(int, Frame&) { return 1; } # ifdef MPI diff --git a/src/Traj_CharmmRestart.cpp b/src/Traj_CharmmRestart.cpp index d77c44bb9d..a14ad9a3f2 100644 --- a/src/Traj_CharmmRestart.cpp +++ b/src/Traj_CharmmRestart.cpp @@ -1,6 +1,9 @@ #include // sscanf #include // atof #include "Traj_CharmmRestart.h" +#include "Topology.h" +#include "Frame.h" +#include "CpptrajFile.h" #include "CpptrajStdio.h" #include "StringRoutines.h" #include "BufferedLine.h" @@ -237,7 +240,7 @@ void Traj_CharmmRestart::WriteHelp() { } /** Process write arguments. */ -int Traj_CharmmRestart::processWriteArgs(ArgList& argIn) { +int Traj_CharmmRestart::processWriteArgs(ArgList& argIn, DataSetList const&) { return 0; } diff --git a/src/Traj_CharmmRestart.h b/src/Traj_CharmmRestart.h index b827bc43b4..64e4853e6e 100644 --- a/src/Traj_CharmmRestart.h +++ b/src/Traj_CharmmRestart.h @@ -21,7 +21,7 @@ class Traj_CharmmRestart : public TrajectoryIO { void Info(); int readVelocity(int, Frame&); int readForce(int, Frame&); - int processWriteArgs(ArgList&); + int processWriteArgs(ArgList&, DataSetList const&); int processReadArgs(ArgList&); // ------------------------------------------- # ifdef MPI diff --git a/src/Traj_Conflib.cpp b/src/Traj_Conflib.cpp index d75d800eb9..265de28d25 100644 --- a/src/Traj_Conflib.cpp +++ b/src/Traj_Conflib.cpp @@ -1,5 +1,7 @@ // Traj_Conflib #include "Traj_Conflib.h" +#include "Topology.h" +#include "Frame.h" #include "CpptrajStdio.h" // CONSTRUCTOR diff --git a/src/Traj_Conflib.h b/src/Traj_Conflib.h index c021b61281..659cbd1d77 100644 --- a/src/Traj_Conflib.h +++ b/src/Traj_Conflib.h @@ -1,7 +1,7 @@ #ifndef INC_TRAJ_CONFLIB_H #define INC_TRAJ_CONFLIB_H #include "TrajectoryIO.h" -// Class: Traj_Conflib +#include "CpptrajFile.h" /// Test TrajectoryIO object for reading conflib file generated by NAB LMOD class Traj_Conflib: public TrajectoryIO { public: @@ -25,7 +25,7 @@ class Traj_Conflib: public TrajectoryIO { void Info(); int readVelocity(int, Frame&) { return 1; } int readForce(int, Frame&) { return 1; } - int processWriteArgs(ArgList&){ return 0; } + int processWriteArgs(ArgList&, DataSetList const&){ return 0; } int processReadArgs(ArgList&) { return 0; } }; #endif diff --git a/src/Traj_GmxTrX.cpp b/src/Traj_GmxTrX.cpp index 301625bbfe..1ebe73233b 100644 --- a/src/Traj_GmxTrX.cpp +++ b/src/Traj_GmxTrX.cpp @@ -1,5 +1,8 @@ #include #include "Traj_GmxTrX.h" +#include "Topology.h" +#include "ArgList.h" +#include "Frame.h" #include "CpptrajStdio.h" #include "ByteRoutines.h" #include "Constants.h" // PIOVER2 @@ -402,7 +405,7 @@ void Traj_GmxTrX::WriteHelp() { } // Traj_GmxTrX::processWriteArgs() -int Traj_GmxTrX::processWriteArgs(ArgList& argIn) { +int Traj_GmxTrX::processWriteArgs(ArgList& argIn, DataSetList const& DSLin) { dt_ = argIn.getKeyDouble( "dt", 1.0 ); isBigEndian_ = true; if (!IsBigEndian()) swapBytes_ = true; diff --git a/src/Traj_GmxTrX.h b/src/Traj_GmxTrX.h index 58abd77fe5..2dcc2a7994 100644 --- a/src/Traj_GmxTrX.h +++ b/src/Traj_GmxTrX.h @@ -1,6 +1,7 @@ #ifndef INC_TRAJ_GMXTRR_H #define INC_TRAJ_GMXTRR_H #include "TrajectoryIO.h" +#include "CpptrajFile.h" /// Read/write Gromacs TRR/TRJ trajectories class Traj_GmxTrX : public TrajectoryIO { public: @@ -24,7 +25,7 @@ class Traj_GmxTrX : public TrajectoryIO { void Info(); int readVelocity(int, Frame&); int readForce(int, Frame&); - int processWriteArgs(ArgList&); + int processWriteArgs(ArgList&, DataSetList const&); int processReadArgs(ArgList&) { return 0; } # ifdef MPI // Parallel functions diff --git a/src/Traj_GmxXtc.cpp b/src/Traj_GmxXtc.cpp index e865324372..40f21f01a0 100644 --- a/src/Traj_GmxXtc.cpp +++ b/src/Traj_GmxXtc.cpp @@ -1,5 +1,9 @@ #include "Traj_GmxXtc.h" #ifndef NO_XDRFILE +#include "Topology.h" +#include "ArgList.h" +#include "Frame.h" +#include "CpptrajFile.h" #include "CpptrajStdio.h" #include "Constants.h" #include // SEEK_SET, SEEK_CUR @@ -162,7 +166,7 @@ void Traj_GmxXtc::WriteHelp() { } // Traj_GmxXtc::processWriteArgs() -int Traj_GmxXtc::processWriteArgs(ArgList& argIn) { +int Traj_GmxXtc::processWriteArgs(ArgList& argIn, DataSetList const& DSLin) { dt_ = argIn.getKeyDouble( "dt", 1.0 ); return 0; } diff --git a/src/Traj_GmxXtc.h b/src/Traj_GmxXtc.h index 760176005f..2e1cc4f06e 100644 --- a/src/Traj_GmxXtc.h +++ b/src/Traj_GmxXtc.h @@ -3,6 +3,7 @@ #include "TrajectoryIO.h" #ifndef NO_XDRFILE # include +# include "FileName.h" #endif /// Read/write Gromacs XTC trajectories class Traj_GmxXtc : public TrajectoryIO { @@ -23,7 +24,7 @@ class Traj_GmxXtc : public TrajectoryIO { void Info(); int readVelocity(int, Frame&); int readForce(int, Frame&); - int processWriteArgs(ArgList&); + int processWriteArgs(ArgList&, DataSetList const&); int processReadArgs(ArgList&) { return 0; } # ifdef MPI // Parallel functions diff --git a/src/Traj_Gro.cpp b/src/Traj_Gro.cpp index be0589671d..03bc13b27b 100644 --- a/src/Traj_Gro.cpp +++ b/src/Traj_Gro.cpp @@ -1,6 +1,9 @@ #include #include #include "Traj_Gro.h" +#include "Topology.h" +#include "Frame.h" +#include "CpptrajFile.h" #include "StringRoutines.h" #include "CpptrajStdio.h" #include "Constants.h" diff --git a/src/Traj_Gro.h b/src/Traj_Gro.h index fcecd532ce..e1f467e527 100644 --- a/src/Traj_Gro.h +++ b/src/Traj_Gro.h @@ -17,7 +17,7 @@ class Traj_Gro : public TrajectoryIO { int readFrame(int,Frame&); int writeFrame(int,Frame const&) { return 1; } void Info(); - int processWriteArgs(ArgList&) { return 0; } + int processWriteArgs(ArgList&, DataSetList const&) { return 0; } int readVelocity(int, Frame&) { return 1; } int readForce(int, Frame&) { return 1; } int processReadArgs(ArgList&) { return 0; } diff --git a/src/Traj_Mol2File.cpp b/src/Traj_Mol2File.cpp index 3212e1bb52..6c5a17bde1 100644 --- a/src/Traj_Mol2File.cpp +++ b/src/Traj_Mol2File.cpp @@ -1,5 +1,8 @@ #include // getenv #include "Traj_Mol2File.h" +#include "Topology.h" +#include "ArgList.h" +#include "Frame.h" #include "CpptrajStdio.h" // CONSTRUCTOR @@ -98,7 +101,7 @@ void Traj_Mol2File::WriteHelp() { } // Traj_Mol2File::processWriteArgs() -int Traj_Mol2File::processWriteArgs(ArgList& argIn) { +int Traj_Mol2File::processWriteArgs(ArgList& argIn, DataSetList const& DSLin) { mol2WriteMode_ = SINGLE; // Default to single writes if (argIn.hasKey("single")) mol2WriteMode_ = MOL; if (argIn.hasKey("multi")) mol2WriteMode_ = MULTI; diff --git a/src/Traj_Mol2File.h b/src/Traj_Mol2File.h index c8836d11b2..1390bc2152 100644 --- a/src/Traj_Mol2File.h +++ b/src/Traj_Mol2File.h @@ -26,7 +26,7 @@ class Traj_Mol2File : public TrajectoryIO { int readFrame(int,Frame&); int writeFrame(int,Frame const&); void Info(); - int processWriteArgs(ArgList&); + int processWriteArgs(ArgList&, DataSetList const&); int readVelocity(int, Frame&) { return 1; } int readForce(int, Frame&) { return 1; } int processReadArgs(ArgList&) { return 0; } diff --git a/src/Traj_NcEnsemble.cpp b/src/Traj_NcEnsemble.cpp index 9731c39720..b8a1db317a 100644 --- a/src/Traj_NcEnsemble.cpp +++ b/src/Traj_NcEnsemble.cpp @@ -1,8 +1,13 @@ #ifdef BINTRAJ #ifdef ENABLE_SINGLE_ENSEMBLE #include "Traj_NcEnsemble.h" +#include "Topology.h" +#include "ArgList.h" +#include "Frame.h" +#include "CpptrajFile.h" #include "CpptrajStdio.h" #include "NC_Routines.h" +#include "FrameArray.h" #ifdef MPI # include "Parallel.h" #endif @@ -37,7 +42,7 @@ void Traj_NcEnsemble::ReadHelp() { } // Traj_NcEnsemble::processWriteArgs() -int Traj_NcEnsemble::processWriteArgs(ArgList& argIn) { +int Traj_NcEnsemble::processWriteArgs(ArgList& argIn, DataSetList const&) { //SetTemperature(argIn.hasKey("remdtraj")); //SetVelocity(argIn.hasKey("velocity")); return 0; diff --git a/src/Traj_NcEnsemble.h b/src/Traj_NcEnsemble.h index db41a6eab5..f2c8b758f0 100644 --- a/src/Traj_NcEnsemble.h +++ b/src/Traj_NcEnsemble.h @@ -4,6 +4,7 @@ #ifdef ENABLE_SINGLE_ENSEMBLE #include "TrajectoryIO.h" #include "NetcdfFile.h" +#include "FileName.h" /// Read/write single NetCDF ensemble trajectory. class Traj_NcEnsemble : public TrajectoryIO, private NetcdfFile { public: @@ -23,7 +24,7 @@ class Traj_NcEnsemble : public TrajectoryIO, private NetcdfFile { int readForce(int, Frame&) { return 1; } //FIXME implement int writeFrame(int,Frame const&); void Info(); - int processWriteArgs(ArgList&); + int processWriteArgs(ArgList&, DataSetList const&); int processReadArgs(ArgList&); bool CanProcessEnsemble() { return true; } int readArray(int, FrameArray&); diff --git a/src/Traj_PDBfile.cpp b/src/Traj_PDBfile.cpp index 2a1023eeea..93bb8609a1 100644 --- a/src/Traj_PDBfile.cpp +++ b/src/Traj_PDBfile.cpp @@ -1,6 +1,12 @@ #include "Traj_PDBfile.h" +#include // min, max +#include "Topology.h" +#include "ArgList.h" +#include "DataSetList.h" #include "CpptrajStdio.h" #include "DistRoutines.h" +#include "Constants.h" +#include "DataSet_1D.h" // for bfacdata, occdata // CONSTRUCTOR Traj_PDBfile::Traj_PDBfile() : @@ -18,8 +24,16 @@ Traj_PDBfile::Traj_PDBfile() : include_ep_(false), prependExt_(false), firstframe_(false), + bfacscale_(false), + occscale_(false), + bfacbyres_(false), + occbyres_(false), pdbTop_(0), - chainchar_(' ') + chainchar_(' '), + bfacdata_(0), + occdata_(0), + bfacmax_(99.99), + occmax_(99.99) {} //------------------------------------------------------------------------ @@ -164,29 +178,37 @@ int Traj_PDBfile::readFrame(int set, Frame& frameIn) } void Traj_PDBfile::WriteHelp() { - mprintf("\tdumpq : Write atom charge/GB radius in occupancy/B-factor columns (PQR format).\n" - "\tparse : Write atom charge/PARSE radius in occupancy/B-factor columns (PQR format).\n" - "\tvdw : Write atom charge/VDW radius in occupancy/B-factor columns (PQR format).\n" - "\tpdbres : Use PDB V3 residue names.\n" - "\tpdbatom : Use PDB V3 atom names.\n" - "\tpdbv3 : Use PDB V3 residue/atom names.\n" - "\tteradvance : Increment record (atom) # for TER records (default no).\n" - "\tterbyres : Print TER cards based on residue sequence instead of molecules.\n" - "\tpdbter : Print TER cards according to original PDB TER (if available).\n" - "\tnoter : Do not write TER cards.\n" - "\tmodel : Write to single file separated by MODEL records.\n" - "\tmulti : Write each frame to separate files.\n" - "\tchainid : Write character 'c' in chain ID column.\n" - "\tsg : Space group for CRYST1 record, only if box coordinates written.\n" - "\tinclude_ep : Include extra points.\n" - "\tconect : Write CONECT records using bond information.\n" - "\tkeepext : Keep filename extension; write '..' instead (implies 'multi').\n" - "\tusecol21 : Use column 21 for 4-letter residue names.\n" + mprintf("\tdumpq : Write atom charge/GB radius in occupancy/B-factor columns (PQR format).\n" + "\tparse : Write atom charge/PARSE radius in occupancy/B-factor columns (PQR format).\n" + "\tvdw : Write atom charge/VDW radius in occupancy/B-factor columns (PQR format).\n" + "\tpdbres : Use PDB V3 residue names.\n" + "\tpdbatom : Use PDB V3 atom names.\n" + "\tpdbv3 : Use PDB V3 residue/atom names.\n" + "\tteradvance : Increment record (atom) # for TER records (default no).\n" + "\tterbyres : Print TER cards based on residue sequence instead of molecules.\n" + "\tpdbter : Print TER cards according to original PDB TER (if available).\n" + "\tnoter : Do not write TER cards.\n" + "\tmodel : Write to single file separated by MODEL records.\n" + "\tmulti : Write each frame to separate files.\n" + "\tchainid : Write character 'c' in chain ID column.\n" + "\tsg : Space group for CRYST1 record, only if box coordinates written.\n" + "\tinclude_ep : Include extra points.\n" + "\tconect : Write CONECT records using bond information.\n" + "\tkeepext : Keep filename extension; write '..' instead (implies 'multi').\n" + "\tusecol21 : Use column 21 for 4-letter residue names.\n" + "\tbfacdata : Use data in for B-factor column.\n" + "\toccdata : Use data in for occupancy column.\n" + "\tbfacbyres : If specified assume X values in B-factor data set are residue numbers.\n" + "\toccbyres : If specified assume X values in occupancy data set are residue numbers.\n" + "\tbfacscale : If specified scale values in B-factor column between 0 and .\n" + "\toccscale : If specified scale values in occupancy column between 0 and .\n" + "\tbfacmax : Max value for bfacscale.\n" + "\toccmax : Max value for occscale.\n" ); } // Traj_PDBfile::processWriteArgs() -int Traj_PDBfile::processWriteArgs(ArgList& argIn) { +int Traj_PDBfile::processWriteArgs(ArgList& argIn, DataSetList const& DSLin) { pdbWriteMode_ = SINGLE; if (argIn.hasKey("dumpq")) { dumpq_ = true; @@ -228,6 +250,115 @@ int Traj_PDBfile::processWriteArgs(ArgList& argIn) { if (!temp.empty()) chainchar_ = temp[0]; if (argIn.hasKey("usecol21")) file_.SetUseCol21( true ); + // Check for data sets + temp = argIn.GetStringKey("bfacdata"); + if (!temp.empty()) { + bfacdata_ = DSLin.GetDataSet( temp ); + if (bfacdata_ == 0) { + mprinterr("Error: No data set selected for 'bfacdata %s'\n", temp.c_str()); + return 1; + } + if (bfacdata_->Group() != DataSet::SCALAR_1D) { + mprinterr("Error: Only scalar 1D data can be used for 'bfacdata'\n"); + return 1; + } + if (dumpq_) + mprintf("Warning: Both a PQR option and 'bfacdata' specified. B-factor column will contain '%s'\n", bfacdata_->legend()); + bfacbyres_ = argIn.hasKey("bfacbyres"); + } + temp = argIn.GetStringKey("occdata"); + if (!temp.empty()) { + occdata_ = DSLin.GetDataSet( temp ); + if (occdata_ == 0) { + mprinterr("Error: No data set selected for 'occdata %s'\n", temp.c_str()); + return 1; + } + if (occdata_->Group() != DataSet::SCALAR_1D) { + mprinterr("Error: Only scalar 1D data can be used for 'occdata'\n"); + return 1; + } + if (dumpq_) + mprintf("Warning: Both a PQR option and 'occdata' specified. Occupancy column will contain '%s'\n", occdata_->legend()); + occbyres_ = argIn.hasKey("occbyres"); + } + bfacscale_ = argIn.hasKey("bfacscale"); + if (bfacscale_) bfacmax_ = argIn.getKeyDouble("bfacmax", 99.99); + occscale_ = argIn.hasKey("occscale"); + if (occscale_) occmax_ = argIn.getKeyDouble("occmax", 99.99); + + return 0; +} + +/// \return true if two double-precision numbers are equivalent with tolerance. +static inline bool Eqv(double d0, double d1) { + double diff = (d1 - d0); + if (diff < 0.0) diff = -diff; + return (diff < Constants::SMALL); +} + +/** Scale data in given set so that it falls within minVal and maxVal. */ +void Traj_PDBfile::ScaleData(Darray& DataOut, double minVal, double maxVal) +const +{ + if (DataOut.empty()) return; + double rangeSize = maxVal - minVal; + // Get original min and max val + double min = DataOut.front(); + double max = DataOut.front(); + for (Darray::const_iterator it = DataOut.begin(); it != DataOut.end(); ++it) { + min = std::min(min, *it); + max = std::max(max, *it); + } + double fac = 1 / (max - min); + // Scale values + for (Darray::iterator it = DataOut.begin(); it != DataOut.end(); ++it) { + double dval = (*it - min) * fac; + *it = (dval * rangeSize) + minVal; + } +} + +/** Assign data to specified output array using given input array. */ +int Traj_PDBfile::AssignData(Darray& DataOut, DataSet* dataIn, Topology const& topIn, bool byres, const char* desc) +const +{ + DataOut.assign(topIn.Natom(), 0); + if ( dataIn->Size() < 1) { + mprinterr("Error: '%s' set '%s' is empty.\n", desc, dataIn->legend()); + return 1; + } + // Set up output data set. Assume X coord of data set matches up + // with atom numbers and that atom numbers start from 1. + DataSet_1D const& data = static_cast( *dataIn ); + unsigned int dsidx = 0; + double dat = 1.0; // Double precision version of atom number for comparing to set X coord + double xcrd = data.Xcrd( dsidx ); + // Advance if necessary + while (xcrd < dat && dsidx < data.Size()) { + xcrd = data.Xcrd( dsidx ); + dsidx++; + } + if (byres) { + for (int ires = 0; ires != topIn.Nres(); ires++) { + if (dsidx >= data.Size()) break; + double xcrd = data.Xcrd( dsidx ); + if ( Eqv(xcrd, dat) ) { + for (int iat = topIn.Res(ires).FirstAtom(); iat < topIn.Res(ires).LastAtom(); iat++) + DataOut[iat] = data.Dval( dsidx ); + dsidx++; + } + dat = dat + 1; // dat is residue num in this context + } + } else { + // Set data for all atoms + for (int iat = 0; iat != topIn.Natom(); iat++) { + if (dsidx >= data.Size()) break; + double xcrd = data.Xcrd( dsidx ); + if ( Eqv(xcrd, dat) ) { + DataOut[iat] = data.Dval( dsidx++ ); + } + dat = dat + 1; + } + } return 0; } @@ -511,17 +642,31 @@ int Traj_PDBfile::setupTrajout(FileName const& fname, Topology* trajParm, if (space_group_.empty()) mprintf("Warning: No PDB space group specified.\n"); } - // Set up radii - if (dumpq_) { - radii_.clear(); + Bfactors_.clear(); + if (bfacdata_ != 0) { + if (AssignData(Bfactors_, bfacdata_, *trajParm, bfacbyres_, "bfacdata")) return 1; + } else if (dumpq_) { + Bfactors_.reserve( trajParm->Natom() ); + // Set up radii for (int iat = 0; iat != trajParm->Natom(); iat++) { switch (radiiMode_) { - case GB: radii_.push_back( (*trajParm)[iat].GBRadius() ); break; - case PARSE: radii_.push_back( (*trajParm)[iat].ParseRadius() ); break; - case VDW: radii_.push_back( trajParm->GetVDWradius(iat) ); break; + case GB: Bfactors_.push_back( (*trajParm)[iat].GBRadius() ); break; + case PARSE: Bfactors_.push_back( (*trajParm)[iat].ParseRadius() ); break; + case VDW: Bfactors_.push_back( trajParm->GetVDWradius(iat) ); break; } } } + Occupancy_.clear(); + if (occdata_ != 0) { + if (AssignData(Occupancy_, occdata_, *trajParm, occbyres_, "occdata")) return 1; + } else if (dumpq_) { + Occupancy_.reserve( trajParm->Natom() ); + // Set up charges + for (Topology::atom_iterator atm = trajParm->begin(); atm != trajParm->end(); ++atm) + Occupancy_.push_back( atm->Charge() ); + } + if (bfacscale_) ScaleData(Bfactors_, 0.0, bfacmax_); + if (occscale_ ) ScaleData(Occupancy_, 0.0, occmax_); // If not including extra points, warn if topology has them. if (!include_ep_) { unsigned int n_not_included = 0; @@ -594,8 +739,8 @@ int Traj_PDBfile::writeFrame(int set, Frame const& frameOut) { if (pdbWriteMode_==MODEL) file_.WriteMODEL(set + 1); - float Occ = 1.0; - float B = 0.0; + float Occ = 1.0; + float Bfac = 0.0; char altLoc = ' '; int anum = 1; // Actual PDB ATOM record number const double *Xptr = frameOut.xAddress(); @@ -610,14 +755,14 @@ int Traj_PDBfile::writeFrame(int set, Frame const& frameOut) { else rectype = PDBfile::ATOM; if (!pdbTop_->Extra().empty()) { - Occ = pdbTop_->Extra()[aidx].Occupancy(); - B = pdbTop_->Extra()[aidx].Bfactor(); + Occ = pdbTop_->Extra()[aidx].Occupancy(); + Bfac = pdbTop_->Extra()[aidx].Bfactor(); altLoc = pdbTop_->Extra()[aidx].AtomAltLoc(); } - if (dumpq_) { - Occ = (float) atom.Charge(); - B = (float) radii_[aidx]; - } + if (!Bfactors_.empty()) + Bfac = (float) Bfactors_[aidx]; + if (!Occupancy_.empty()) + Occ = (float) Occupancy_[aidx]; // If pdbatom change amber atom names to pdb v3 NameType atomName = atom.Name(); if (pdbatom_) { @@ -639,7 +784,7 @@ int Traj_PDBfile::writeFrame(int set, Frame const& frameOut) { file_.WriteCoord(rectype, anum, atomName, altLoc, resNames_[res], chainID_[res], pdbTop_->Res(res).OriginalResNum(), pdbTop_->Res(res).Icode(), - Xptr[0], Xptr[1], Xptr[2], Occ, B, + Xptr[0], Xptr[1], Xptr[2], Occ, Bfac, atom.ElementName(), 0, dumpq_); if (conectMode_ != NO_CONECT) atrec_[aidx] = anum; // Store ATOM record # @@ -680,15 +825,20 @@ void Traj_PDBfile::Info() { else if (pdbWriteMode_==MODEL) mprintf(" (1 MODEL per frame)"); if (conectMode_ != NO_CONECT) mprintf(" with CONECT records"); - if (dumpq_) { - mprintf(", writing charges to occupancy column and "); + if (bfacdata_ != 0) + mprintf(", B-factor data from '%s'", bfacdata_->legend()); + else if (dumpq_) { + mprintf(", B-factor column contains "); switch (radiiMode_) { case GB: mprintf("GB radii"); break; case PARSE: mprintf("PARSE radii"); break; case VDW: mprintf("vdW radii"); break; } - mprintf(" to B-factor column"); } + if (occdata_ != 0) + mprintf(", occupancy data from '%s'", occdata_->legend()); + else if (dumpq_) + mprintf(", occupancy column contains charges"); if (pdbres_ && pdbatom_) mprintf(", using PDB V3 res/atom names"); else if (pdbres_) diff --git a/src/Traj_PDBfile.h b/src/Traj_PDBfile.h index f199959739..261b49d7d7 100644 --- a/src/Traj_PDBfile.h +++ b/src/Traj_PDBfile.h @@ -2,7 +2,8 @@ #define INC_TRAJ_PDBFILE_H #include "TrajectoryIO.h" #include "PDBfile.h" -// Class: Traj_PDBfile +// Forward declarations +class DataSet; /// TrajectoryIO class for reading coordinates from PDB files. class Traj_PDBfile: public TrajectoryIO { public: @@ -19,6 +20,8 @@ class Traj_PDBfile: public TrajectoryIO { static BaseIOtype* Alloc() { return (BaseIOtype*)new Traj_PDBfile(); } static void WriteHelp(); private: + typedef std::vector Iarray; + typedef std::vector Darray; // Inherited functions bool ID_TrajFormat(CpptrajFile&); int setupTrajin(FileName const&, Topology*); @@ -28,7 +31,7 @@ class Traj_PDBfile: public TrajectoryIO { int readFrame(int,Frame&); int writeFrame(int,Frame const&); void Info(); - int processWriteArgs(ArgList&); + int processWriteArgs(ArgList&, DataSetList const&); int readVelocity(int, Frame&) { return 1; } int readForce(int, Frame&) { return 1; } int processReadArgs(ArgList&) { return 0; } @@ -40,10 +43,14 @@ class Traj_PDBfile: public TrajectoryIO { int parallelWriteFrame(int, Frame const&); void parallelCloseTraj() {} # endif + void WriteDisulfides(Frame const&); void WriteBonds(); + /// Used to set up B-factor/occupancy data from DataSets + int AssignData(Darray&, DataSet*, Topology const&, bool, const char*) const; + /// Used to scale Bfactor/occupancy data between set values + void ScaleData(Darray&, double, double) const; - typedef std::vector Iarray; typedef PDBfile::SSBOND SSBOND; enum TER_Mode { BY_MOL = 0, BY_RES, ORIGINAL_PDB, NO_TER }; enum Radii_Mode { GB = 0, PARSE, VDW }; @@ -62,11 +69,16 @@ class Traj_PDBfile: public TrajectoryIO { bool include_ep_; ///< If true include extra points. bool prependExt_; bool firstframe_; ///< Set to false after first call to writeFrame + bool bfacscale_; ///< If specified scale B-factor data + bool occscale_; ///< If specified scale occupancy data + bool bfacbyres_; ///< If true do bfactor data by residue + bool occbyres_; ///< If true do occupancy data by residue std::string space_group_; - std::vector radii_; ///< Hold radii for PQR format. - Iarray TER_idxs_; ///< TER card indices. - Iarray atrec_; ///< Hold ATOM record #s for CONECT - std::vector resIsHet_; ///< True if residue needs HETATM records + Darray Bfactors_; ///< Hold data for B-factor column. + Darray Occupancy_; ///< Hold data for occupancy column. + Iarray TER_idxs_; ///< TER card indices. + Iarray atrec_; ///< Hold ATOM record #s for CONECT + std::vector resIsHet_; ///< True if residue needs HETATM records std::vector ss_residues_; Iarray ss_atoms_; Topology *pdbTop_; @@ -74,5 +86,9 @@ class Traj_PDBfile: public TrajectoryIO { std::vector chainID_; ///< Hold chainID for each residue. std::vector resNames_; ///< Hold residue names. char chainchar_; + DataSet* bfacdata_; + DataSet* occdata_; + double bfacmax_; + double occmax_; }; #endif diff --git a/src/Traj_SDF.cpp b/src/Traj_SDF.cpp index 9ce7ea1a84..0d9e63acbe 100644 --- a/src/Traj_SDF.cpp +++ b/src/Traj_SDF.cpp @@ -1,4 +1,6 @@ #include "Traj_SDF.h" +#include "Topology.h" +#include "Frame.h" #include "CpptrajStdio.h" bool Traj_SDF::ID_TrajFormat(CpptrajFile& fileIn) { diff --git a/src/Traj_SDF.h b/src/Traj_SDF.h index 91f92a043e..fba57ade6a 100644 --- a/src/Traj_SDF.h +++ b/src/Traj_SDF.h @@ -19,7 +19,7 @@ class Traj_SDF : public TrajectoryIO { void Info(); int readVelocity(int, Frame&) { return 1; } int readForce(int, Frame&) { return 1; } - int processWriteArgs(ArgList&){ return 0; } + int processWriteArgs(ArgList&, DataSetList const&){ return 0; } int processReadArgs(ArgList&) { return 0; } SDFfile file_; diff --git a/src/Traj_SQM.cpp b/src/Traj_SQM.cpp index ef2af35497..10d896c485 100644 --- a/src/Traj_SQM.cpp +++ b/src/Traj_SQM.cpp @@ -1,4 +1,7 @@ #include "Traj_SQM.h" +#include "Topology.h" +#include "ArgList.h" +#include "Frame.h" #include "CpptrajStdio.h" #include "StringRoutines.h" // integerToString @@ -7,7 +10,7 @@ void Traj_SQM::WriteHelp() { } // Traj_SQM::processWriteArgs() -int Traj_SQM::processWriteArgs(ArgList& argIn) { +int Traj_SQM::processWriteArgs(ArgList& argIn, DataSetList const&) { if (argIn.Contains("charge")) { charge_ = argIn.getKeyInt( "charge", 0 ); chargeIsSet_ = true; diff --git a/src/Traj_SQM.h b/src/Traj_SQM.h index ce11a9a68b..2d28db9233 100644 --- a/src/Traj_SQM.h +++ b/src/Traj_SQM.h @@ -1,6 +1,7 @@ #ifndef INC_TRAJ_SQM_H #define INC_TRAJ_SQM_H #include "TrajectoryIO.h" +#include "CpptrajFile.h" /// Write out sqm input file. class Traj_SQM : public TrajectoryIO { public: @@ -17,7 +18,7 @@ class Traj_SQM : public TrajectoryIO { int readVelocity(int, Frame&) { return 1; } int readForce(int, Frame&) { return 1; } void closeTraj() { return; } - int processWriteArgs(ArgList&); + int processWriteArgs(ArgList&, DataSetList const&); int setupTrajout(FileName const&, Topology*, CoordinateInfo const&,int, bool); int writeFrame(int,Frame const&); void Info(); diff --git a/src/Traj_Tinker.cpp b/src/Traj_Tinker.cpp index 56b769db63..d22c332613 100644 --- a/src/Traj_Tinker.cpp +++ b/src/Traj_Tinker.cpp @@ -1,4 +1,6 @@ #include "Traj_Tinker.h" +#include "Topology.h" +#include "Frame.h" #include "CpptrajStdio.h" // CONSTRUCTOR diff --git a/src/Traj_Tinker.h b/src/Traj_Tinker.h index f9f95cd2bd..730c33ef2d 100644 --- a/src/Traj_Tinker.h +++ b/src/Traj_Tinker.h @@ -20,7 +20,7 @@ class Traj_Tinker : public TrajectoryIO { int readFrame(int,Frame&); int writeFrame(int,Frame const&); void Info(); - int processWriteArgs(ArgList&) { return 0; } + int processWriteArgs(ArgList&, DataSetList const&) { return 0; } int readVelocity(int, Frame&) { return 1; } int readForce(int, Frame&) { return 1; } int processReadArgs(ArgList&) { return 0; } diff --git a/src/Traj_XYZ.cpp b/src/Traj_XYZ.cpp index 03eeda1583..d41fb387c2 100644 --- a/src/Traj_XYZ.cpp +++ b/src/Traj_XYZ.cpp @@ -1,5 +1,9 @@ #include #include "Traj_XYZ.h" +#include "Topology.h" +#include "ArgList.h" +#include "Frame.h" +#include "CpptrajFile.h" #include "CpptrajStdio.h" #include "StringRoutines.h" #include "TextFormat.h" @@ -219,7 +223,7 @@ void Traj_XYZ::WriteHelp() { } /** Process write arguments. */ -int Traj_XYZ::processWriteArgs(ArgList& argIn) { +int Traj_XYZ::processWriteArgs(ArgList& argIn, DataSetList const& DSLin) { std::string arg = argIn.GetStringKey("ftype"); if (!arg.empty()) { if (arg == "xyz") diff --git a/src/Traj_XYZ.h b/src/Traj_XYZ.h index 0f02c5278d..5524e6bd93 100644 --- a/src/Traj_XYZ.h +++ b/src/Traj_XYZ.h @@ -21,7 +21,7 @@ class Traj_XYZ : public TrajectoryIO { void Info(); int readVelocity(int, Frame&); int readForce(int, Frame&); - int processWriteArgs(ArgList&); + int processWriteArgs(ArgList&, DataSetList const&); int processReadArgs(ArgList&); // ------------------------------------------- # ifdef MPI diff --git a/src/TrajectoryFile.h b/src/TrajectoryFile.h index c52d0aa1a3..dee41b56ba 100644 --- a/src/TrajectoryFile.h +++ b/src/TrajectoryFile.h @@ -1,7 +1,9 @@ #ifndef INC_TRAJECTORYFILE_H #define INC_TRAJECTORYFILE_H -#include "TrajectoryIO.h" #include "FileTypes.h" +#include "FileName.h" +// Forward declarations +class TrajectoryIO; /// Base class that all input and output trajectories will inherit. /** There are 3 steps to adding new trajectory types: * - 1) Create the TrajectoryIO-derived class for the format and include diff --git a/src/TrajectoryIO.h b/src/TrajectoryIO.h index 68d20670bd..02a87b0e54 100644 --- a/src/TrajectoryIO.h +++ b/src/TrajectoryIO.h @@ -1,14 +1,25 @@ #ifndef INC_TRAJECTORYIO_H #define INC_TRAJECTORYIO_H -#include "Topology.h" // Box -#include "FrameArray.h" -#include "FramePtrArray.h" -#include "CpptrajFile.h" -#include "ArgList.h" +#include #include "BaseIOtype.h" +#include "CoordinateInfo.h" #ifdef MPI # include "Parallel.h" #endif +#ifdef ENABLE_SINGLE_ENSEMBLE + // This is not forward declared because it is a typedef, not a class +# include "FramePtrArray.h" +#endif +// Forward declarations +class CpptrajFile; +class FileName; +class Topology; +class Frame; +class ArgList; +class DataSetList; +#ifdef ENABLE_SINGLE_ENSEMBLE +class FrameArray; +#endif /// Abstract base class for performing trajectory reading and writing. /** This is the generic interface for a trajectory format used by * TrajectoryFile-derived classes. @@ -31,13 +42,15 @@ class TrajectoryIO : public BaseIOtype { */ virtual int setupTrajin(FileName const&, Topology*) = 0; /// Set up and open trajectory IO for WRITE/APPEND - /** Called on the first write call. Args are: 1) trajectory file name, - * 2) Topology associated with this trajectory, 3) coordinate metadata - * (velocities, temperatures, etc), 4) number of frames expected to be - * written out, 5) whether trajectory should be appended to. + /** Called on the first write call. Args are: + * - Trajectory file name + * - Topology associated with this trajectory + * - Coordinate metadata (velocities, temperatures, etc) + * - Number of frames expected to be written out + * - whether trajectory should be appended to. * \return 0 on success, 1 on error. */ - virtual int setupTrajout(FileName const&,Topology*,CoordinateInfo const&,int,bool) = 0; + virtual int setupTrajout(FileName const&, Topology*, CoordinateInfo const&, int, bool) = 0; /// Open previously set-up input trajectory, prepare for IO. virtual int openTrajin() = 0; /// Read a frame from trajectory @@ -68,7 +81,7 @@ class TrajectoryIO : public BaseIOtype { * implemented as functions that can be called independently if need be * (e.g. setting the write mode for PDB files). */ - virtual int processWriteArgs(ArgList&) = 0; + virtual int processWriteArgs(ArgList&, DataSetList const&) = 0; /// Process arguments relevant to reading trajectory (optional) virtual int processReadArgs(ArgList&) = 0; # ifdef ENABLE_SINGLE_ENSEMBLE diff --git a/src/Trajin.h b/src/Trajin.h index ae8232b73b..361c8abd2c 100644 --- a/src/Trajin.h +++ b/src/Trajin.h @@ -4,6 +4,9 @@ #ifdef MPI # include "Parallel.h" #endif +// Forward declarations +class Frame; +class CoordinateInfo; /// Read in 1 frame at a time. class Trajin { public: diff --git a/src/TrajinList.cpp b/src/TrajinList.cpp index 2ac6ffa22f..10f08f1554 100644 --- a/src/TrajinList.cpp +++ b/src/TrajinList.cpp @@ -1,4 +1,5 @@ #include "TrajinList.h" +#include "Topology.h" #include "CpptrajStdio.h" #include "TrajectoryFile.h" #include "Trajin_Single.h" diff --git a/src/Trajin_Multi.cpp b/src/Trajin_Multi.cpp index 6fb96d7381..51910a4d1f 100644 --- a/src/Trajin_Multi.cpp +++ b/src/Trajin_Multi.cpp @@ -1,4 +1,6 @@ #include "Trajin_Multi.h" +#include "ArgList.h" +#include "Topology.h" #include "StringRoutines.h" // convertToInteger #include "CpptrajStdio.h" diff --git a/src/Trajin_Multi.h b/src/Trajin_Multi.h index 77f3e0e75c..8aefc17297 100644 --- a/src/Trajin_Multi.h +++ b/src/Trajin_Multi.h @@ -3,6 +3,11 @@ #include "Trajin.h" #include "TrajIOarray.h" #include "ReplicaInfo.h" +#include "Frame.h" // For RemdIdxType +// Forward declares +class ArgList; +class Topology; +class FileName; /// Read in 1 frame at a time from multiple files. class Trajin_Multi : public Trajin { public: @@ -24,7 +29,7 @@ class Trajin_Multi : public Trajin { // --------------------------------------------- private: /// Type that will hold REMD indices - typedef Frame::RemdIdxType RemdIdxType; + typedef Frame::RemdIdxType RemdIdxType; // TODO put in ReplicaInfo TrajIOarray REMDtraj_; CoordinateInfo cInfo_; ///< Collective coord information for all replicas TODO Trajin? diff --git a/src/Trajin_Single.cpp b/src/Trajin_Single.cpp index a5950dc3fe..39c4cc4df7 100644 --- a/src/Trajin_Single.cpp +++ b/src/Trajin_Single.cpp @@ -1,4 +1,6 @@ #include "Trajin_Single.h" +#include "Topology.h" +#include "TrajectoryIO.h" #include "TrajectoryFile.h" #include "CpptrajStdio.h" @@ -15,6 +17,9 @@ Trajin_Single::~Trajin_Single() { if (frcio_!=0) delete frcio_; } +/** \return Trajectory title. */ +std::string const& Trajin_Single::Title() const { return trajio_->Title(); } //TODO Check for segfault + /** Used to set up separate traj for forces/velocities. */ TrajectoryIO* Trajin_Single::SetupSeparateTraj(FileName const& fname, const char* type) const { diff --git a/src/Trajin_Single.h b/src/Trajin_Single.h index 233e8b403c..6754966dcd 100644 --- a/src/Trajin_Single.h +++ b/src/Trajin_Single.h @@ -1,7 +1,9 @@ #ifndef INC_TRAJIN_SINGLE_H #define INC_TRAJIN_SINGLE_H #include "Trajin.h" -#include "TrajectoryIO.h" +#include "CoordinateInfo.h" +// Forward declarations +class TrajectoryIO; /// Read in 1 frame at a time from a single file. class Trajin_Single : public Trajin { public: @@ -21,7 +23,7 @@ class Trajin_Single : public Trajin { /// \return trajectory metadata. CoordinateInfo const& TrajCoordInfo() const { return cInfo_; } // --------------------------------------------- - std::string const& Title() const { return trajio_->Title(); } //TODO Check for segfault + std::string const& Title() const; # ifdef MPI int ParallelBeginTraj( Parallel::Comm const& ); int ParallelReadTrajFrame(int, Frame&); diff --git a/src/TrajoutList.cpp b/src/TrajoutList.cpp index 43df2ff518..2ec9e8e8b8 100644 --- a/src/TrajoutList.cpp +++ b/src/TrajoutList.cpp @@ -1,6 +1,20 @@ #include "TrajoutList.h" +#include "Trajout_Single.h" +#include "Topology.h" #include "CpptrajStdio.h" +// FIXME for pytraj compatibility +#include "DataSetList.h" +/// CONSTRUCTOR +TrajoutList::TrajoutList() : debug_(0) {} + +/// DESTRUCTOR +TrajoutList::~TrajoutList() { Clear(); } + +/** Set the list debug level; passed to new output trajectories. */ +void TrajoutList::SetDebug(int d) { debug_ = d; } + +/** Clear the output trajectory list, free all memory. */ void TrajoutList::Clear() { for (ListType::iterator traj = trajout_.begin(); traj != trajout_.end(); ++traj) delete *traj; @@ -10,12 +24,19 @@ void TrajoutList::Clear() { open_.clear(); } +// FIXME legacy function to maintain pytraj compatibility +int TrajoutList::AddTrajout(std::string const& filename, ArgList const& argIn, Topology* tParm) +{ + DataSetList blank; + return AddTrajout(filename, argIn, blank, tParm); +} + /** Add output trajectory to list as single output trajectory. Associate it * with the given Topology but no Topology-dependent setup will occur. This * is because during the course of a Run the Topology may be modified, by * e.g. a 'strip' command. */ -int TrajoutList::AddTrajout(std::string const& filename, ArgList const& argIn, Topology* tParm) +int TrajoutList::AddTrajout(std::string const& filename, ArgList const& argIn, DataSetList const& DSLin, Topology* tParm) { if (tParm == 0) { mprinterr("Error: No topology information.\n"); @@ -39,7 +60,7 @@ int TrajoutList::AddTrajout(std::string const& filename, ArgList const& argIn, T to->SetDebug( debug_ ); // Initialize output trajectory ArgList args = argIn; - if (to->InitTrajWrite(filename, args, TrajectoryFile::UNKNOWN_TRAJ)) { + if (to->InitTrajWrite(filename, args, DSLin, TrajectoryFile::UNKNOWN_TRAJ)) { mprinterr("Error: Could not set up output trajectory.\n"); delete to; return 1; diff --git a/src/TrajoutList.h b/src/TrajoutList.h index f1accdce8d..2dba9a6fad 100644 --- a/src/TrajoutList.h +++ b/src/TrajoutList.h @@ -1,15 +1,28 @@ #ifndef INC_TRAJOUTLIST_H #define INC_TRAJOUTLIST_H -#include "Trajout_Single.h" +#include +#include +#ifdef MPI +# include "Parallel.h" +#endif +// Forward declarations +class Trajout_Single; +class Topology; +class ArgList; +class DataSetList; +class CoordinateInfo; +class Frame; /// Hold output trajectories for a run. class TrajoutList { public: - TrajoutList() : debug_(0) {} - ~TrajoutList() { Clear(); } - void SetDebug(int d) { debug_ = d; } + TrajoutList(); + ~TrajoutList(); + void SetDebug(int); void Clear(); - /// Add output trajectory to the list and associate with given topology. + /// FIXME legacy function to maintain pytraj compatibility int AddTrajout(std::string const&, ArgList const&, Topology*); + /// Add output trajectory to the list and associate with given topology. + int AddTrajout(std::string const&, ArgList const&, DataSetList const&, Topology*); /// Set up trajectories for given topology. int SetupTrajout(Topology*, CoordinateInfo const&, int); /// Write frame to normal output trajectories. diff --git a/src/Trajout_Single.cpp b/src/Trajout_Single.cpp index 5e0be850ff..9fdea91bd3 100644 --- a/src/Trajout_Single.cpp +++ b/src/Trajout_Single.cpp @@ -1,4 +1,6 @@ #include "Trajout_Single.h" +#include "TrajectoryIO.h" +#include "Topology.h" #include "CpptrajStdio.h" #include "StringRoutines.h" // AppendNumber @@ -13,6 +15,7 @@ Trajout_Single::~Trajout_Single() { * process arguments. */ int Trajout_Single::InitTrajWrite(FileName const& tnameIn, ArgList const& argIn, + DataSetList const& DSLin, TrajectoryFile::TrajFormatType writeFormatIn) { // Require a filename @@ -20,22 +23,24 @@ int Trajout_Single::InitTrajWrite(FileName const& tnameIn, ArgList const& argIn, mprinterr("Internal Error: InitTrajWrite: No filename given.\n"); return 1; } - return InitTrajout(tnameIn, argIn, writeFormatIn); + return InitTrajout(tnameIn, argIn, DSLin, writeFormatIn); } // Trajout_Single::PrepareStdoutTrajWrite() /** Initialize and set up output trajectory for STDOUT write. */ -int Trajout_Single::PrepareStdoutTrajWrite(ArgList const& argIn, Topology *tparmIn, +int Trajout_Single::PrepareStdoutTrajWrite(ArgList const& argIn, DataSetList const& DSLin, + Topology *tparmIn, CoordinateInfo const& cInfoIn, int nFrames, TrajectoryFile::TrajFormatType writeFormatIn) { - if (InitTrajout("", argIn, writeFormatIn)) return 1; + if (InitTrajout("", argIn, DSLin, writeFormatIn)) return 1; if (SetupTrajWrite(tparmIn, cInfoIn, nFrames)) return 1; return 0; } /** Initialize trajectory for write. Append ensemble number to filename if given. */ int Trajout_Single::InitEnsembleTrajWrite(FileName const& tnameIn, ArgList const& argIn, + DataSetList const& DSLin, TrajectoryFile::TrajFormatType fmtIn, int ensembleNum) { ArgList args = argIn; @@ -47,25 +52,27 @@ int Trajout_Single::InitEnsembleTrajWrite(FileName const& tnameIn, ArgList const fmt = TrajectoryFile::WriteFormatFromFname( tnameIn, TrajectoryFile::UNKNOWN_TRAJ ); int err = 0; if (ensembleNum > -1) - err = InitTrajWrite( AppendNumber(tnameIn.Full(), ensembleNum), args, fmt ); + err = InitTrajWrite( AppendNumber(tnameIn.Full(), ensembleNum), args, DSLin, fmt ); else - err = InitTrajWrite( tnameIn, args, fmt ); + err = InitTrajWrite( tnameIn, args, DSLin, fmt ); if (err != 0) return 1; return 0; } // Trajout_Single::PrepareTrajWrite() int Trajout_Single::PrepareTrajWrite(FileName const& tnameIn, ArgList const& argIn, + DataSetList const& DSLin, Topology* tparmIn, CoordinateInfo const& cInfoIn, int nFrames, TrajectoryFile::TrajFormatType fmtIn) { - if (InitTrajWrite(tnameIn, argIn, fmtIn)) return 1; + if (InitTrajWrite(tnameIn, argIn, DSLin, fmtIn)) return 1; if (SetupTrajWrite(tparmIn, cInfoIn, nFrames)) return 1; return 0; } // Trajout_Single::InitTrajout() int Trajout_Single::InitTrajout(FileName const& tnameIn, ArgList const& argIn, + DataSetList const& DSLin, TrajectoryFile::TrajFormatType writeFormatIn) { ArgList trajout_args = argIn; @@ -89,7 +96,7 @@ int Trajout_Single::InitTrajout(FileName const& tnameIn, ArgList const& argIn, trajio_->SetTitle( traj_.Title() ); // Process any write arguments specific to certain formats not related // to parm file. Options related to parm file are handled in SetupTrajWrite - if (trajio_->processWriteArgs(trajout_args)) { + if (trajio_->processWriteArgs(trajout_args, DSLin)) { mprinterr("Error: trajout %s: Could not process arguments.\n", traj_.Filename().full()); return 1; } diff --git a/src/Trajout_Single.h b/src/Trajout_Single.h index 8bc16c2445..7c161cbede 100644 --- a/src/Trajout_Single.h +++ b/src/Trajout_Single.h @@ -1,6 +1,9 @@ #ifndef INC_TRAJOUT_SINGLE_H #define INC_TRAJOUT_SINGLE_H #include "OutputTrajCommon.h" +// Forward declarations +class Frame; +class DataSetList; /// Write out 1 frame at a time to a single file. /** Note that unlike Trajin, there is really no point in having * a single frame written to multiple files since this is handled @@ -20,7 +23,7 @@ class Trajout_Single { void SetDebug(int d) { debug_ = d; } // ----- Inherited functions ----------------- /// Prepare trajectory for writing to the given format, but no Topology setup. - int InitTrajWrite(FileName const&, ArgList const&, TrajectoryFile::TrajFormatType); + int InitTrajWrite(FileName const&, ArgList const&, DataSetList const& DSLin, TrajectoryFile::TrajFormatType); /// Peform Topology-related setup for trajectory and open. TODO const& int SetupTrajWrite(Topology*, CoordinateInfo const&, int); /// Close output trajectory. @@ -33,20 +36,20 @@ class Trajout_Single { OutputTrajCommon Traj() const { return traj_; } bool IsInitialized() const { return trajio_ != 0; } /// Init and setup/open traj. - int PrepareTrajWrite(FileName const&, ArgList const&, Topology*, + int PrepareTrajWrite(FileName const&, ArgList const&, DataSetList const&, Topology*, CoordinateInfo const&, int, TrajectoryFile::TrajFormatType); /// Init and setup/open traj for writing to STDOUT (e.g. ambpdb mode) - int PrepareStdoutTrajWrite(ArgList const&, Topology*, CoordinateInfo const&, int, - TrajectoryFile::TrajFormatType); + int PrepareStdoutTrajWrite(ArgList const&, DataSetList const&, Topology*, + CoordinateInfo const&, int, TrajectoryFile::TrajFormatType); /// Init traj; if given, append ensemble number to name (use in Actions) - int InitEnsembleTrajWrite(FileName const&, ArgList const&, + int InitEnsembleTrajWrite(FileName const&, ArgList const&, DataSetList const&, TrajectoryFile::TrajFormatType, int); # ifdef MPI // Set the parallel communicator. int SetTrajComm(Parallel::Comm const& c) { trajComm_ = c; return 0; } # endif private: - int InitTrajout(FileName const&, ArgList const&, TrajectoryFile::TrajFormatType); + int InitTrajout(FileName const&, ArgList const&, DataSetList const&, TrajectoryFile::TrajFormatType); # ifdef MPI /// Peform Topology-related setup for trajectory and open in parallel. int ParallelSetupTrajWrite(); diff --git a/src/Version.h b/src/Version.h index 93e2c0b2ee..cd2e723a24 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 "V4.14.3" +#define CPPTRAJ_INTERNAL_VERSION "V4.14.4" /// PYTRAJ relies on this #define CPPTRAJ_VERSION_STRING CPPTRAJ_INTERNAL_VERSION #endif diff --git a/src/ViewRst.cpp b/src/ViewRst.cpp index 456b86c7ad..cc8d668eb3 100644 --- a/src/ViewRst.cpp +++ b/src/ViewRst.cpp @@ -1,4 +1,5 @@ #include "ViewRst.h" +#include "DataSetList.h" #include "CpptrajStdio.h" #include "Trajout_Single.h" #include "ParmFile.h" @@ -68,7 +69,7 @@ int ViewRst::WriteRstMol2(std::string const& mol2out, Frame const& frameIn) { for (unsigned int nt = 0; nt != Pseudo_.size(); nt++) { Trajout_Single trajout; - if (trajout.PrepareTrajWrite(OutNames[nt], ArgList(), &(Pseudo_[nt]), CoordinateInfo(), 1, + if (trajout.PrepareTrajWrite(OutNames[nt], ArgList(), DataSetList(), &(Pseudo_[nt]), CoordinateInfo(), 1, TrajectoryFile::MOL2FILE)) return 1; if (trajout.WriteSingle(0, frameIn)) return 1; diff --git a/src/cpptrajdepend b/src/cpptrajdepend index 0e4dfacd3a..766bda7614 100644 --- a/src/cpptrajdepend +++ b/src/cpptrajdepend @@ -8,7 +8,7 @@ Action_AtomMap.o : Action_AtomMap.cpp Action.h ActionState.h Action_AtomMap.h Ar 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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.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 BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TrajectoryIO.h Trajout_Single.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h Vec3.h @@ -40,11 +40,11 @@ Action_HydrogenBond.o : Action_HydrogenBond.cpp Action.h ActionState.h Action_Hy Action_Image.o : Action_Image.cpp Action.h ActionState.h Action_Image.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.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 BaseIOtype.h Box.h CharMask.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h ProgressBar.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.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 BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TrajectoryIO.h Trajout_Single.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.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 BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.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 BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TrajectoryIO.h Trajout_Single.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.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 BaseIOtype.h Box.h CharMask.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h Vec3.h molsurf.h @@ -54,9 +54,9 @@ Action_NAstruct.o : Action_NAstruct.cpp Action.h ActionState.h Action_NAstruct.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 BaseIOtype.h Box.h BufferedLine.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 FrameArray.h FramePtrArray.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TrajectoryIO.h Trajout_Single.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.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 BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 FrameArray.h FramePtrArray.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PDBfile.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TrajectoryIO.h Trajout_Single.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 BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 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 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 BaseIOtype.h Box.h CharMask.h ComplexArray.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_1D.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.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 BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.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 BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Vec3.h @@ -64,7 +64,7 @@ Action_Radgyr.o : Action_Radgyr.cpp Action.h ActionState.h Action_Radgyr.h ArgLi Action_Radial.o : Action_Radial.cpp Action.h ActionState.h Action_Radial.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h Vec3.h Action_Remap.o : Action_Remap.cpp Action.h ActionState.h Action_Remap.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h BondSearch.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h ParmFile.h ParmIO.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h Vec3.h -Action_ReplicateCell.o : Action_ReplicateCell.cpp Action.h ActionFrameCounter.h ActionState.h Action_ReplicateCell.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h BondSearch.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 FrameArray.h FramePtrArray.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h ParmFile.h ParmIO.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TrajectoryIO.h Trajout_Single.h Vec3.h +Action_ReplicateCell.o : Action_ReplicateCell.cpp Action.h ActionFrameCounter.h ActionState.h Action_ReplicateCell.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h BondSearch.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h ParmFile.h ParmIO.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.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 BaseIOtype.h Box.h CharMask.h ComplexArray.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.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 BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h Vec3.h @@ -90,7 +90,7 @@ AnalysisList.o : AnalysisList.cpp ActionState.h Analysis.h AnalysisList.h Analys 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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.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 BaseIOtype.h Box.h CharMask.h ComplexArray.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.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 BaseIOtype.h Box.h CharMask.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 CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 FrameArray.h FramePtrArray.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.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 TrajectoryIO.h Trajout_Single.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 BaseIOtype.h Box.h CharMask.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 CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 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 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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.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 BaseIOtype.h Box.h CharMask.h ComplexArray.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h Vec3.h @@ -100,7 +100,7 @@ Analysis_CurveFit.o : Analysis_CurveFit.cpp ActionState.h Analysis.h AnalysisSta 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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.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 BaseIOtype.h Box.h CharMask.h ComplexArray.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.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 BaseIOtype.h BondSearch.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 FrameArray.h FramePtrArray.h Grid.h GridBin.h HistBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h ParmFile.h ParmIO.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TrajectoryIO.h Trajout_Single.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 BaseIOtype.h BondSearch.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h ParmFile.h ParmIO.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.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 BaseIOtype.h Box.h CharMask.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.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 BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h Vec3.h @@ -108,8 +108,8 @@ Analysis_Lifetime.o : Analysis_Lifetime.cpp ActionState.h Analysis.h AnalysisSta 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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.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 BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 FrameArray.h FramePtrArray.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TrajectoryIO.h Trajout_Single.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 FrameArray.h FramePtrArray.h HistBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TrajectoryIO.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 BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.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 BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h Vec3.h @@ -125,7 +125,7 @@ Analysis_Statistics.o : Analysis_Statistics.cpp ActionState.h Analysis.h Analysi 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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.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 BaseIOtype.h Box.h CharMask.h ComplexArray.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.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 BaseIOtype.h Box.h CharMask.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.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 BaseIOtype.h BondSearch.h Box.h CharMask.h ClusterMap.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 FrameArray.h FramePtrArray.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h ParmFile.h ParmIO.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 TrajectoryIO.h Trajout_Single.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 BaseIOtype.h BondSearch.h Box.h CharMask.h ClusterMap.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h ParmFile.h ParmIO.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 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 Box.h CharMask.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h Vec3.h AssociatedData.o : AssociatedData.cpp ArgList.h AssociatedData.h CpptrajStdio.h @@ -156,19 +156,19 @@ Cluster_ReadInfo.o : Cluster_ReadInfo.cpp ArgList.h ArrayIterator.h AssociatedDa 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 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_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_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_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 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 Constraints.h Control.h CoordinateInfo.h Corr.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 EnsembleOut.h EnsembleOutList.h Ewald.h Exec.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_GenerateAmberRst.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_PrintData.h Exec_ReadData.h Exec_ReadEnsembleData.h Exec_ReadInput.h Exec_RotateDihedral.h Exec_RunAnalysis.h Exec_ScaleDihedralK.h Exec_SequenceAlign.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 FrameArray.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 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 TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h VariableArray.h Vec3.h molsurf.h +Command.o : Command.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.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_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_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_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 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 Constraints.h Control.h CoordinateInfo.h Corr.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 Ewald.h Exec.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_GenerateAmberRst.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_PrintData.h Exec_ReadData.h Exec_ReadEnsembleData.h Exec_ReadInput.h Exec_RotateDihedral.h Exec_RunAnalysis.h Exec_ScaleDihedralK.h Exec_SequenceAlign.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 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 VariableArray.h Vec3.h molsurf.h ComplexArray.o : ComplexArray.cpp ArrayIterator.h ComplexArray.h Constraints.o : Constraints.cpp ArgList.h Atom.h AtomExtra.h AtomMask.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 ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h Vec3.h -Control.o : Control.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 BaseIOtype.h Box.h CharMask.h Control.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOut.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 OutputTrajCommon.h Parallel.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 TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h VariableArray.h Vec3.h +Control.o : Control.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.h Control.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 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 VariableArray.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 ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h BondSearch.h Box.h CharMask.h Cmd.h CmdInput.h CmdList.h Command.h Control.h CoordinateInfo.h Cpptraj.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOut.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 OutputTrajCommon.h Parallel.h ParameterTypes.h ParmFile.h ParmIO.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 TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h VariableArray.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 BaseIOtype.h BondSearch.h Box.h CharMask.h Cmd.h CmdInput.h CmdList.h Command.h Control.h CoordinateInfo.h Cpptraj.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h ParmFile.h ParmIO.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 VariableArray.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 ActionFrameCounter.h ActionList.h ActionState.h Action_CreateCrd.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 EnsembleOut.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 OutputTrajCommon.h Parallel.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 TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 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 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 BaseIOtype.h Box.h BufferedLine.h CharMask.h ClusterDist.h ClusterSieve.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_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 FrameArray.h FramePtrArray.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Cmatrix.h NameType.h Parallel.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 TrajectoryIO.h Vec3.h +DataFile.o : DataFile.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h CharMask.h ClusterDist.h ClusterSieve.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_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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Vec3.h DataFileList.o : DataFileList.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Vec3.h DataIO.o : DataIO.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h Vec3.h DataIO_CCP4.o : DataIO_CCP4.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h ByteRoutines.h CharMask.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h Vec3.h @@ -186,7 +186,7 @@ DataIO_NC_Cmatrix.o : DataIO_NC_Cmatrix.cpp ArgList.h ArrayIterator.h Associated DataIO_OpenDx.o : DataIO_OpenDx.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h CharMask.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_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 ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h Vec3.h DataIO_RemLog.o : DataIO_RemLog.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h CharMask.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 ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Vec3.h DataIO_Std.o : DataIO_Std.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h CharMask.h ClusterDist.h ClusterSieve.h ComplexArray.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_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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h Vec3.h -DataIO_VecTraj.o : DataIO_VecTraj.cpp ActionFrameCounter.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h BondSearch.h Box.h CharMask.h ComplexArray.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_VecTraj.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h ParmFile.h ParmIO.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TrajectoryIO.h Trajout_Single.h Vec3.h +DataIO_VecTraj.o : DataIO_VecTraj.cpp ActionFrameCounter.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h BondSearch.h Box.h CharMask.h ComplexArray.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_VecTraj.h DataSet.h DataSetList.h DataSet_1D.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 ParameterTypes.h ParmFile.h ParmIO.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Vec3.h DataIO_XVG.o : DataIO_XVG.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h CharMask.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h Vec3.h DataIO_Xplor.o : DataIO_Xplor.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h CharMask.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 ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h Vec3.h DataSet.o : DataSet.cpp ArgList.h AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h @@ -199,8 +199,8 @@ DataSet_Cmatrix_MEM.o : DataSet_Cmatrix_MEM.cpp ArgList.h ArrayIterator.h Associ DataSet_Cmatrix_NOMEM.o : DataSet_Cmatrix_NOMEM.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h Box.h CharMask.h ClusterDist.h ClusterSieve.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 ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Topology.h Vec3.h DataSet_Coords.o : DataSet_Coords.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h Box.h CharMask.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 ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Topology.h Vec3.h DataSet_Coords_CRD.o : DataSet_Coords_CRD.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h Box.h CharMask.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 ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Vec3.h -DataSet_Coords_REF.o : DataSet_Coords_REF.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Topology.h TrajFrameCounter.h TrajectoryIO.h Trajin.h Trajin_Single.h Vec3.h -DataSet_Coords_TRJ.o : DataSet_Coords_TRJ.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_TRJ.h Dimension.h FileIO.h FileName.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Topology.h TrajFrameCounter.h TrajFrameIndex.h TrajectoryIO.h Trajin.h Trajin_Single.h Vec3.h +DataSet_Coords_REF.o : DataSet_Coords_REF.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h Box.h CharMask.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 ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Topology.h TrajFrameCounter.h Trajin.h Trajin_Single.h Vec3.h +DataSet_Coords_TRJ.o : DataSet_Coords_TRJ.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h Box.h CharMask.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 ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h Trajin_Single.h Vec3.h DataSet_GridDbl.o : DataSet_GridDbl.cpp ArgList.h 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 ArgList.h 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 ArgList.h 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 @@ -225,57 +225,57 @@ DihedralSearch.o : DihedralSearch.cpp ArgList.h AssociatedData.h Atom.h AtomExtr 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 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 ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h TorsionRoutines.h Vec3.h Energy_Sander.o : Energy_Sander.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h BondSearch.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h Energy_Sander.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmFile.h ParmIO.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h Vec3.h -EnsembleIn.o : EnsembleIn.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h Box.h CharMask.h CoordinateInfo.h CpptrajStdio.h EnsembleIn.h FileName.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h Timer.h Topology.h TrajFrameCounter.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataIO.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 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 Vec3.h -EnsembleIn_Single.o : EnsembleIn_Single.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h EnsembleIn.h EnsembleIn_Single.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Vec3.h -EnsembleNavigator.o : EnsembleNavigator.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h Box.h CharMask.h CoordinateInfo.h CpptrajStdio.h EnsembleIn.h EnsembleNavigator.h FileName.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TrajinList.h Vec3.h -EnsembleOut.o : EnsembleOut.cpp ActionFrameCounter.h ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h EnsembleOut.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h Vec3.h -EnsembleOutList.o : EnsembleOutList.cpp ActionFrameCounter.h ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h EnsembleOut.h EnsembleOutList.h EnsembleOut_Multi.h EnsembleOut_Single.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h Vec3.h -EnsembleOut_Multi.o : EnsembleOut_Multi.cpp ActionFrameCounter.h ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h EnsembleOut.h EnsembleOut_Multi.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h Vec3.h -EnsembleOut_Single.o : EnsembleOut_Single.cpp ActionFrameCounter.h ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h EnsembleOut.h EnsembleOut_Single.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h Vec3.h +EnsembleIn_Single.o : EnsembleIn_Single.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.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 ParameterTypes.h Range.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.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 +EnsembleOut.o : EnsembleOut.cpp ActionFrameCounter.h ArgList.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 BaseIOtype.h Box.h CharMask.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 ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h TrajectoryFile.h Vec3.h +EnsembleOut_Multi.o : EnsembleOut_Multi.cpp ActionFrameCounter.h ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.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 ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h Vec3.h +EnsembleOut_Single.o : EnsembleOut_Single.cpp ActionFrameCounter.h ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.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 ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h Vec3.h Ewald.o : Ewald.cpp Atom.h AtomExtra.h AtomMask.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 ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Spline.h StringRoutines.h SymbolExporting.h Timer.h Topology.h Vec3.h Ewald_ParticleMesh.o : Ewald_ParticleMesh.cpp Atom.h AtomExtra.h AtomMask.h Box.h CharMask.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 ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Timer.h Topology.h Vec3.h helpme_standalone.h Ewald_Regular.o : Ewald_Regular.cpp Atom.h AtomExtra.h AtomMask.h Box.h CharMask.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 ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h Timer.h Topology.h Vec3.h -Exec_Analyze.o : Exec_Analyze.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 BaseIOtype.h Box.h CharMask.h Cmd.h CmdList.h Command.h Control.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOut.h EnsembleOutList.h Exec.h Exec_Analyze.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 OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h VariableArray.h Vec3.h -Exec_Calc.o : Exec_Calc.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOut.h EnsembleOutList.h Exec.h Exec_Calc.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 OutputTrajCommon.h Parallel.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 TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Vec3.h -Exec_CatCrd.o : Exec_CatCrd.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOut.h EnsembleOutList.h Exec.h Exec_CatCrd.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 OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Vec3.h -Exec_Change.o : Exec_Change.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOut.h EnsembleOutList.h Exec.h Exec_Change.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 OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Vec3.h -Exec_ClusterMap.o : Exec_ClusterMap.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.h ClusterMap.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOut.h EnsembleOutList.h Exec.h Exec_ClusterMap.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Vec3.h -Exec_CombineCoords.o : Exec_CombineCoords.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOut.h EnsembleOutList.h Exec.h Exec_CombineCoords.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 OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Vec3.h -Exec_Commands.o : Exec_Commands.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOut.h EnsembleOutList.h Exec.h Exec_Commands.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 OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Vec3.h -Exec_CompareTop.o : Exec_CompareTop.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 BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOut.h EnsembleOutList.h Exec.h Exec_CompareTop.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 OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Vec3.h -Exec_CrdAction.o : Exec_CrdAction.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 BaseIOtype.h Box.h CharMask.h Cmd.h CmdList.h Command.h Control.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOut.h EnsembleOutList.h Exec.h Exec_CrdAction.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 OutputTrajCommon.h Parallel.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 TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h VariableArray.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOut.h EnsembleOutList.h Exec.h Exec_CrdOut.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 OutputTrajCommon.h Parallel.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 TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Vec3.h -Exec_CreateSet.o : Exec_CreateSet.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOut.h EnsembleOutList.h Exec.h Exec_CreateSet.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 OutputTrajCommon.h Parallel.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 TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Vec3.h -Exec_DataFile.o : Exec_DataFile.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOut.h EnsembleOutList.h Exec.h Exec_DataFile.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 OutputTrajCommon.h Parallel.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 TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Vec3.h -Exec_DataFilter.o : Exec_DataFilter.cpp Action.h ActionFrameCounter.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOut.h EnsembleOutList.h Exec.h Exec_DataFilter.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 OutputTrajCommon.h Parallel.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 TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Vec3.h -Exec_DataSetCmd.o : Exec_DataSetCmd.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.h ComplexArray.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Vector.h DataSet_string.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOut.h EnsembleOutList.h Exec.h Exec_DataSetCmd.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.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 TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Vec3.h -Exec_GenerateAmberRst.o : Exec_GenerateAmberRst.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 BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h EnsembleIn.h EnsembleOut.h EnsembleOutList.h Exec.h Exec_GenerateAmberRst.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 OutputTrajCommon.h Parallel.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 TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Vec3.h -Exec_Help.o : Exec_Help.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 BaseIOtype.h BondSearch.h Box.h CharMask.h Cmd.h CmdList.h Command.h Control.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOut.h EnsembleOutList.h Exec.h Exec_Help.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 OutputTrajCommon.h Parallel.h ParameterTypes.h ParmFile.h ParmIO.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h VariableArray.h Vec3.h -Exec_LoadCrd.o : Exec_LoadCrd.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOut.h EnsembleOutList.h Exec.h Exec_LoadCrd.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 OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Trajout_Single.h Vec3.h -Exec_LoadTraj.o : Exec_LoadTraj.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOut.h EnsembleOutList.h Exec.h Exec_LoadTraj.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 OutputTrajCommon.h Parallel.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 TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Vec3.h -Exec_ParallelAnalysis.o : Exec_ParallelAnalysis.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOut.h EnsembleOutList.h Exec.h Exec_ParallelAnalysis.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 OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Vec3.h -Exec_ParmBox.o : Exec_ParmBox.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOut.h EnsembleOutList.h Exec.h Exec_ParmBox.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 OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Vec3.h -Exec_ParmSolvent.o : Exec_ParmSolvent.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOut.h EnsembleOutList.h Exec.h Exec_ParmSolvent.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 OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Vec3.h -Exec_ParmStrip.o : Exec_ParmStrip.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOut.h EnsembleOutList.h Exec.h Exec_ParmStrip.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 OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Vec3.h -Exec_ParmWrite.o : Exec_ParmWrite.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 BaseIOtype.h BondSearch.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOut.h EnsembleOutList.h Exec.h Exec_ParmWrite.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 OutputTrajCommon.h Parallel.h ParameterTypes.h ParmFile.h ParmIO.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.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 BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 EnsembleOut.h EnsembleOutList.h Exec.h Exec_PermuteDihedrals.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h ImagedAction.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PairList.h Parallel.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 TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Vec3.h -Exec_Precision.o : Exec_Precision.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOut.h EnsembleOutList.h Exec.h Exec_Precision.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 OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Vec3.h -Exec_PrintData.o : Exec_PrintData.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOut.h EnsembleOutList.h Exec.h Exec_PrintData.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 OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Vec3.h -Exec_ReadData.o : Exec_ReadData.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOut.h EnsembleOutList.h Exec.h Exec_ReadData.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 OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Vec3.h -Exec_ReadEnsembleData.o : Exec_ReadEnsembleData.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOut.h EnsembleOutList.h Exec.h Exec_ReadEnsembleData.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 OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Vec3.h -Exec_ReadInput.o : Exec_ReadInput.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 BaseIOtype.h Box.h CharMask.h Cmd.h CmdList.h Command.h Control.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOut.h EnsembleOutList.h Exec.h Exec_ReadInput.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 OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h VariableArray.h Vec3.h -Exec_RotateDihedral.o : Exec_RotateDihedral.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 BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOut.h EnsembleOutList.h Exec.h Exec_RotateDihedral.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 OutputTrajCommon.h Parallel.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 TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Vec3.h -Exec_RunAnalysis.o : Exec_RunAnalysis.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 BaseIOtype.h Box.h CharMask.h Cmd.h CmdList.h Command.h Control.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOut.h EnsembleOutList.h Exec.h Exec_RunAnalysis.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 OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h VariableArray.h Vec3.h -Exec_ScaleDihedralK.o : Exec_ScaleDihedralK.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOut.h EnsembleOutList.h Exec.h Exec_ScaleDihedralK.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 OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.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 BaseIOtype.h Box.h BufferedLine.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOut.h EnsembleOutList.h Exec.h Exec_SequenceAlign.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 OutputTrajCommon.h Parallel.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 TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Vec3.h -Exec_SortEnsembleData.o : Exec_SortEnsembleData.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 EnsembleOut.h EnsembleOutList.h Exec.h Exec_SortEnsembleData.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 OutputTrajCommon.h Parallel.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 TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Vec3.h -Exec_SplitCoords.o : Exec_SplitCoords.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOut.h EnsembleOutList.h Exec.h Exec_SplitCoords.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 OutputTrajCommon.h Parallel.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 TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Vec3.h -Exec_System.o : Exec_System.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOut.h EnsembleOutList.h Exec.h Exec_System.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 OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Vec3.h -Exec_Top.o : Exec_Top.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 BaseIOtype.h BondSearch.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOut.h EnsembleOutList.h Exec.h Exec_Top.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 OutputTrajCommon.h Parallel.h ParameterTypes.h ParmFile.h ParmIO.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h TopInfo.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOut.h EnsembleOutList.h Exec.h Exec_Traj.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 OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Vec3.h -Exec_UpdateParameters.o : Exec_UpdateParameters.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 AtomTypeArray.h BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOut.h EnsembleOutList.h Exec.h Exec_UpdateParameters.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 OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Vec3.h -Exec_ViewRst.o : Exec_ViewRst.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 BaseIOtype.h Box.h BufferedLine.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOut.h EnsembleOutList.h Exec.h Exec_ViewRst.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 OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Vec3.h ViewRst.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 BaseIOtype.h Box.h CharMask.h Cmd.h CmdList.h Command.h Control.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 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 VariableArray.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 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 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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 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 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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 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 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 BaseIOtype.h Box.h CharMask.h ClusterMap.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 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 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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 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 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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 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 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 BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 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 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 BaseIOtype.h Box.h CharMask.h Cmd.h CmdList.h Command.h Control.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 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 VariableArray.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 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 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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 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 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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 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 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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.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 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 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 BaseIOtype.h Box.h CharMask.h ComplexArray.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.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 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 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 BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 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 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 BaseIOtype.h BondSearch.h Box.h CharMask.h Cmd.h CmdList.h Command.h Control.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h ParmFile.h ParmIO.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 VariableArray.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 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 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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 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 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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 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 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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 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 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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 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 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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 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 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 BaseIOtype.h BondSearch.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h ParmFile.h ParmIO.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 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 BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 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 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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 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 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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 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 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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 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 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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 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 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 BaseIOtype.h Box.h CharMask.h Cmd.h CmdList.h Command.h Control.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 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 VariableArray.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 BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 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 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 BaseIOtype.h Box.h CharMask.h Cmd.h CmdList.h Command.h Control.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 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 VariableArray.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 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 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 BaseIOtype.h Box.h BufferedLine.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 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 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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 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 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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 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 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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 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 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 BaseIOtype.h BondSearch.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 ParameterTypes.h ParmFile.h ParmIO.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 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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 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 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 AtomTypeArray.h BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.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 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 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 BaseIOtype.h Box.h BufferedLine.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 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 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 @@ -289,7 +289,7 @@ 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 AtomExtra.h AtomMask.h Box.h CharMask.h CoordinateInfo.h DistRoutines.h FileName.h Frame.h ImageRoutines.h ImageTypes.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h Vec3.h -InputTrajCommon.o : InputTrajCommon.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h Box.h CharMask.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h TrajFrameCounter.h Vec3.h +InputTrajCommon.o : InputTrajCommon.cpp CpptrajStdio.h FileName.h InputTrajCommon.h TrajFrameCounter.h KDE.o : KDE.cpp ArgList.h 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 Box.h CharMask.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h Vec3.h @@ -302,7 +302,7 @@ NC_Cmatrix.o : NC_Cmatrix.cpp CpptrajStdio.h FileName.h NC_Cmatrix.h NC_Routines NC_Routines.o : NC_Routines.cpp CpptrajStdio.h NC_Routines.h NameType.o : NameType.cpp 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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h Vec3.h +OutputTrajCommon.o : OutputTrajCommon.cpp ActionFrameCounter.h ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.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 ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.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 Box.h CharMask.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h Timer.h Topology.h Vec3.h Parallel.o : Parallel.cpp Parallel.h @@ -322,7 +322,7 @@ 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 Box.h CharMask.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 ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.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 ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.h Cmd.h CmdInput.h CmdList.h Command.h Control.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOut.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 OutputTrajCommon.h Parallel.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 TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h VariableArray.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 BaseIOtype.h Box.h CharMask.h Cmd.h CmdInput.h CmdList.h Command.h Control.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.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 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 VariableArray.h Vec3.h ReferenceAction.o : ReferenceAction.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h Box.h CharMask.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 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 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 Residue.o : Residue.cpp NameType.h Residue.h @@ -341,36 +341,36 @@ TopInfo.o : TopInfo.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.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 ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h Topology.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryFile.h TrajectoryIO.h Vec3.h -Traj_AmberCoord.o : Traj_AmberCoord.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h BufferedFrame.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FrameArray.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Topology.h Traj_AmberCoord.h TrajectoryIO.h Vec3.h -Traj_AmberNetcdf.o : Traj_AmberNetcdf.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.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 ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h Traj_AmberNetcdf.h TrajectoryIO.h Vec3.h -Traj_AmberRestart.o : Traj_AmberRestart.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h BufferedFrame.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FrameArray.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Traj_AmberRestart.h TrajectoryIO.h Vec3.h -Traj_AmberRestartNC.o : Traj_AmberRestartNC.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.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 ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h Topology.h Traj_AmberRestartNC.h TrajectoryIO.h Vec3.h -Traj_Binpos.o : Traj_Binpos.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FrameArray.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h Traj_Binpos.h TrajectoryIO.h Vec3.h -Traj_CIF.o : Traj_CIF.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h CIFfile.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FrameArray.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h Topology.h Traj_CIF.h TrajectoryIO.h Vec3.h -Traj_CharmmCor.o : Traj_CharmmCor.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FrameArray.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h Topology.h Traj_CharmmCor.h TrajectoryIO.h Vec3.h -Traj_CharmmDcd.o : Traj_CharmmDcd.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h ByteRoutines.h CharMask.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 NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h Traj_CharmmDcd.h TrajectoryIO.h Vec3.h -Traj_CharmmRestart.o : Traj_CharmmRestart.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h BufferedFrame.h BufferedLine.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FrameArray.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Traj_CharmmRestart.h TrajectoryIO.h Vec3.h -Traj_Conflib.o : Traj_Conflib.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FrameArray.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h Traj_Conflib.h TrajectoryIO.h Vec3.h -Traj_GmxTrX.o : Traj_GmxTrX.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h ByteRoutines.h CharMask.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 NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h Traj_GmxTrX.h TrajectoryIO.h Vec3.h -Traj_GmxXtc.o : Traj_GmxXtc.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.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 NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h Traj_GmxXtc.h TrajectoryIO.h Vec3.h -Traj_Gro.o : Traj_Gro.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h CharMask.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 NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h Topology.h Traj_Gro.h TrajectoryIO.h Vec3.h -Traj_Mol2File.o : Traj_Mol2File.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FrameArray.h FramePtrArray.h MaskToken.h Matrix_3x3.h Mol2File.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h Traj_Mol2File.h TrajectoryIO.h Vec3.h +TrajIOarray.o : TrajIOarray.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryFile.h TrajectoryIO.h Vec3.h +Traj_AmberCoord.o : Traj_AmberCoord.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h BufferedFrame.h CharMask.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 ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Topology.h Traj_AmberCoord.h TrajectoryIO.h Vec3.h +Traj_AmberNetcdf.o : Traj_AmberNetcdf.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.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 ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h Traj_AmberNetcdf.h TrajectoryIO.h Vec3.h +Traj_AmberRestart.o : Traj_AmberRestart.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h BufferedFrame.h CharMask.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 ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Traj_AmberRestart.h TrajectoryIO.h Vec3.h +Traj_AmberRestartNC.o : Traj_AmberRestartNC.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.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 ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h Topology.h Traj_AmberRestartNC.h TrajectoryIO.h Vec3.h +Traj_Binpos.o : Traj_Binpos.cpp Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.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 ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h Traj_Binpos.h TrajectoryIO.h Vec3.h +Traj_CIF.o : Traj_CIF.cpp Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h CIFfile.h CharMask.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 ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h Topology.h Traj_CIF.h TrajectoryIO.h Vec3.h +Traj_CharmmCor.o : Traj_CharmmCor.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.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 ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h Topology.h Traj_CharmmCor.h TrajectoryIO.h Vec3.h +Traj_CharmmDcd.o : Traj_CharmmDcd.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h ByteRoutines.h CharMask.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 ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h Traj_CharmmDcd.h TrajectoryIO.h Vec3.h +Traj_CharmmRestart.o : Traj_CharmmRestart.cpp Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h BufferedFrame.h BufferedLine.h CharMask.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 ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Traj_CharmmRestart.h TrajectoryIO.h Vec3.h +Traj_Conflib.o : Traj_Conflib.cpp Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.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 ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h Traj_Conflib.h TrajectoryIO.h Vec3.h +Traj_GmxTrX.o : Traj_GmxTrX.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h ByteRoutines.h CharMask.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 ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h Traj_GmxTrX.h TrajectoryIO.h Vec3.h +Traj_GmxXtc.o : Traj_GmxXtc.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.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 ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h Traj_GmxXtc.h TrajectoryIO.h Vec3.h +Traj_Gro.o : Traj_Gro.cpp Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h CharMask.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 ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h Topology.h Traj_Gro.h TrajectoryIO.h Vec3.h +Traj_Mol2File.o : Traj_Mol2File.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.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 ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h Traj_Mol2File.h TrajectoryIO.h Vec3.h Traj_NcEnsemble.o : Traj_NcEnsemble.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.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 ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h Traj_NcEnsemble.h TrajectoryIO.h Vec3.h -Traj_PDBfile.o : Traj_PDBfile.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DistRoutines.h FileIO.h FileName.h Frame.h FrameArray.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h Traj_PDBfile.h TrajectoryIO.h Vec3.h -Traj_SDF.o : Traj_SDF.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FrameArray.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SDFfile.h SymbolExporting.h Topology.h Traj_SDF.h TrajectoryIO.h Vec3.h -Traj_SQM.o : Traj_SQM.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FrameArray.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h Topology.h Traj_SQM.h TrajectoryIO.h Vec3.h -Traj_Tinker.o : Traj_Tinker.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FrameArray.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h TinkerFile.h Topology.h Traj_Tinker.h TrajectoryIO.h Vec3.h -Traj_XYZ.o : Traj_XYZ.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FrameArray.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Traj_XYZ.h TrajectoryIO.h Vec3.h -TrajectoryFile.o : TrajectoryFile.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h BufferedFrame.h BufferedLine.h CIFfile.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h MaskToken.h Matrix_3x3.h Mol2File.h Molecule.h NameType.h NetcdfFile.h PDBfile.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SDFfile.h SymbolExporting.h TextFormat.h TinkerFile.h Topology.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_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 -TrajectoryIO.o : TrajectoryIO.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h FileIO.h FileName.h Frame.h FrameArray.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h TrajectoryIO.h Vec3.h -TrajinList.o : TrajinList.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.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 FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.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 Vec3.h -Trajin_Multi.o : Trajin_Multi.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.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 Vec3.h -Trajin_Single.o : Trajin_Single.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Trajin.h Trajin_Single.h Vec3.h -TrajoutList.o : TrajoutList.cpp ActionFrameCounter.h ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h TrajoutList.h Trajout_Single.h Vec3.h -Trajout_Single.o : Trajout_Single.cpp ActionFrameCounter.h ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h Trajout_Single.h Vec3.h +Traj_PDBfile.o : Traj_PDBfile.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.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 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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h Traj_PDBfile.h TrajectoryIO.h Vec3.h +Traj_SDF.o : Traj_SDF.cpp Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.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 ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SDFfile.h SymbolExporting.h Topology.h Traj_SDF.h TrajectoryIO.h Vec3.h +Traj_SQM.o : Traj_SQM.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.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 ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h Topology.h Traj_SQM.h TrajectoryIO.h Vec3.h +Traj_Tinker.o : Traj_Tinker.cpp Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h CharMask.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 ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h TinkerFile.h Topology.h Traj_Tinker.h TrajectoryIO.h Vec3.h +Traj_XYZ.o : Traj_XYZ.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h BufferedLine.h CharMask.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 ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Traj_XYZ.h TrajectoryIO.h Vec3.h +TrajectoryFile.o : TrajectoryFile.cpp ArgList.h 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_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 +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 BaseIOtype.h Box.h CharMask.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 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 Vec3.h +Trajin_Multi.o : Trajin_Multi.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.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 Vec3.h +Trajin_Single.o : Trajin_Single.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.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 ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Trajin.h Trajin_Single.h Vec3.h +TrajoutList.o : TrajoutList.cpp ActionFrameCounter.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.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 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 Vec3.h +Trajout_Single.o : Trajout_Single.cpp ActionFrameCounter.h ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h Box.h CharMask.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 ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h Trajout_Single.h Vec3.h VariableArray.o : VariableArray.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.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 ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h VariableArray.h Vec3.h Vec3.o : Vec3.cpp Constants.h CpptrajStdio.h Vec3.h -ViewRst.o : ViewRst.cpp ActionFrameCounter.h ArgList.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h BondSearch.h Box.h CharMask.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h ParmFile.h ParmIO.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h Trajout_Single.h Vec3.h ViewRst.h -main.o : main.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h Cpptraj.h CpptrajFile.h CpptrajState.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOut.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 OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Vec3.h +ViewRst.o : ViewRst.cpp ActionFrameCounter.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h BaseIOtype.h BondSearch.h Box.h CharMask.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 ParameterTypes.h ParmFile.h ParmIO.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.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 BaseIOtype.h Box.h CharMask.h CoordinateInfo.h Cpptraj.h CpptrajFile.h CpptrajState.h DataFile.h DataFileList.h DataIO.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 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 Vec3.h molsurf.o : molsurf.c molsurf.h diff --git a/test/Test_AtomicFluct/RunTest.sh b/test/Test_AtomicFluct/RunTest.sh index ec901c8be3..417bd24f4e 100755 --- a/test/Test_AtomicFluct/RunTest.sh +++ b/test/Test_AtomicFluct/RunTest.sh @@ -2,13 +2,15 @@ . ../MasterTest.sh -CleanFiles atomic.in fluct.*.dat dpdp.fluct.dat dpdp.adp.dat +CleanFiles atomic.in fluct.*.dat dpdp.fluct.dat dpdp.adp.dat \ + fluct.2.pdb occ.2.pdb scale.2.pdb fluct.1.pdb TESTNAME='Atomic fluctuations tests' Requires netcdf + INPUT="atomic.in" -TOP="../tz2.parm7" WriteInput() { + TOP="../tz2.parm7" cat > $INPUT < $INPUT <