diff --git a/devtools/Template.sh b/devtools/Template.sh
index bbf82916b7..901d6bd76b 100755
--- a/devtools/Template.sh
+++ b/devtools/Template.sh
@@ -419,6 +419,7 @@ elif [ "$TYPE" = 'DataSet' ] ; then
     void Add(size_t, const void*)                          { return; }
     void WriteBuffer(CpptrajFile&, SizeArray const&) const { return; }
     int Append(DataSet*)                                   { return 1; }
+    size_t MemUsageInBytes()                         const { return 0; }
 #   ifdef MPI
     int Sync(size_t, std::vector<int> const&, Parallel::Comm const&) { return 1; }
 #   endif
diff --git a/doc/cpptraj.lyx b/doc/cpptraj.lyx
index ad71d98000..10d4db2630 100644
--- a/doc/cpptraj.lyx
+++ b/doc/cpptraj.lyx
@@ -1924,11 +1924,25 @@ script
  variables and 'for' loops.
  Script variables are referred to by a dollar sign ('$') prefix and are
  replaced when they are processed.
- Note that to use script variables in CPPTRAJ input that is also inside
- e.g.
- a BASH script, they can be escaped with the '
+ These are stored in the master data set list like other data and are assigned
+ the type 
+\begin_inset Quotes eld
+\end_inset
+
+string variable
+\begin_inset Quotes erd
+\end_inset
+
+.
+ 
+\series bold
+Note that to use script variables in CPPTRAJ input that is inside another
+ script (e.g.
+ a BASH script), they must be escaped with the '
 \backslash
-' character, e.g.
+' character,
+\series default
+ e.g.
 \end_layout
 
 \begin_layout LyX-Code
@@ -1944,13 +1958,13 @@ cpptraj <<EOF
 \end_layout
 
 \begin_layout LyX-Code
-set topname=$TOP
+set topname=$TOP # TOP is a BASH script variable
 \end_layout
 
 \begin_layout LyX-Code
 parm 
 \backslash
-$topname
+$topname   # topname is a CPPTRAJ script variable
 \end_layout
 
 \begin_layout LyX-Code
@@ -2069,14 +2083,25 @@ for { {atoms|residues|molecules|molfirstres|mollastres}
 \end_layout
 
 \begin_layout LyX-Code
-	    <var> inmask <mask> [parm <name> | parmindex <#> | <#>] ...
- |
+	    <var> inmask <mask> [parm <name> | parmindex <#> | <#>] |
 \end_layout
 
 \begin_layout LyX-Code
       <var> in <list> |
 \end_layout
 
+\begin_layout LyX-Code
+      <var> oversets <list> |
+\end_layout
+
+\begin_layout LyX-Code
+      <var> datasetblocks <set> blocksize <#> [blockoffset <#>]
+\end_layout
+
+\begin_layout LyX-Code
+        [cumulative [firstblock <#>]] |
+\end_layout
+
 \begin_layout LyX-Code
 	  <var>=<start>;[<var><end OP><end>;]<var><increment OP>[<value>] ...
  }
@@ -2087,7 +2112,7 @@ for { {atoms|residues|molecules|molfirstres|mollastres}
 \end_layout
 
 \begin_layout LyX-Code
-  Available 'end OP'       : '<' '>'
+  Available 'end OP'       : '<' '>' '<=' '>='
 \end_layout
 
 \begin_layout LyX-Code
@@ -2160,6 +2185,65 @@ in
  File name wildcards can be used.
 \end_layout
 
+\begin_layout Description
+<var>
+\begin_inset space ~
+\end_inset
+
+oversets
+\begin_inset space ~
+\end_inset
+
+<list> Loop over sets selected by comma-separated list of names.
+ Data set wildcards can be used.
+\end_layout
+
+\begin_layout Description
+<var>
+\begin_inset space ~
+\end_inset
+
+datasetblocks
+\begin_inset space ~
+\end_inset
+
+<set> Loop over blocks in specified DataSet.
+\end_layout
+
+\begin_deeper
+\begin_layout Description
+blocksize
+\begin_inset space ~
+\end_inset
+
+<#> Size of blocks to use.
+\end_layout
+
+\begin_layout Description
+[blockoffset
+\begin_inset space ~
+\end_inset
+
+<#>] Offset between blocks.
+\end_layout
+
+\begin_layout Description
+[cumulative] Instead of blocks of fixed size, use blocks of increasing size
+ incremented by blocksize.
+\end_layout
+
+\begin_deeper
+\begin_layout Description
+[firstblock
+\begin_inset space ~
+\end_inset
+
+<#>] When cumulative, the size of the first block (default is first data
+ set element).
+\end_layout
+
+\end_deeper
+\end_deeper
 \begin_layout Description
 <var>=<start>;[<var><end
 \begin_inset space ~
@@ -2188,11 +2272,32 @@ OP>[<value>] Loop over integer script variable
 .
 \end_layout
 
+\begin_layout Standard
+Data Sets Created (datasetblocks loops):
+\end_layout
+
+\begin_layout Description
+<var>[block]:<start
+\begin_inset space \space{}
+\end_inset
+
+idx> (Data set blocks only) Data set block of blocksize starting at <start
+ idx>.
+\end_layout
+
+\begin_layout Description
+<var>[cumul]:<end
+\begin_inset space ~
+\end_inset
+
+idx> (Cumulative data set blocks only) Data set block starting at firstblock
+ and ending at <end idx>.
+\end_layout
+
 \end_deeper
 \begin_layout Standard
-Create a for loop using one or more mask expressions or integers.
- Loops can be nested, but currently inner loops cannot refer to output loop
- variables.
+Create a for loop using one or more mask expressions, integers, etc.
+ Loops can be nested inside each other.
  Integer loops may be used without an end condition, but in that case at
  least one descriptor in the loop should have an end condition or refer
  to a mask.
@@ -2201,16 +2306,13 @@ Create a for loop using one or more mask expressions or integers.
 done
 \series default
  keyword.
- Note that unlike C-style for loops the variable is not incremented on the
- final execution, so the final value of 
-\series bold
-<var>
-\series default
- will be 
-\series bold
-<end>
-\series default
- (or the last selection in the mask).
+ 
+\end_layout
+
+\begin_layout Standard
+Note that non-integer variables (e.g.
+ 'inmask' loops) are NOT incremented after the final loop iteration, i.e.
+ these loop variables always retain their final value.
 \end_layout
 
 \begin_layout Standard
@@ -2383,8 +2485,24 @@ trajin
 \end_deeper
 \begin_layout Standard
 Set (<OP> = '=') or append (<OP> = '+=') a script variable.
- Script variables are referred to in CPPTRAJ input by using a dollar sign
- '$' prefix.
+ Script variables are character strings, and are referred to in CPPTRAJ
+ input by using a dollar sign '$' prefix.
+\end_layout
+
+\begin_layout Standard
+For example, the following input will load files my.parm7 and my.rst7:
+\end_layout
+
+\begin_layout LyX-Code
+set PREFIX = my
+\end_layout
+
+\begin_layout LyX-Code
+trajin $PREFIX.parm7
+\end_layout
+
+\begin_layout LyX-Code
+trajin $PREFIX.rst7
 \end_layout
 
 \begin_layout Standard
@@ -2413,11 +2531,13 @@ show
 \end_layout
 
 \begin_layout LyX-Code
-show
+show [<var1> ...]
 \end_layout
 
 \begin_layout Standard
-Show all current script variables and their values.
+If no variable names specified, show all current script variables and their
+ values.
+ Otherwise, show the values of the specified script variables.
 \end_layout
 
 \begin_layout Section
@@ -4918,7 +5038,7 @@ Write
 \end_layout
 
 \begin_layout LyX-Code
-[invert] [xydy]
+[invert] [xydy] [<label set>]
 \begin_inset Separator latexpar
 \end_inset
 
@@ -4937,6 +5057,14 @@ invert Normally, data is written out with X-values pertaining to frames
 xydy Combine consecutive pairs of sets into XYDY sets.
 \end_layout
 
+\begin_layout Description
+<label
+\begin_inset space ~
+\end_inset
+
+set> If a string dataset is specified, assume it has data point labels.
+\end_layout
+
 \end_deeper
 \begin_layout Standard
 If a single string data set is specified when writing Grace format, it is
diff --git a/src/Action_InfraredSpectrum.cpp b/src/Action_InfraredSpectrum.cpp
index c62b114a45..0118324e24 100644
--- a/src/Action_InfraredSpectrum.cpp
+++ b/src/Action_InfraredSpectrum.cpp
@@ -3,6 +3,7 @@
 #include "ProgressBar.h"
 #include "Constants.h"
 #include "DataSet_double.h"
+#include "DataSet_Vector.h"
 #include "Corr.h"
 #ifdef _OPENMP
 #  include <omp.h>
diff --git a/src/Action_InfraredSpectrum.h b/src/Action_InfraredSpectrum.h
index 218f1ac734..6f3425ce7c 100644
--- a/src/Action_InfraredSpectrum.h
+++ b/src/Action_InfraredSpectrum.h
@@ -1,7 +1,7 @@
 #ifndef INC_ACTION_INFRAREDSPECTRUM_H
 #define INC_ACTION_INFRAREDSPECTRUM_H
 #include "Action.h"
-#include "DataSet_Vector.h"
+class DataSet_Vector;
 /// <Enter description of Action_InfraredSpectrum here>
 class Action_InfraredSpectrum : public Action {
   public:
@@ -14,8 +14,7 @@ class Action_InfraredSpectrum : public Action {
     Action::RetType DoAction(int, ActionFrame&);
     void Print();
 
-    typedef DataSet_Vector VelArray;
-    VelArray* Vel_;         ///< Hold velocity*charge for selected atoms at each frame.
+    DataSet_Vector* Vel_; ///< Hold velocity*charge for selected atoms at each frame.
     DataSet* VAC_;
     AtomMask mask_;         ///< Atoms to calculate VAC fn for.
     Topology* currentTop_;
diff --git a/src/Action_Matrix.cpp b/src/Action_Matrix.cpp
index 3ed531e5e7..99156812d8 100644
--- a/src/Action_Matrix.cpp
+++ b/src/Action_Matrix.cpp
@@ -95,7 +95,7 @@ Action::RetType Action_Matrix::Init(ArgList& actionArgs, ActionInit& init, int d
       return Action::ERR;
     }
     for ( DataSetList::const_iterator DS = init.DSL().begin(); DS != init.DSL().end(); ++DS) {
-      if ( (*DS)->Type() == DataSet::VECTOR && (*DS)->Meta().ScalarType() == MetaData::IREDVEC )
+      if ( (*DS)->Group() == DataSet::VECTOR_1D && (*DS)->Meta().ScalarType() == MetaData::IREDVEC )
         IredVectors_.push_back( (DataSet_Vector*)*DS );
     }
     if (IredVectors_.empty()) {
diff --git a/src/Action_MultiVector.cpp b/src/Action_MultiVector.cpp
index c0db2a0186..47618abb97 100644
--- a/src/Action_MultiVector.cpp
+++ b/src/Action_MultiVector.cpp
@@ -1,5 +1,6 @@
 #include "Action_MultiVector.h"
 #include "CpptrajStdio.h"
+#include "DataSet_Vector.h"
 
 Action_MultiVector::Action_MultiVector() :
   debug_(0),
@@ -120,7 +121,7 @@ Action::RetType Action_MultiVector::DoAction(int frameNum, ActionFrame& frm) {
     Vec3 CXYZ( frm.Frm().CRD( CrdIdx1_[nv] ) );
     Vec3 VXYZ( frm.Frm().CRD( CrdIdx2_[nv] ) );
     VXYZ -= CXYZ;
-    data_[nv]->AddVxyz(VXYZ, CXYZ);
+    data_[nv]->AddVxyzo(VXYZ, CXYZ);
   }
 
   return Action::OK;
diff --git a/src/Action_MultiVector.h b/src/Action_MultiVector.h
index 4358c6bdad..a926ec0675 100644
--- a/src/Action_MultiVector.h
+++ b/src/Action_MultiVector.h
@@ -1,8 +1,8 @@
 #ifndef INC_MULTIVECTOR_H
 #define INC_MULTIVECTOR_H
 #include "Action.h"
-#include "DataSet_Vector.h"
 #include "Range.h"
+class DataSet_Vector;
 class Action_MultiVector : public Action {
   public:
     Action_MultiVector();
diff --git a/src/Action_Principal.cpp b/src/Action_Principal.cpp
index d8b8222e34..6967a5f562 100644
--- a/src/Action_Principal.cpp
+++ b/src/Action_Principal.cpp
@@ -1,6 +1,7 @@
 #include "Action_Principal.h"
 #include "CpptrajStdio.h"
-#include "Matrix_3x3.h"
+#include "DataSet_Mat3x3.h"
+#include "DataSet_Vector.h"
 
 // CONSTRUCTOR
 Action_Principal::Action_Principal() :
diff --git a/src/Action_Principal.h b/src/Action_Principal.h
index ee0d6da535..eb45178c82 100644
--- a/src/Action_Principal.h
+++ b/src/Action_Principal.h
@@ -1,8 +1,8 @@
 #ifndef INC_ACTION_PRINCIPAL_H
 #define INC_ACTION_PRINCIPAL_H
 #include "Action.h"
-#include "DataSet_Mat3x3.h"
-#include "DataSet_Vector.h"
+class DataSet_Mat3x3;
+class DataSet_Vector;
 class Action_Principal : public Action {
   public:
     Action_Principal();
diff --git a/src/Action_Rmsd.cpp b/src/Action_Rmsd.cpp
index 5a665e4a29..23c6b2a1d4 100644
--- a/src/Action_Rmsd.cpp
+++ b/src/Action_Rmsd.cpp
@@ -2,6 +2,7 @@
 #include "CpptrajStdio.h"
 #include "StringRoutines.h" // integerToString
 #include "DataSet_Mesh.h"
+#include "DataSet_Vector.h"
 
 // CONSTRUCTOR
 Action_Rmsd::Action_Rmsd() :
@@ -123,6 +124,10 @@ Action::RetType Action_Rmsd::Init(ArgList& actionArgs, ActionInit& init, int deb
       return Action::ERR;
     }
     tvecs_ = (DataSet_Vector*)init.DSL().AddSet(DataSet::VECTOR, md);
+    //if (tvecType_ == COMBINED)
+    //  tvecs_ = (DataSet_Vector*)init.DSL().AddSet(DataSet::VEC_XYZ, md);
+    //else // SEPARATE
+    //  tvecs_ = (DataSet_Vector*)init.DSL().AddSet(DataSet::VEC_OXYZ, md);
     if (tvecs_ == 0) return Action::ERR;
     if (vecsOut != 0) vecsOut->AddDataSet( tvecs_ );
   }
@@ -373,7 +378,7 @@ Action::RetType Action_Rmsd::DoAction(int frameNum, ActionFrame& frm) {
     if (tvecType_ == COMBINED)
       tvecs_->AddVxyz( tgtTrans_ + REF_.RefTrans() );
     else if (tvecType_ == SEPARATE)
-      tvecs_->AddVxyz( tgtTrans_, REF_.RefTrans() );
+      tvecs_->AddVxyzo( tgtTrans_, REF_.RefTrans() );
     switch (mode_) {
       case ROT_AND_TRANS:
         frm.ModifyFrm().Trans_Rot_Trans(tgtTrans_, rot_, REF_.RefTrans());
diff --git a/src/Action_Rmsd.h b/src/Action_Rmsd.h
index 3b16ae58e5..85dbf62349 100644
--- a/src/Action_Rmsd.h
+++ b/src/Action_Rmsd.h
@@ -3,8 +3,8 @@
 #include "Action.h"
 #include "Range.h"
 #include "ReferenceAction.h"
-#include "DataSet_1D.h"
-#include "DataSet_Vector.h"
+class DataSet_1D;
+class DataSet_Vector;
 /// Action to calculate the RMSD between frame and a reference frame.
 class Action_Rmsd: public Action {
   public:
diff --git a/src/Action_Vector.cpp b/src/Action_Vector.cpp
index ce75a689ce..098f5cc75e 100644
--- a/src/Action_Vector.cpp
+++ b/src/Action_Vector.cpp
@@ -4,6 +4,7 @@
 #include "Action_Vector.h"
 #include "CpptrajStdio.h"
 #include "DistRoutines.h" // MinImagedVec, includes Matrix_3x3 for principal
+#include "DataSet_Vector.h"
 
 // CONSTRUCTOR
 Action_Vector::Action_Vector() :
@@ -43,13 +44,20 @@ Action_Vector::~Action_Vector() {
   if (vcorr_!=0) delete[] vcorr_;
 }
 
-const char* Action_Vector::ModeString[] = {
+const char* Action_Vector::ModeString_[] = {
   "NO_OP", "Principal X", "Principal Y", "Principal Z",
-  "Dipole", "Box", "Mask", "Ired",
+  "Dipole", "Box", "Mask",
   "CorrPlane", "Center", "Unit cell X", "Unit cell Y", "Unit cell Z",
   "Box Center", "MinImage", "Momentum", "Velocity", "Force"
 };
 
+const bool Action_Vector::NeedsOrigin_[] = {
+  false, true, true, true,
+  true, false, true,
+  true, false, true, true, true,
+  false, true, false, false, false
+};
+
 static Action::RetType WarnDeprecated() {
   mprinterr("Error: Vector: 'corrired' and 'corr' are deprecated.\n"
             "Error: 'corrired' functionality is now part of the\n"
@@ -140,7 +148,7 @@ Action::RetType Action_Vector::Init(ArgList& actionArgs, ActionInit& init, int d
     std::string maskexpr = actionArgs.GetMaskNext();
     if (maskexpr.empty()) {
       mprinterr("Error: Specified vector mode (%s) requires a second mask.\n",
-                ModeString[ mode_ ]);
+                ModeString_[ mode_ ]);
       return Action::ERR;
     }
     if (mask2_.SetMaskString( maskexpr )) return Action::ERR;
@@ -148,7 +156,12 @@ Action::RetType Action_Vector::Init(ArgList& actionArgs, ActionInit& init, int d
   // Set up vector dataset and IRED status
   MetaData md(actionArgs.GetStringNext(), MetaData::M_VECTOR);
   if (isIred) md.SetScalarType( MetaData::IREDVEC );
-  Vec_ = (DataSet_Vector*)init.DSL().AddSet(DataSet::VECTOR, md, "Vec");
+  DataSet::DataType vtype = DataSet::VECTOR;
+  //if (NeedsOrigin_[mode_])
+  //  vtype = DataSet::VEC_OXYZ;
+  //else
+  //  vtype = DataSet::VEC_XYZ;
+  Vec_ = (DataSet_Vector*)init.DSL().AddSet(vtype, md, "Vec");
   if (Vec_ == 0) return Action::ERR;
   // Add set to output file if not doing ptraj-compatible output
   if (!ptrajoutput_ && df != 0)
@@ -160,7 +173,7 @@ Action::RetType Action_Vector::Init(ArgList& actionArgs, ActionInit& init, int d
     if (df != 0) df->AddDataSet( Magnitude_ );
   }
   
-  mprintf("    VECTOR: Type %s", ModeString[ mode_ ]);
+  mprintf("    VECTOR: Type %s", ModeString_[ mode_ ]);
   if (calc_magnitude)
     mprintf(" (with magnitude)");
   if (isIred)
@@ -193,11 +206,11 @@ Action::RetType Action_Vector::Setup(ActionSetup& setup) {
   }
   // Check for velocity/force
   if ((mode_ == MOMENTUM || mode_ == VELOCITY) && !setup.CoordInfo().HasVel()) {
-    mprintf("Warning: vector %s requires velocity information. Skipping.\n", ModeString[mode_]);
+    mprintf("Warning: vector %s requires velocity information. Skipping.\n", ModeString_[mode_]);
     return Action::SKIP;
   }
   if (mode_ == FORCE && !setup.CoordInfo().HasForce()) {
-    mprintf("Warning: vector %s requires force information. Skipping.\n", ModeString[mode_]);
+    mprintf("Warning: vector %s requires force information. Skipping.\n", ModeString_[mode_]);
     return Action::SKIP;
   }
   if (mask_.MaskStringSet()) {
@@ -344,7 +357,7 @@ void Action_Vector::Mask(Frame const& currentFrame) {
   Vec3 CXYZ = currentFrame.VCenterOfMass(mask_);
   Vec3 VXYZ = currentFrame.VCenterOfMass(mask2_);
   VXYZ -= CXYZ;
-  Vec_->AddVxyz(VXYZ, CXYZ);
+  Vec_->AddVxyzo(VXYZ, CXYZ);
 }
 
 // Action_Vector::Dipole()
@@ -364,7 +377,7 @@ void Action_Vector::Dipole(Frame const& currentFrame) {
     VXYZ += ( XYZ );
   }
   CXYZ /= total_mass;
-  Vec_->AddVxyz( VXYZ, CXYZ );
+  Vec_->AddVxyzo( VXYZ, CXYZ );
 }
 
 // Action_Vector::Principal()
@@ -376,14 +389,15 @@ void Action_Vector::Principal(Frame const& currentFrame) {
   Vec3 OXYZ = currentFrame.CalculateInertia( mask_, Inertia );
   // NOTE: Diagonalize_Sort_Chirality places sorted eigenvectors in rows.
   Inertia.Diagonalize_Sort_Chirality( Eval, 0 );
-  // Eval.Print("PRINCIPAL EIGENVALUES");
-  // Inertia.Print("PRINCIPAL EIGENVECTORS (Rows)");
+  //Eval.Print("PRINCIPAL EIGENVALUES");
+  //Inertia.Print("PRINCIPAL EIGENVECTORS (Rows)");
+  DataSet_Vector& vec = static_cast<DataSet_Vector&>( *Vec_ );
   if ( mode_ == PRINCIPAL_X ) 
-    Vec_->AddVxyz( Inertia.Row1(), OXYZ ); // First row = first eigenvector
+    vec.AddVxyzo( Inertia.Row1(), OXYZ ); // First row = first eigenvector
   else if ( mode_ == PRINCIPAL_Y )
-    Vec_->AddVxyz( Inertia.Row2(), OXYZ ); // Second row = second eigenvector
+    vec.AddVxyzo( Inertia.Row2(), OXYZ ); // Second row = second eigenvector
   else // PRINCIPAL_Z
-    Vec_->AddVxyz( Inertia.Row3(), OXYZ ); // Third row = third eigenvector
+    vec.AddVxyzo( Inertia.Row3(), OXYZ ); // Third row = third eigenvector
 }
 
 // Action_Vector::CorrPlane()
@@ -400,7 +414,7 @@ void Action_Vector::CorrPlane(Frame const& currentFrame) {
     vcorr_[idx++] = XYZ[2];
   }
   Vec3 VXYZ = leastSquaresPlane(idx, vcorr_);
-  Vec_->AddVxyz(VXYZ, CXYZ);
+  Vec_->AddVxyzo(VXYZ, CXYZ);
 }
 
 //  Action_Vector::UnitCell()
@@ -408,9 +422,9 @@ void Action_Vector::UnitCell(Box const& box) {
   Matrix_3x3 ucell, recip;
   box.ToRecip( ucell, recip );
   switch ( mode_ ) {
-    case BOX_X: Vec_->AddVxyz( ucell.Row1(), DataSet_Vector::ZERO ); break;
-    case BOX_Y: Vec_->AddVxyz( ucell.Row2(), DataSet_Vector::ZERO ); break;
-    case BOX_Z: Vec_->AddVxyz( ucell.Row3(), DataSet_Vector::ZERO ); break;
+    case BOX_X: Vec_->AddVxyzo( ucell.Row1(), Vec3(0.0) ); break;
+    case BOX_Y: Vec_->AddVxyzo( ucell.Row2(), Vec3(0.0) ); break;
+    case BOX_Z: Vec_->AddVxyzo( ucell.Row3(), Vec3(0.0) ); break;
     case BOX_CTR: Vec_->AddVxyz( ucell.TransposeMult(Vec3(0.5)) ); break;
     default: return;
   }
@@ -421,7 +435,7 @@ void Action_Vector::MinImage(Frame const& frm) {
   Matrix_3x3 ucell, recip;
   frm.BoxCrd().ToRecip( ucell, recip );
   Vec3 com1 = frm.VCenterOfMass(mask_);
-  Vec_->AddVxyz( MinImagedVec(com1, frm.VCenterOfMass(mask2_), ucell, recip), com1 );
+  Vec_->AddVxyzo( MinImagedVec(com1, frm.VCenterOfMass(mask2_), ucell, recip), com1 );
 }
 
 /// \return The center of selected elements in given array.
@@ -473,13 +487,27 @@ void Action_Vector::Print() {
     outfile_->Printf("# FORMAT: frame vx vy vz cx cy cz cx+vx cy+vy cz+vz\n"
                    "# FORMAT where v? is vector, c? is center of mass...\n");
     int totalFrames = Vec_->Size();
-    for (int i=0; i < totalFrames; ++i) {
-      Vec3 const& vxyz = (*Vec_)[i];
-      Vec3 const& cxyz = Vec_->OXYZ(i);
-      Vec3 txyz  = cxyz + vxyz;
-      outfile_->Printf("%i %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f\n",
-              i+1, vxyz[0], vxyz[1], vxyz[2], cxyz[0], cxyz[1], cxyz[2],
-              txyz[0], txyz[1], txyz[2]);
+    if (Vec_->HasOrigins()) {
+      DataSet_Vector const& vec =
+        static_cast<DataSet_Vector const&>( *Vec_ );
+      for (int i=0; i < totalFrames; ++i) {
+        Vec3 const& vxyz = vec[i];
+        Vec3 const& cxyz = vec.OXYZ(i);
+        Vec3 txyz  = cxyz + vxyz;
+        outfile_->Printf("%i %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f\n",
+                i+1, vxyz[0], vxyz[1], vxyz[2], cxyz[0], cxyz[1], cxyz[2],
+                txyz[0], txyz[1], txyz[2]);
+      }
+    } else {
+      // No origin
+      for (int i=0; i < totalFrames; ++i) {
+        Vec3 const& vxyz = (*Vec_)[i];
+        const Vec3 cxyz(0.0);
+        Vec3 txyz  = cxyz + vxyz;
+        outfile_->Printf("%i %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f\n",
+                i+1, vxyz[0], vxyz[1], vxyz[2], cxyz[0], cxyz[1], cxyz[2],
+                txyz[0], txyz[1], txyz[2]);
+      }
     }
   }
 }
diff --git a/src/Action_Vector.h b/src/Action_Vector.h
index a30dccf262..efbf91d1e3 100644
--- a/src/Action_Vector.h
+++ b/src/Action_Vector.h
@@ -1,7 +1,7 @@
 #ifndef INC_ACTION_VECTOR_H
 #define INC_ACTION_VECTOR_H
 #include "Action.h"
-#include "DataSet_Vector.h"
+class DataSet_Vector;
 class Action_Vector : public Action {
   public:
     Action_Vector();
@@ -11,11 +11,12 @@ class Action_Vector : public Action {
   private:
     enum vectorMode {
       NO_OP=0,   PRINCIPAL_X, PRINCIPAL_Y, PRINCIPAL_Z,
-      DIPOLE,    BOX,         MASK,        IRED,
+      DIPOLE,    BOX,         MASK,
       CORRPLANE, CENTER,      BOX_X,       BOX_Y,       BOX_Z,
       BOX_CTR,   MINIMAGE,    MOMENTUM,    VELOCITY,    FORCE
     };
-    static const char* ModeString[];
+    static const char* ModeString_[];
+    static const bool NeedsOrigin_[];
 
     Action::RetType Init(ArgList&, ActionInit&, int);
     Action::RetType Setup(ActionSetup&);
diff --git a/src/Analysis_AutoCorr.cpp b/src/Analysis_AutoCorr.cpp
index 5ea5fff5ce..af855a7fc3 100644
--- a/src/Analysis_AutoCorr.cpp
+++ b/src/Analysis_AutoCorr.cpp
@@ -1,6 +1,7 @@
 #include "Analysis_AutoCorr.h"
 #include "CpptrajStdio.h"
 #include "DataSet_Vector.h"
+#include "DataSet_1D.h"
 
 // CONSTRUCTOR
 Analysis_AutoCorr::Analysis_AutoCorr() :
@@ -30,7 +31,7 @@ Analysis::RetType Analysis_AutoCorr::Setup(ArgList& analyzeArgs, AnalysisSetup&
   for (ArgList::const_iterator dsa = dsetArgs.begin(); dsa != dsetArgs.end(); ++dsa) {
     DataSetList setsIn = setup.DSL().GetMultipleSets( *dsa );
     for (DataSetList::const_iterator ds = setsIn.begin(); ds != setsIn.end(); ++ds) {
-      if ( (*ds)->Group() != DataSet::SCALAR_1D && (*ds)->Type() != DataSet::VECTOR )
+      if ( (*ds)->Group() != DataSet::SCALAR_1D && (*ds)->Group() != DataSet::VECTOR_1D )
         mprintf("Warning: Set '%s' type not supported in AUTOCORR - skipping.\n",
                 (*ds)->legend());
       else
@@ -83,7 +84,7 @@ Analysis::RetType Analysis_AutoCorr::Analyze() {
   for (unsigned int ids = 0; ids != dsets_.size(); ids++) {
     mprintf("\t\tCalculating AutoCorrelation for set %s\n", dsets_[ids]->legend());
     DataSet_1D& Ct = static_cast<DataSet_1D&>( *outputData_[ids] );
-    if (dsets_[ids]->Type() == DataSet::VECTOR) {
+    if (dsets_[ids]->Group() == DataSet::VECTOR_1D) {
       DataSet_Vector const& set = static_cast<DataSet_Vector const&>( *dsets_[ids] );
       set.CalcVectorCorr( set, Ct, lagmax_ );
     } else {
diff --git a/src/Analysis_Corr.cpp b/src/Analysis_Corr.cpp
index 7099cb4f0a..94810633cd 100644
--- a/src/Analysis_Corr.cpp
+++ b/src/Analysis_Corr.cpp
@@ -1,6 +1,7 @@
 #include "Analysis_Corr.h"
 #include "CpptrajStdio.h"
 #include "DataSet_Vector.h"
+#include "DataSet_1D.h"
 
 // CONSTRUCTOR
 Analysis_Corr::Analysis_Corr() :
@@ -59,7 +60,7 @@ Analysis::RetType Analysis_Corr::Setup(ArgList& analyzeArgs, AnalysisSetup& setu
     mprinterr("Error: Corr: Could not get dataset named %s\n",D2name.c_str());
     return Analysis::ERR;
   }
-  if (D1_->Type() == DataSet::VECTOR && D2_->Type() != DataSet::VECTOR)
+  if (D1_->Group() == DataSet::VECTOR_1D && D2_->Group() != DataSet::VECTOR_1D)
   {
     mprinterr("Error: Vector cross correlation requires 2 vector data sets.\n");
     return Analysis::ERR;
@@ -76,7 +77,7 @@ Analysis::RetType Analysis_Corr::Setup(ArgList& analyzeArgs, AnalysisSetup& setu
   }
   outfile->AddDataSet( Ct_ );
   Coeff_ = 0;
-  if (D1_->Type() != DataSet::VECTOR) {
+  if (D1_->Group() != DataSet::VECTOR_1D) {
     Coeff_ = setup.DSL().AddSet( DataSet::DOUBLE, MetaData(Ct_->Meta().Name(), "coeff") );
     if (Coeff_ == 0) return Analysis::ERR;
     Coeff_->Allocate( DataSet::SizeArray(1, 1) );
@@ -121,7 +122,7 @@ Analysis::RetType Analysis_Corr::Analyze() {
   mprintf("    CORR: %zu elements, max lag %i\n",Nelements,lagmax_);
 
   Analysis::RetType err = Analysis::OK;
-  if (D1_->Type() == DataSet::VECTOR) {
+  if (D1_->Group() == DataSet::VECTOR_1D) {
     DataSet_Vector const& set1 = static_cast<DataSet_Vector const&>( *D1_ );
     DataSet_Vector const& set2 = static_cast<DataSet_Vector const&>( *D2_ );
     set1.CalcVectorCorr(set2, *((DataSet_1D*)Ct_), lagmax_);
diff --git a/src/Analysis_IRED.cpp b/src/Analysis_IRED.cpp
index 53b556daeb..ae0b4a523f 100644
--- a/src/Analysis_IRED.cpp
+++ b/src/Analysis_IRED.cpp
@@ -4,6 +4,8 @@
 #include "Corr.h"
 #include "DataSet_double.h" // Access to Resize and [] op
 #include "DataSet_MatrixDbl.h" // Access to AddElement
+#include "DataSet_Vector.h"
+#include "DataSet_Modes.h"
 #ifdef TIMER
 # include "Timer.h"
 #endif
@@ -45,7 +47,7 @@ Analysis::RetType Analysis_IRED::Setup(ArgList& analyzeArgs, AnalysisSetup& setu
   debug_ = debugIn;
   // Count and store the number of previously defined IRED vectors.
   for ( DataSetList::const_iterator DS = setup.DSL().begin(); DS != setup.DSL().end(); ++DS) {
-    if ( (*DS)->Type() == DataSet::VECTOR && (*DS)->Meta().ScalarType() == MetaData::IREDVEC)
+    if ( (*DS)->Group() == DataSet::VECTOR_1D && (*DS)->Meta().ScalarType() == MetaData::IREDVEC)
       IredVectors_.push_back( (DataSet_Vector*)*DS );
   }
   if (IredVectors_.empty()) {
diff --git a/src/Analysis_IRED.h b/src/Analysis_IRED.h
index 86e197b718..293193b5c2 100644
--- a/src/Analysis_IRED.h
+++ b/src/Analysis_IRED.h
@@ -1,8 +1,8 @@
 #ifndef INC_ANALYSIS_IRED_H
 #define INC_ANALYSIS_IRED_H
 #include "Analysis.h"
-#include "DataSet_Vector.h"
-#include "DataSet_Modes.h"
+class DataSet_Vector;
+class DataSet_Modes;
 /** \author Original Code by Alrun N. Koller & H. Gohlke
   * \author Adapted by DRR
   */
diff --git a/src/Analysis_Rotdif.cpp b/src/Analysis_Rotdif.cpp
index 1513fb4baa..57be404300 100644
--- a/src/Analysis_Rotdif.cpp
+++ b/src/Analysis_Rotdif.cpp
@@ -11,6 +11,7 @@
 #include "Corr.h"
 #include "CurveFit.h"
 #include "SimplexMin.h"
+#include "DataSet_Mat3x3.h"
 
 #ifndef NO_MATHLIB
 // Definition of Fortran subroutines called from this class
@@ -356,9 +357,10 @@ static void Diagonalize(Matrix_3x3& Mat, Vec3& Vec) {
   */
 // NOTE: Theta could also be generated in the same way as phi. Currently done
 //       to be consistent with the original implementation in randvec.F90
+// NOTE: This function cannot be const since the RNG is modified when called.
 DataSet_Vector Analysis_Rotdif::RandomVectors() {
   DataSet_Vector XYZ;
-  XYZ.ReserveVecs( nvecs_ );
+  XYZ.Allocate( DataSet::SizeArray(1, nvecs_) );
   // ----- Read nvecs vectors from a file
   if (!randvecIn_.empty()) {
     CpptrajFile vecIn;
@@ -1247,7 +1249,7 @@ int Analysis_Rotdif::DetermineDeffsAlt() {
   D_eff_.reserve( random_vectors_.Size() );
   // Hold vectors after rotation with Rmatrices
   DataSet_Vector rotated_vectors;
-  rotated_vectors.ReserveVecs( vLength );
+  rotated_vectors.Allocate( DataSet::SizeArray(1, vLength) );
   // Hold single vector autocorrelation
   CurveFit::Darray Ct;
   Ct.reserve( ctMax );
@@ -1541,7 +1543,7 @@ int Analysis_Rotdif::DetermineDeffs() {
   D_eff_.reserve( nvecs_ );
   // Allocate memory to hold rotated vectors. Need +1 since the original
   // vector is stored at position 0. 
-  rotated_vectors.ReserveVecs( itotframes + 1 );
+  rotated_vectors.Allocate( DataSet::SizeArray(1, itotframes + 1) );
   // Allocate memory for C(t)
   pY.reserve( maxdat );
   pX.reserve( maxdat );
diff --git a/src/Analysis_Rotdif.h b/src/Analysis_Rotdif.h
index a2397dc190..ec0c501b38 100644
--- a/src/Analysis_Rotdif.h
+++ b/src/Analysis_Rotdif.h
@@ -3,7 +3,7 @@
 #include "Analysis.h"
 #include "Random.h"
 #include "DataSet_Vector.h"
-#include "DataSet_Mat3x3.h"
+class DataSet_Mat3x3;
 /// Estimate rotational diffusion tensors from MD simulations
 /** To estimate rotational diffusion tensors from MD simulations along the
   * lines described by Wong & Case, (Evaluating rotational diffusion from
@@ -62,7 +62,7 @@ class Analysis_Rotdif: public Analysis {
     // Variables used by the random number generator
     Random_Number RNgen_;
 
-    DataSet_Mat3x3* Rmatrices_;      ///< Store rotation matrices
+    DataSet_Mat3x3* Rmatrices_;     ///< Store rotation matrices
     DataSet_Vector random_vectors_; ///< Hold nvecs random vectors
     std::vector<double> D_eff_;     ///< Hold calculated effective D values for each vector
 //    std::vector<double> sumc2_;      
diff --git a/src/Analysis_Timecorr.cpp b/src/Analysis_Timecorr.cpp
index 5d380d266d..d580e07a7b 100644
--- a/src/Analysis_Timecorr.cpp
+++ b/src/Analysis_Timecorr.cpp
@@ -2,6 +2,7 @@
 #include "Analysis_Timecorr.h"
 #include "CpptrajStdio.h"
 #include "DataSet_double.h"
+#include "DataSet_Vector.h"
 
 /// Strings corresponding to modes, used in output.
 const char* Analysis_Timecorr::ModeString[] = { 
@@ -97,7 +98,7 @@ Analysis::RetType Analysis_Timecorr::Setup(ArgList& analyzeArgs, AnalysisSetup&
     mprinterr("Error: no vec1 given, ignoring command\n");
     return Analysis::ERR;
   }
-  vinfo1_ = (DataSet_Vector*)setup.DSL().FindSetOfType( vec1name, DataSet::VECTOR );
+  vinfo1_ = (DataSet_Vector*)setup.DSL().FindSetOfGroup( vec1name, DataSet::VECTOR_1D );
   if (vinfo1_==0) {
     mprinterr("Error: vec1: no vector with name %s found.\n", 
               vec1name.c_str());
@@ -105,7 +106,7 @@ Analysis::RetType Analysis_Timecorr::Setup(ArgList& analyzeArgs, AnalysisSetup&
   }
   std::string vec2name = analyzeArgs.GetStringKey("vec2");
   if (!vec2name.empty()) {
-    vinfo2_ = (DataSet_Vector*)setup.DSL().FindSetOfType( vec2name, DataSet::VECTOR );
+    vinfo2_ = (DataSet_Vector*)setup.DSL().FindSetOfGroup( vec2name, DataSet::VECTOR_1D );
     if (vinfo2_==0) {
       mprinterr("Error: vec2: no vector with name %s found.\n", 
                 vec2name.c_str());
diff --git a/src/Analysis_Timecorr.h b/src/Analysis_Timecorr.h
index 4440ace1e2..6775ba4b41 100644
--- a/src/Analysis_Timecorr.h
+++ b/src/Analysis_Timecorr.h
@@ -1,8 +1,8 @@
 #ifndef INC_ANALYSIS_TIMECORR_H
 #define INC_ANALYSIS_TIMECORR_H
 #include "Analysis.h"
-#include "DataSet_Vector.h"
 #include "Corr.h"
+class DataSet_Vector;
 /** \author Original Code by Alrun N. Koller & H. Gohlke
   * \author Adapted by DRR
   */
diff --git a/src/Analysis_VectorMath.cpp b/src/Analysis_VectorMath.cpp
index 3740c235bc..18b42b3b16 100644
--- a/src/Analysis_VectorMath.cpp
+++ b/src/Analysis_VectorMath.cpp
@@ -27,14 +27,14 @@ void Analysis_VectorMath::Help() const {
 Analysis::RetType Analysis_VectorMath::Setup(ArgList& analyzeArgs, AnalysisSetup& setup, int debugIn)
 {
   // Get Vectors
-  DataSetList vsets1 = setup.DSL().GetSetsOfType( analyzeArgs.GetStringKey("vec1"),
-                                                  DataSet::VECTOR );
+  DataSetList vsets1 = setup.DSL().SelectGroupSets( analyzeArgs.GetStringKey("vec1"),
+                                                  DataSet::VECTOR_1D );
   if (vsets1.empty()) {
     mprinterr("Error: 'vec1' not found.\n");
     return Analysis::ERR;
   }
-  DataSetList vsets2 = setup.DSL().GetSetsOfType( analyzeArgs.GetStringKey("vec2"),
-                                                  DataSet::VECTOR );
+  DataSetList vsets2 = setup.DSL().SelectGroupSets( analyzeArgs.GetStringKey("vec2"),
+                                                  DataSet::VECTOR_1D );
   if (vsets2.empty()) {
     mprinterr("Error: 'vec2' not found.\n");
     return Analysis::ERR;
@@ -131,7 +131,7 @@ int Analysis_VectorMath::CrossProduct(DataSet* Dout, DataSet_Vector& V1, DataSet
 const
 {
   DataSet_Vector& Out = static_cast<DataSet_Vector&>( *Dout );
-  Out.ReserveVecs( V1.Size() );
+  Out.Allocate( DataSet::SizeArray(1, V1.Size()) );
   unsigned int v1 = 0;
   unsigned int v2 = 0;
   for (unsigned int v = 0; v < vmax; ++v, v1 += v1inc, v2 += v2inc) {
diff --git a/src/ArgList.cpp b/src/ArgList.cpp
index 35fe7584b3..3185e6cc7c 100644
--- a/src/ArgList.cpp
+++ b/src/ArgList.cpp
@@ -224,13 +224,6 @@ void ArgList::RemoveFirstArg() {
   marked_.erase( marked_.begin() );
 }
 
-/** Replace argument at position with given argument. Update ArgLine. */
-void ArgList::ChangeArg(unsigned int idx, std::string const& arg) {
-  size_t pos = argline_.find( arglist_[idx], 0 ); 
-  argline_.replace(pos, arglist_[idx].size(), arg);
-  arglist_[idx] = arg;
-}
-
 // ArgList::Command()
 /* \return pointer to the first argument
  */
diff --git a/src/ArgList.h b/src/ArgList.h
index 48729b3509..d53be09988 100644
--- a/src/ArgList.h
+++ b/src/ArgList.h
@@ -65,8 +65,6 @@ class ArgList {
     void PrintDebug() const;
     /// Remove the first argument
     void RemoveFirstArg();
-    /// Change argument at position to new argument
-    void ChangeArg(unsigned int, std::string const&);
     /// \return the first argument
     const char *Command() const;
     /// \return true if the first argument matches key
diff --git a/src/AssociatedData.cpp b/src/AssociatedData.cpp
index f5eccea427..80f791d13d 100644
--- a/src/AssociatedData.cpp
+++ b/src/AssociatedData.cpp
@@ -1,5 +1,6 @@
 #include "AssociatedData.h"
 #include "CpptrajStdio.h"
+#include "ArgList.h"
 
 const char* AssociatedData_NOE::HelpText = 
   "[bound <lower> bound <upper>] [rexp <expected>] [noe_strong] [noe_medium] [noe_weak]";
diff --git a/src/AssociatedData.h b/src/AssociatedData.h
index 82b70415bc..615e9dcc96 100644
--- a/src/AssociatedData.h
+++ b/src/AssociatedData.h
@@ -1,6 +1,6 @@
 #ifndef INC_ASSOCIATEDDATA_H
 #define INC_ASSOCIATEDDATA_H
-#include "ArgList.h"
+class ArgList;
 class AssociatedData {
   public:
     /// Destructor. Virtual since this class is inherited.
diff --git a/src/AxisType.cpp b/src/AxisType.cpp
index 54c10409ba..5cfacfaeac 100644
--- a/src/AxisType.cpp
+++ b/src/AxisType.cpp
@@ -5,6 +5,10 @@
 #include "TorsionRoutines.h" // pucker calc
 #include "Constants.h" // pucker calc
 #include "PDBfile.h" // load base reference
+#include "ArgList.h"
+#include "Topology.h"
+#include "DataSetList.h"
+#include "DataSet_1D.h"
 // ---------- NA_Reference -----------------------------------------------------
 /** Add all common variations of NA base name given single letter X:
   * DX/DX3/DX5 (not for U), RX/RX3/RX5 (not for T), X3/X5, X
diff --git a/src/AxisType.h b/src/AxisType.h
index ea307ecd22..980976a00a 100644
--- a/src/AxisType.h
+++ b/src/AxisType.h
@@ -1,8 +1,14 @@
 #ifndef INC_AXISTYPE_H
 #define INC_AXISTYPE_H
-#include "Topology.h"
-#include "DataSetList.h"
-#include "DataSet_1D.h"
+#include "Matrix_3x3.h"
+#include "Vec3.h"
+#include "Frame.h"
+#include "NameType.h"
+#include "AtomMask.h"
+class Topology;
+class DataSetList;
+class DataSet_1D;
+class FileName;
 /*! \file AxisType.h
     \brief Hold classes and functions used for NA structure analysis.
  */
diff --git a/src/Cmd.h b/src/Cmd.h
index 7cd6ad32b9..10b30180c4 100644
--- a/src/Cmd.h
+++ b/src/Cmd.h
@@ -11,8 +11,8 @@
 class Cmd {
   public:
     typedef std::vector< std::string > Sarray; // TODO put in common header?
-    /// Command destinations. EXEcute, ACTion, ANAlysis, ConTroL, BLocK, DEPrecated.
-    enum DestType { EXE = 0, ACT, ANA, CTL, BLK, DEP };
+    /// Command destinations. EXEcute, ACTion, ANAlysis, BLocK, DEPrecated.
+    enum DestType { EXE = 0, ACT, ANA, BLK, DEP };
     /// CONSTRUCTOR
     Cmd() : object_(0), dest_(EXE) {}
     /// CONSTRUCTOR - takes destination, DispatchObject pointer, and keywords.
diff --git a/src/Command.cpp b/src/Command.cpp
index b0923e42ba..92eccfac76 100644
--- a/src/Command.cpp
+++ b/src/Command.cpp
@@ -7,7 +7,8 @@
 #include "CmdInput.h"     // ProcessInput()
 #include "RPNcalc.h"
 #include "Deprecated.h"
-#include "Control.h"
+#include "ControlBlock.h"
+#include "ControlBlock_For.h"
 #include "Parallel.h"
 // ----- GENERAL ---------------------------------------------------------------
 #include "Exec_Analyze.h"
@@ -30,6 +31,8 @@
 #include "Exec_SortEnsembleData.h"
 #include "Exec_SequenceAlign.h"
 #include "Exec_ViewRst.h"
+#include "Exec_Set.h"
+#include "Exec_Show.h"
 // ----- SYSTEM ----------------------------------------------------------------
 #include "Exec_System.h"
 // ----- COORDS ----------------------------------------------------------------
@@ -193,8 +196,6 @@ Command::CtlArray Command::control_ = Command::CtlArray();
 
 int Command::ctlidx_ = -1;
 
-VariableArray Command::CurrentVars_ = VariableArray();
-
 /** Initialize all commands. Should only be called once as program starts. */
 void Command::Init() {
   // GENERAL
@@ -406,8 +407,8 @@ void Command::Init() {
   Command::AddCmd( new Analysis_Wavelet(),     Cmd::ANA, 1, "wavelet" );
   // CONTROL STRUCTURES
   Command::AddCmd( new ControlBlock_For(),     Cmd::BLK, 1, "for" );
-  Command::AddCmd( new Control_Set(),          Cmd::CTL, 1, "set" );
-  Command::AddCmd( new Control_Show(),         Cmd::CTL, 1, "show" );
+  Command::AddCmd( new Exec_Set(),             Cmd::EXE, 1, "set" );
+  Command::AddCmd( new Exec_Show(),            Cmd::EXE, 1, "show" );
   // DEPRECATED COMMANDS
   Command::AddCmd( new Deprecated_AvgCoord(),    Cmd::DEP, 1, "avgcoord" );
   Command::AddCmd( new Deprecated_DihScan(),     Cmd::DEP, 1, "dihedralscan" );
@@ -548,6 +549,7 @@ void Command::ListCommands(DispatchObject::Otype typeIn) {
     ListCommandsForType( typeIn );
 }
 
+// ----- Control block functions -----------------------------------------------
 /** \return true if any control blocks remain. */
 bool Command::UnterminatedControl() {
   if (!control_.empty()) {
@@ -563,7 +565,7 @@ bool Command::UnterminatedControl() {
 int Command::AddControlBlock(ControlBlock* ctl, CpptrajState& State, ArgList& cmdArg) {
   if ( ctl->SetupBlock( State, cmdArg ) )
     return 1;
-  if (ctlidx_ == -1) mprintf("CONTROL: Starting control block.\n");
+  if (ctlidx_ == -1) mprintf("CONTROL: Parsing control block.\n");
   control_.push_back( ctl );
   ctlidx_++;
   mprintf("  BLOCK %2i: ", ctlidx_);
@@ -578,11 +580,11 @@ int Command::AddControlBlock(ControlBlock* ctl, CpptrajState& State, ArgList& cm
 /** Execute the specified control block. */
 int Command::ExecuteControlBlock(int block, CpptrajState& State)
 {
-  control_[block]->Start();
-  ControlBlock::DoneType ret = control_[block]->CheckDone(CurrentVars_);
+  if (control_[block]->Start(State.DSL())) return 1;
+  ControlBlock::DoneType ret = control_[block]->CheckDone(State.DSL());
   if (State.Debug() > 0) {
     mprintf("DEBUG: Start: CurrentVars:");
-    CurrentVars_.PrintVariables();
+    State.DSL().ListStringVar();
   }
   while (ret == ControlBlock::NOT_DONE) {
     for (ControlBlock::const_iterator it = control_[block]->begin();
@@ -597,12 +599,14 @@ int Command::ExecuteControlBlock(int block, CpptrajState& State)
         if ( ExecuteCommand(State, *it) != CpptrajState::OK ) return 1;
       }
     }
-    ret = control_[block]->CheckDone(CurrentVars_);
+    ret = control_[block]->CheckDone(State.DSL());
   }
   if (ret == ControlBlock::ERROR) return 1;
   return 0;
 }
 
+// ----- END Control block functions -------------------------------------------
+
 /** Handle the given command. If inside a control block, if the command is
   * a control command a new block will be created, otherwise the command will
   * be added to the current control block. Once all control blocks are
@@ -662,14 +666,26 @@ CpptrajState::RetType Command::Dispatch(CpptrajState& State, std::string const&
 #undef NEW_BLOCK
 
 /** Search for the given command and execute it. Replace any variables in
-  * command with their values. EXE and CTL commands are executed immediately
+  * command with their values. EXE commands are executed immediately
   * and then freed. ACT and ANA commands are sent to the CpptrajState for later
   * execution. BLK commands set up control blocks which will be executed when
   * the outer control block is completed.
+  * TODO just take a string and do all tokenizing here?
   */
 CpptrajState::RetType Command::ExecuteCommand( CpptrajState& State, ArgList const& cmdArgIn ) {
   // Replace variable names in command with entries from CurrentVars
-  ArgList cmdArg = CurrentVars_.ReplaceVariables( cmdArgIn, State.DSL(), State.Debug() );
+  ArgList cmdArg;
+  std::string argline2;
+  int nReplaced = State.DSL().ReplaceVariables( argline2, cmdArgIn.ArgLineStr() );
+  // TODO trap replace errors?
+  if (nReplaced > 0) {
+    if (State.Debug() > 0)
+      mprintf("DEBUG: %i variables replaced with values in: '%s'\n",
+        nReplaced, cmdArgIn.ArgLine());
+    cmdArg = ArgList(argline2);
+    cmdArg.MarkArg(0);
+  } else
+    cmdArg = cmdArgIn;
   if (cmdArg.empty()) return CpptrajState::ERR;
   // Print modified command
   mprintf("  [%s]\n", cmdArg.ArgLine());
@@ -691,10 +707,6 @@ CpptrajState::RetType Command::ExecuteCommand( CpptrajState& State, ArgList cons
   } else {
     DispatchObject* obj = cmd.Alloc();
     switch (cmd.Destination()) {
-      case Cmd::CTL:
-        ret_val = ((Control*)obj)->SetupControl(State, cmdArg, CurrentVars_);
-        delete obj;
-        break;
       case Cmd::BLK:
         if (AddControlBlock( (ControlBlock*)obj, State, cmdArg )) {
           delete obj;
diff --git a/src/Command.h b/src/Command.h
index 2d9ea426b7..037386c4c8 100644
--- a/src/Command.h
+++ b/src/Command.h
@@ -2,7 +2,7 @@
 #define INC_COMMAND_H
 #include "CmdList.h"
 #include "CpptrajState.h"
-#include "Control.h"
+class ControlBlock;
 class Command {
   public:
     static void Init();
@@ -44,7 +44,5 @@ class Command {
     typedef std::vector<ControlBlock*> CtlArray;
     static CtlArray control_; ///< Array of control blocks
     static int ctlidx_;       ///< Point to current control block
-    /// Array of script variables and their current values.
-    static VariableArray CurrentVars_;
 };
 #endif
diff --git a/src/Control.cpp b/src/Control.cpp
deleted file mode 100644
index e299cedfc1..0000000000
--- a/src/Control.cpp
+++ /dev/null
@@ -1,468 +0,0 @@
-#include <algorithm> // std::min
-#include "Control.h"
-#include "CpptrajStdio.h"
-#include "StringRoutines.h"
-
-void ControlBlock_For::Help() const {
-  mprintf("\t{ {atoms|residues|molecules|molfirstres|mollastres}\n"
-          "\t    <var> inmask <mask> [%s] ... |\n"
-          "\t    <var> in <list>\n"
-          "\t  <var>=<start>;[<var><end OP><end>;]<var><increment OP>[<value>] ... }\n",
-          DataSetList::TopIdxArgs);
-  mprintf("\tEND KEYWORD: 'done'\n");
-  mprintf("  Create a 'for' loop around specified mask(s), comma-separated list of\n"
-          "  strings and/or integer value(s). Any number and combination of masks,\n"
-          "  lists, and integers can be specified. Strings in lists can be file\n"
-          "  names containing wildcard characters ('*' or '?').\n"
-          "  Variables created in the for loop can be referenced by prefacing\n"
-          "  the name with a '$' character.\n"
-          "  Available 'end OP'       : '<' '>'\n"
-          "  Available 'increment OP' : '++', '--', '+=', '-='\n"
-          "  Note that variables are NOT incremented after the final loop iteration,\n"
-          "  i.e. loop variables always retain their final value.\n"
-          "  Examples:\n"
-          "\tfor atoms A0 inmask :1-27&!@H= i=1;i++\n"
-          "\t  distance d$i :TCS $A0 out $i.dat\n"
-          "\tdone\n"
-          "\tfor TRAJ in trajA*.nc,trajB*.nc\n"
-          "\t  trajin $TRAJ 1 last 10\n"
-          "\tdone\n"
-          );
-}
-
-/** Set up each mask/integer loop. */
-int ControlBlock_For::SetupBlock(CpptrajState& State, ArgList& argIn) {
-  mprintf("    Setting up 'for' loop.\n");
-  Vars_.clear();
-  Topology* currentTop = 0;
-  static const char* TypeStr[] = { "ATOMS ", "RESIDUES ", "MOLECULES ",
-                                   "MOL_FIRST_RES ", "MOL_LAST_RES " };
-  static const char* OpStr[] = {"+=", "-=", "<", ">"};
-  description_.assign("for (");
-  int MaxIterations = -1;
-  int iarg = 0;
-  while (iarg < argIn.Nargs())
-  {
-    // Advance to next unmarked argument.
-    while (iarg < argIn.Nargs() && argIn.Marked(iarg)) iarg++;
-    if (iarg == argIn.Nargs()) break;
-    // Determine 'for' type
-    ForType ftype = UNKNOWN;
-    bool isMaskFor = true;
-    int argToMark = iarg;
-    if      ( argIn[iarg] == "atoms"       ) ftype = ATOMS;
-    else if ( argIn[iarg] == "residues"    ) ftype = RESIDUES;
-    else if ( argIn[iarg] == "molecules"   ) ftype = MOLECULES;
-    else if ( argIn[iarg] == "molfirstres" ) ftype = MOLFIRSTRES;
-    else if ( argIn[iarg] == "mollastres"  ) ftype = MOLLASTRES;
-    else if ( argIn[iarg].find(";") != std::string::npos ) {
-      isMaskFor = false;
-      ftype = INTEGER;
-    }
-    // If type is still unknown, check for list.
-    if (ftype == UNKNOWN) {
-      if (iarg+1 < argIn.Nargs() && argIn[iarg+1] == "in") {
-        ftype = LIST;
-        isMaskFor = false;
-        argToMark = iarg+1;
-      }
-    }
-    // Exit if type could not be determined.
-    if (ftype == UNKNOWN) {
-      mprinterr("Error: for loop type not specfied.\n");
-      return 1;
-    }
-    argIn.MarkArg(argToMark);
-    Vars_.push_back( LoopVar() );
-    LoopVar& MH = Vars_.back();
-    int Niterations = -1;
-    // Set up for specific type
-    if (description_ != "for (") description_.append(", ");
-    // -------------------------------------------
-    if (isMaskFor)
-    {
-      // {atoms|residues|molecules} <var> inmask <mask> [TOP KEYWORDS]
-      if (argIn[iarg+2] != "inmask") {
-        mprinterr("Error: Expected 'inmask', got %s\n", argIn[iarg+2].c_str());
-        return 1;
-      }
-      AtomMask currentMask;
-      if (currentMask.SetMaskString( argIn.GetStringKey("inmask") )) return 1;
-      MH.varType_ = ftype;
-      Topology* top = State.DSL().GetTopByIndex( argIn );
-      if (top != 0) currentTop = top;
-      if (currentTop == 0) return 1;
-      MH.varname_ = argIn.GetStringNext();
-      if (MH.varname_.empty()) {
-        mprinterr("Error: 'for inmask': missing variable name.\n");
-        return 1;
-      }
-      MH.varname_ = "$" + MH.varname_;
-      // Set up mask
-      if (currentTop->SetupIntegerMask( currentMask )) return 1;
-      currentMask.MaskInfo();
-      if (currentMask.None()) return 1;
-      // Set up indices
-      if (MH.varType_ == ATOMS)
-        MH.Idxs_ = currentMask.Selected();
-      else if (MH.varType_ == RESIDUES) {
-        int curRes = -1;
-        for (AtomMask::const_iterator at = currentMask.begin(); at != currentMask.end(); ++at) {
-          int res = (*currentTop)[*at].ResNum();
-          if (res != curRes) {
-            MH.Idxs_.push_back( res );
-            curRes = res;
-          }
-        }
-      } else if (MH.varType_ == MOLECULES ||
-                 MH.varType_ == MOLFIRSTRES ||
-                 MH.varType_ == MOLLASTRES)
-      {
-        int curMol = -1;
-        for (AtomMask::const_iterator at = currentMask.begin(); at != currentMask.end(); ++at) {
-          int mol = (*currentTop)[*at].MolNum();
-          if (mol != curMol) {
-            if (MH.varType_ == MOLECULES)
-              MH.Idxs_.push_back( mol );
-            else {
-              int res;
-              if (MH.varType_ == MOLFIRSTRES)
-                res = (*currentTop)[ currentTop->Mol( mol ).BeginAtom() ].ResNum();
-              else // MOLLASTRES
-                res = (*currentTop)[ currentTop->Mol( mol ).EndAtom()-1 ].ResNum();
-              MH.Idxs_.push_back( res );
-            }
-            curMol = mol;
-          }
-        }
-      }
-      Niterations = (int)MH.Idxs_.size();
-      description_.append(std::string(TypeStr[MH.varType_]) +
-                        MH.varname_ + " inmask " + currentMask.MaskExpression());
-    // -------------------------------------------
-    } else if (ftype == INTEGER) {
-      // [<var>=<start>;[<var><OP><end>;]<var><OP>[<value>]]
-      MH.varType_ = ftype;
-      ArgList varArg( argIn[iarg], ";" );
-      if (varArg.Nargs() < 2 || varArg.Nargs() > 3) {
-        mprinterr("Error: Malformed 'for' loop variable.\n"
-                  "Error: Expected '[<var>=<start>;[<var><OP><end>;]<var><OP>[<value>]]'\n"
-                  "Error: Got '%s'\n", argIn[iarg].c_str());
-        return 1;
-      }
-      // First argument: <var>=<start>
-      ArgList startArg( varArg[0], "=" );
-      if (startArg.Nargs() != 2) {
-        mprinterr("Error: Malformed 'start' argument.\n"
-                  "Error: Expected <var>=<start>, got '%s'\n", varArg[0].c_str());
-        return 1;
-      }
-      MH.varname_ = startArg[0];
-      if (!validInteger(startArg[1])) {
-        // TODO allow variables
-        mprinterr("Error: Start argument must be an integer.\n");
-        return 1;
-      } else
-        MH.start_ = convertToInteger(startArg[1]);
-      // Second argument: <var><OP><end>
-      size_t pos0 = MH.varname_.size();
-      size_t pos1 = pos0 + 1;
-      MH.endOp_ = NO_OP;
-      int iargIdx = 1;
-      if (varArg.Nargs() == 3) {
-        iargIdx = 2;
-        if ( varArg[1][pos0] == '<' )
-          MH.endOp_ = LESS_THAN;
-        else if (varArg[1][pos0] == '>')
-          MH.endOp_ = GREATER_THAN;
-        if (MH.endOp_ == NO_OP) {
-          mprinterr("Error: Unrecognized end op: '%s'\n",
-                    varArg[1].substr(pos0, pos1-pos0).c_str());
-          return 1;
-        }
-        std::string endStr = varArg[1].substr(pos1);
-        if (!validInteger(endStr)) {
-          // TODO allow variables
-          mprinterr("Error: End argument must be an integer.\n");
-          return 1;
-        } else
-          MH.end_ = convertToInteger(endStr);
-      }
-      // Third argument: <var><OP>[<value>]
-      pos1 = pos0 + 2;
-      MH.incOp_ = NO_OP;
-      bool needValue = false;
-      if ( varArg[iargIdx][pos0] == '+' ) {
-        if (varArg[iargIdx][pos0+1] == '+') {
-          MH.incOp_ = INCREMENT;
-          MH.inc_ = 1;
-        } else if (varArg[iargIdx][pos0+1] == '=') {
-          MH.incOp_ = INCREMENT;
-          needValue = true;
-        }
-      } else if ( varArg[iargIdx][pos0] == '-' ) {
-        if (varArg[iargIdx][pos0+1] == '-' ) {
-          MH.incOp_ = DECREMENT;
-          MH.inc_ = 1;
-        } else if (varArg[iargIdx][pos0+1] == '=') {
-          MH.incOp_ = DECREMENT;
-          needValue = true;
-        }
-      }
-      if (MH.incOp_ == NO_OP) {
-        mprinterr("Error: Unrecognized increment op: '%s'\n",
-                  varArg[iargIdx].substr(pos0, pos1-pos0).c_str());
-        return 1;
-      }
-      if (needValue) {
-        std::string incStr = varArg[iargIdx].substr(pos1);
-        if (!validInteger(incStr)) {
-          mprinterr("Error: increment value is not a valid integer.\n");
-          return 1;
-        }
-        MH.inc_ = convertToInteger(incStr);
-        if (MH.inc_ < 1) {
-          mprinterr("Error: Extra '-' detected in increment.\n");
-          return 1;
-        }
-      }
-      // Description
-      MH.varname_ = "$" + MH.varname_;
-      std::string sval = integerToString(MH.start_);
-      description_.append("(" + MH.varname_ + "=" + sval + "; ");
-      std::string eval;
-      if (iargIdx == 2) {
-        // End argument present
-        eval = integerToString(MH.end_);
-        description_.append(MH.varname_ + std::string(OpStr[MH.endOp_]) + eval + "; ");
-        // Check end > start for increment, start > end for decrement
-        int maxval, minval;
-        if (MH.incOp_ == INCREMENT) {
-          if (MH.start_ >= MH.end_) {
-            mprinterr("Error: start must be less than end for increment.\n");
-            return 1;
-          }
-          minval = MH.start_;
-          maxval = MH.end_;
-        } else {
-          if (MH.end_ >= MH.start_) {
-            mprinterr("Error: end must be less than start for decrement.\n");
-            return 1;
-          }
-          minval = MH.end_;
-          maxval = MH.start_;
-        }
-        // Figure out number of iterations
-        Niterations = (maxval - minval) / MH.inc_;
-        if (((maxval-minval) % MH.inc_) > 0) Niterations++;
-      }
-      description_.append( MH.varname_ + std::string(OpStr[MH.incOp_]) +
-                           integerToString(MH.inc_) + ")" );
-      // If decrementing just negate value
-      if (MH.incOp_ == DECREMENT)
-        MH.inc_ = -MH.inc_;
-      // DEBUG
-      //mprintf("DEBUG: start=%i endOp=%i end=%i incOp=%i val=%i startArg=%s endArg=%s\n",
-      //        MH.start_, (int)MH.endOp_, MH.end_, (int)MH.incOp_, MH.inc_,
-      //        MH.startArg_.c_str(), MH.endArg_.c_str());
-    // -------------------------------------------
-    } else if (ftype == LIST) {
-      // <var> in <string0>[,<string1>...]
-      MH.varType_ = ftype;
-      // Variable name
-      MH.varname_ = argIn.GetStringNext();
-      if (MH.varname_.empty()) {
-        mprinterr("Error: 'for in': missing variable name.\n");
-        return 1;
-      }
-      MH.varname_ = "$" + MH.varname_;
-      // Comma-separated list of strings
-      std::string listArg = argIn.GetStringNext();
-      if (listArg.empty()) {
-        mprinterr("Error: 'for in': missing comma-separated list of strings.\n");
-        return 1;
-      }
-      ArgList list(listArg, ",");
-      if (list.Nargs() < 1) {
-        mprinterr("Error: Could not parse '%s' for 'for in'\n", listArg.c_str());
-        return 1;
-      }
-      for (int il = 0; il != list.Nargs(); il++) {
-        // Check if file name expansion should occur
-        if (list[il].find_first_of("*?") != std::string::npos) {
-          File::NameArray files = File::ExpandToFilenames( list[il] );
-          for (File::NameArray::const_iterator fn = files.begin(); fn != files.end(); ++fn)
-            MH.List_.push_back( fn->Full() );
-        } else
-          MH.List_.push_back( list[il] );
-      }
-      Niterations = (int)MH.List_.size();
-      // Description
-      description_.append( MH.varname_ + " in " + listArg );
-
-    }
-    // Check number of values
-    if (MaxIterations == -1)
-      MaxIterations = Niterations;
-    else if (Niterations != -1 && Niterations != MaxIterations) {
-      mprintf("Warning: # iterations %i != previous # iterations %i\n",
-              Niterations, MaxIterations);
-      MaxIterations = std::min(Niterations, MaxIterations);
-    }
-  }
-  mprintf("\tLoop will execute for %i iterations.\n", MaxIterations);
-  if (MaxIterations < 1) {
-    mprinterr("Error: Loop has less than 1 iteration.\n");
-    return 1; 
-  }
-  description_.append(") do");
-
-  return 0;
-}
-
-/** For each mask initialize iterator. For each integer set to start value. */
-void ControlBlock_For::Start() {
-  for (Marray::iterator MH = Vars_.begin(); MH != Vars_.end(); ++MH) {
-    if (MH->varType_ == INTEGER)
-      MH->currentVal_ = MH->start_; // TODO search currentvars
-    else if ( MH->varType_ == LIST)
-      MH->sdx_ = MH->List_.begin();
-    else
-      MH->idx_ = MH->Idxs_.begin();
-  }
-}
-
-/** For each mask check if done, then update CurrentVars, then increment. */
-ControlBlock::DoneType ControlBlock_For::CheckDone(Varray& CurrentVars) {
-  static const char* prefix[] = {"@", ":", "^", ":", ":"};
-  for (Marray::iterator MH = Vars_.begin(); MH != Vars_.end(); ++MH) {
-    // Exit as soon as one is done TODO check all?
-    if (MH->varType_ == INTEGER) {
-      if (MH->endOp_ == LESS_THAN) {
-        if (MH->currentVal_ >= MH->end_) return DONE;
-      } else if (MH->endOp_ == GREATER_THAN) {
-        if (MH->currentVal_ <= MH->end_) return DONE;
-      }
-      // Get variable value and update CurrentVars
-      CurrentVars.UpdateVariable( MH->varname_, integerToString( MH->currentVal_ ));
-      // Increment
-      MH->currentVal_ += MH->inc_;
-    } else if (MH->varType_ == LIST) {
-      if (MH->sdx_ == MH->List_.end()) return DONE;
-      // Get variable value
-      CurrentVars.UpdateVariable( MH->varname_, *(MH->sdx_) );
-      // Increment
-      ++(MH->sdx_);
-    } else {
-      if (MH->idx_ == MH->Idxs_.end()) return DONE;
-      // Get variable value
-      std::string maskStr = prefix[MH->varType_] + integerToString(*(MH->idx_) + 1);
-      //mprintf("DEBUG: ControlBlock_For: %s\n", maskStr.c_str());
-      // Update CurrentVars
-      CurrentVars.UpdateVariable( MH->varname_, maskStr );
-      // Increment
-      ++(MH->idx_);
-    }
-  }
-  return NOT_DONE;
-}
-
-// =============================================================================
-void Control_Set::Help() const {
-  mprintf("\t{ <variable> <OP> <value> |\n"
-          "\t  <variable> <OP> {atoms|residues|molecules} inmask <mask>\n"
-          "\t    [%s]\n"
-          "\t  <variable> <OP> trajinframes }\n",
-          DataSetList::TopIdxArgs);
-  mprintf("  Set (<OP> = '=') or append (<OP> = '+=') a script variable.\n"
-          "  - Set script variable <variable> to value <value>.\n"
-          "  - Set script variable to the number of atoms/residues/molecules in\n"
-          "     the given atom mask.\n"
-          "  - Set script variable to the current number of frames that will\n"
-          "     be read from all previous 'trajin' statements.\n");
-}
-
-/** Set up variable with value. In this case allow any amount of whitespace,
-  * so re-tokenize the original argument line (minus the command).
-  */
-CpptrajState::RetType
-  Control_Set::SetupControl(CpptrajState& State, ArgList& argIn, Varray& CurrentVars)
-{
-  ArgList remaining = argIn.RemainingArgs();
-  size_t pos0 = remaining.ArgLineStr().find_first_of("=");
-  if (pos0 == std::string::npos) {
-    mprinterr("Error: Expected <var>=<value>\n");
-    return CpptrajState::ERR;
-  }
-  size_t pos1 = pos0;
-  bool append = false;
-  if (pos0 > 0 && remaining.ArgLineStr()[pos0-1] == '+') {
-    pos0--;
-    append = true;
-  }
-  std::string variable = NoWhitespace( remaining.ArgLineStr().substr(0, pos0) );
-  if (variable.empty()) {
-    mprinterr("Error: No variable name.\n");
-    return CpptrajState::ERR;
-  }
-  ArgList equals( NoLeadingWhitespace(remaining.ArgLineStr().substr(pos1+1)) );
-  std::string value;
-  if (equals.Contains("inmask")) {
-    AtomMask mask( equals.GetStringKey("inmask") );
-    Topology* top = State.DSL().GetTopByIndex( equals );
-    if (top == 0) return CpptrajState::ERR;
-    if (top->SetupIntegerMask( mask )) return CpptrajState::ERR;
-    if (equals.hasKey("atoms"))
-      value = integerToString( mask.Nselected() );
-    else if (equals.hasKey("residues")) {
-      int curRes = -1;
-      int nres = 0;
-      for (AtomMask::const_iterator at = mask.begin(); at != mask.end(); ++at) {
-        int res = (*top)[*at].ResNum();
-        if (res != curRes) {
-          nres++;
-          curRes = res;
-        }
-      }
-      value = integerToString( nres );
-    } else if (equals.hasKey("molecules")) {
-      int curMol = -1;
-      int nmol = 0;
-      for (AtomMask::const_iterator at = mask.begin(); at != mask.end(); ++at) {
-        int mol = (*top)[*at].MolNum();
-        if (mol != curMol) {
-          nmol++;
-          curMol = mol;
-        }
-      }
-      value = integerToString( nmol );
-    } else {
-      mprinterr("Error: Expected 'atoms', 'residues', or 'molecules'.\n");
-      return CpptrajState::ERR;
-    }
-  } else if (equals.hasKey("trajinframes")) {
-    value = integerToString(State.InputTrajList().MaxFrames());
-  } else
-    value = equals.ArgLineStr();
-  if (append)
-    CurrentVars.AppendVariable( "$" + variable, value );
-  else
-    CurrentVars.UpdateVariable( "$" + variable, value );
-  mprintf("\tVariable '%s' set to '%s'\n", variable.c_str(), value.c_str());
-  for (int iarg = 0; iarg < argIn.Nargs(); iarg++)
-    argIn.MarkArg( iarg );
-  return CpptrajState::OK;
-}
-
-// -----------------------------------------------------------------------------
-void Control_Show::Help() const {
-  mprintf("  Show all current script variables and their values.\n");
-}
-
-CpptrajState::RetType
-  Control_Show::SetupControl(CpptrajState& State, ArgList& argIn, Varray& CurrentVars)
-{
-  for (Varray::const_iterator it = CurrentVars.begin(); it != CurrentVars.end(); ++it)
-    mprintf("\t%s = '%s'\n", it->first.c_str(), it->second.c_str());
-  return CpptrajState::OK;
-}
diff --git a/src/Control.h b/src/Control.h
deleted file mode 100644
index 09eb0157f2..0000000000
--- a/src/Control.h
+++ /dev/null
@@ -1,107 +0,0 @@
-#ifndef INC_CONTROL_H
-#define INC_CONTROL_H
-#include "CpptrajState.h"
-#include "VariableArray.h"
-/// Control block structures.
-class ControlBlock : public DispatchObject {
-  public:
-    typedef std::vector<ArgList> ArgArray;
-    typedef ArgArray::const_iterator const_iterator;
-    /// Hold variable/value pairs
-    typedef VariableArray Varray;
-    /// Control block states
-    enum DoneType { DONE = 0, NOT_DONE, ERROR };
-
-    ControlBlock() : DispatchObject(CONTROL) {}
-    virtual ~ControlBlock() {}
-    /// \return Description of control block.
-    std::string const& Description() const { return description_; }
-    /// Set up control block.
-    virtual int SetupBlock(CpptrajState&, ArgList&) = 0;
-    /// Check for control block end command.
-    virtual bool EndBlock(ArgList const&) const = 0;
-    /// Add command to control block.
-    virtual void AddCommand(ArgList const&) = 0;
-    /// \return iterator to first command in the block.
-    virtual const_iterator begin() const = 0;
-    /// \return iterator to last command in the block.
-    virtual const_iterator end() const = 0;
-    /// Start control block. Init internal variables if necessary.
-    virtual void Start() = 0;
-    /// Add/update variables and increment, check block state.
-    virtual DoneType CheckDone(Varray&) = 0;
-  protected:
-    std::string description_; ///< Describe control TODO private?
-};
-
-/// Loop over mask expression or integer 
-class ControlBlock_For : public ControlBlock {
-  public:
-    ControlBlock_For() {}
-    void Help() const;
-    DispatchObject* Alloc() const { return (DispatchObject*)new ControlBlock_For(); }
-
-    int SetupBlock(CpptrajState&, ArgList&);
-    bool EndBlock(ArgList const& a) const { return (a.CommandIs("done")); }
-    void AddCommand(ArgList const& c) { commands_.push_back(c); }
-    const_iterator begin() const { return commands_.begin(); }
-    const_iterator end()   const { return commands_.end();   }
-    void Start();
-    DoneType CheckDone(Varray&);
-  private:
-    enum ForType {ATOMS=0, RESIDUES, MOLECULES, MOLFIRSTRES, MOLLASTRES, INTEGER, LIST, UNKNOWN};
-    enum OpType { INCREMENT=0, DECREMENT, LESS_THAN, GREATER_THAN, NO_OP };
-    typedef std::vector<int> Iarray;
-    typedef std::vector<std::string> Sarray;
-    class LoopVar {
-      public:
-      LoopVar() : varType_(UNKNOWN) {}
-      Iarray Idxs_;                ///< (MASK only) Selected atom/residue/molecule indices
-      Iarray::const_iterator idx_; ///< (MASK only) Current atom/residue/molecule index
-      Sarray List_;                ///< (LIST only) List of strings to iterate over.
-      Sarray::const_iterator sdx_; ///< (LIST only) Iterator to current list item.
-      std::string varname_;        ///< Loop variable name
-      ForType varType_;            ///< Loop variable type
-      OpType endOp_;               ///< (INTEGER only) end operator
-      OpType incOp_;               ///< (INTEGER only) increment operator
-      int start_;                  ///< (INTEGER only) initial value
-      int end_;                    ///< (INTEGER only) end value
-      int inc_;                    ///< (INTEGER only) increment value
-      int currentVal_;             ///< (INTEGER only) current value
-    };
-    typedef std::vector<LoopVar> Marray;
-    Marray Vars_;
-    ArgArray commands_;
-};
-// =============================================================================
-/// Work with script variables
-class Control : public DispatchObject {
-  public:
-    /// Hold variable/value pairs
-    typedef VariableArray Varray;
-
-    Control() : DispatchObject(CONTROL) {}
-    virtual ~Control() {}
-    virtual CpptrajState::RetType SetupControl(CpptrajState&, ArgList&, Varray&) = 0;
-};
-
-/// Create/update script variables
-class Control_Set : public Control {
-  public:
-    Control_Set() {}
-    void Help() const;
-    DispatchObject* Alloc() const { return (DispatchObject*)new Control_Set(); }
-
-    CpptrajState::RetType SetupControl(CpptrajState&, ArgList&, Varray&);
-};
-
-/// List all variables and values.
-class Control_Show : public Control {
-  public:
-    Control_Show() {}
-    void Help() const;
-    DispatchObject* Alloc() const { return (DispatchObject*)new Control_Show(); }
-
-    CpptrajState::RetType SetupControl(CpptrajState&, ArgList&, Varray&);
-};
-#endif
diff --git a/src/ControlBlock.h b/src/ControlBlock.h
new file mode 100644
index 0000000000..160705b387
--- /dev/null
+++ b/src/ControlBlock.h
@@ -0,0 +1,38 @@
+#ifndef INC_CONTROLBLOCK_H
+#define INC_CONTROLBLOCK_H
+#include <vector>
+#include <string>
+#include "DispatchObject.h"
+class CpptrajState;
+class DataSetList;
+class ArgList;
+/// Abstract base class for control block structures.
+class ControlBlock : public DispatchObject {
+  public:
+    typedef std::vector<ArgList> ArgArray;
+    typedef ArgArray::const_iterator const_iterator;
+    /// Control block states
+    enum DoneType { DONE = 0, NOT_DONE, ERROR };
+
+    ControlBlock() : DispatchObject(CONTROL) {}
+    virtual ~ControlBlock() {}
+    /// \return Description of control block.
+    std::string const& Description() const { return description_; }
+    /// Set up control block.
+    virtual int SetupBlock(CpptrajState&, ArgList&) = 0;
+    /// Check for control block end command.
+    virtual bool EndBlock(ArgList const&) const = 0;
+    /// Add command to control block.
+    virtual void AddCommand(ArgList const&) = 0;
+    /// \return iterator to first command in the block.
+    virtual const_iterator begin() const = 0;
+    /// \return iterator to last command in the block.
+    virtual const_iterator end() const = 0;
+    /// Start control block. Init internal variables if necessary.
+    virtual int Start(DataSetList const&) = 0;
+    /// Add/update variables and increment, check block state, create sets if needed
+    virtual DoneType CheckDone(DataSetList&) = 0;
+  protected:
+    std::string description_; ///< Describe control TODO private?
+};
+#endif
diff --git a/src/ControlBlock_For.cpp b/src/ControlBlock_For.cpp
new file mode 100644
index 0000000000..7decc9056c
--- /dev/null
+++ b/src/ControlBlock_For.cpp
@@ -0,0 +1,203 @@
+#include <algorithm> // std::min
+#include "ControlBlock_For.h"
+#include "CpptrajStdio.h"
+#include "ArgList.h"
+#include "CpptrajState.h"
+// For loop types
+#include "ForLoop.h"
+#include "ForLoop_integer.h"
+#include "ForLoop_mask.h"
+#include "ForLoop_list.h"
+#include "ForLoop_dataSetBlocks.h"
+#include "ForLoop_overSets.h"
+
+/// DESTRUCTOR
+ControlBlock_For::~ControlBlock_For() {
+  for (Marray::iterator it = Vars_.begin(); it != Vars_.end(); ++it)
+    delete *it;
+  Vars_.clear();
+}
+
+void ControlBlock_For::Help() const {
+  mprintf("\t<loop spec.> ...\n"
+          "  Create a 'for' loop of one or more types:\n"
+          "    <loop spec> = mask, list, integer, datasetblocks, oversets\n"
+          "  Type help 'for <loop spec.>' for more info on each type.\n"
+          "  Note that non-integer variables (e.g. for mask loops) are NOT incremented\n"
+          "  after the final loop iteration, i.e. these loop variables always retain\n"
+          "  their final value.\n"
+          "  Examples:\n"
+          "\tfor atoms A0 inmask :1-27&!@H= i=1;i++\n"
+          "\t  distance d$i :TCS $A0 out $i.dat\n"
+          "\tdone\n"
+          "\tfor TRAJ in trajA*.nc,trajB*.nc\n"
+          "\t  trajin $TRAJ 1 last 10\n"
+          "\tdone\n"
+          );
+}
+
+void ControlBlock_For::Help(ArgList& argIn) const {
+  if (argIn.hasKey("datasetblocks"))
+    ForLoop_dataSetBlocks::helpText();
+  else if (argIn.hasKey("integer"))
+    ForLoop_integer::helpText();
+  else if (argIn.hasKey("list"))
+    ForLoop_list::helpText();
+  else if (argIn.hasKey("mask"))
+    ForLoop_mask::helpText();
+  else if (argIn.hasKey("oversets"))
+    ForLoop_overSets::helpText();
+  else
+    Help();
+}
+
+/** Set up each mask/integer loop. */
+int ControlBlock_For::SetupBlock(CpptrajState& State, ArgList& argIn) {
+  mprintf("    Setting up 'for' loop.\n");
+  Vars_.clear();
+  description_.assign("for (");
+  // Parse out each component of this for block. E.g.
+  //               .               .                 .          .
+  //   for atoms X inmask :30 name in var1,var2,var3 i=0;i++ DS datasetblocks blocksize 10
+  //   0   1     2 3      4   5    6  7              8       9  10            11        12
+  //       *                  *                      *       *
+  // component 1: 1,2,3,4
+  // component 2: 5,6,7
+  // component 3: 8
+  argIn.MarkArg(0);
+  std::vector<int> forLoopIdxs;
+  for (int iarg = 1; iarg < argIn.Nargs(); iarg++) {
+    if (argIn[iarg] == "inmask") {
+      int idx = iarg - 2;
+      if (idx < 1) {
+        mprinterr("Error: Malformed 'inmask' for loop.\n");
+        return 1;
+      }
+      forLoopIdxs.push_back( idx );
+      Vars_.push_back( static_cast<ForLoop*>( new ForLoop_mask() ) );
+    } else if (argIn[iarg] == "in") {
+      int idx = iarg - 1;
+      if (idx < 1) {
+        mprinterr("Error: Malformed 'in' for loop.\n");
+        return 1;
+      }
+      forLoopIdxs.push_back( idx );
+      Vars_.push_back( static_cast<ForLoop*>( new ForLoop_list() ) );
+    } else if (argIn[iarg] == "oversets") {
+      int idx = iarg -1 ;
+      if (idx < 1) {
+        mprinterr("Error: Malformed 'oversets' for loop.\n");
+        return 1;
+      }
+      forLoopIdxs.push_back( idx );
+      Vars_.push_back( static_cast<ForLoop*>( new ForLoop_overSets() ) );
+    } else if (argIn[iarg] == "datasetblocks") {
+      int idx = iarg - 1;
+      if (idx < 1) {
+        mprinterr("Error: Malformed 'datasetblocks' for loop.\n");
+        return 1;
+      }
+      forLoopIdxs.push_back( idx );
+      Vars_.push_back( static_cast<ForLoop*>( new ForLoop_dataSetBlocks() ) );
+    } else if ( argIn[iarg].find(";") != std::string::npos ) {
+      forLoopIdxs.push_back( iarg );
+      Vars_.push_back( static_cast<ForLoop*>( new ForLoop_integer() ) );
+    }
+    argIn.MarkArg(iarg);
+  }
+  forLoopIdxs.push_back( argIn.Nargs() );
+  //mprintf("DEBUG: For loop indices:");
+  //for (std::vector<int>::const_iterator it = forLoopIdxs.begin();
+  //                                      it != forLoopIdxs.end(); ++it)
+  //  mprintf(" %i", *it);
+  //mprintf("\n");
+  if (forLoopIdxs.size() < 2) {
+    mprinterr("Error: No recognized for loop arguments.\n");
+    return 1;
+  }
+  // Set up each individual for loop.
+  for (unsigned int idx = 1; idx < forLoopIdxs.size(); ++idx)
+  {
+    ArgList forLoopArgs;
+    for (int jdx = forLoopIdxs[idx-1]; jdx < forLoopIdxs[idx]; ++jdx)
+      forLoopArgs.AddArg( argIn[jdx] );
+    if (State.Debug() > 0)
+      forLoopArgs.PrintDebug();
+    ForLoop& forloop = static_cast<ForLoop&>( *(Vars_[idx-1]) );
+    if ( forloop.SetupFor( State, forLoopArgs ) ) {
+      mprinterr("Error: For loop setup failed.\n");
+      return 1;
+    }
+    if ( !forloop.IsSetup() ) {
+      mprinterr("Internal Error: For loop variable was not properly set up.\n");
+      return 1;
+    }
+    if (forLoopArgs.CheckForMoreArgs()) {
+      if (State.ExitOnError()) {
+        mprinterr("Error: Not all for loop arguments handled.\n");
+        return 1;
+      } else
+        mprintf("Warning: Not all for loop arguments handled.\n");
+    }
+    // Append description
+    description_.append( forloop.Description() );
+    // TODO check variable name
+  }
+
+  description_.append(") do");
+
+  return 0;
+}
+
+/** \return true if the given command will finish this block. */
+bool ControlBlock_For::EndBlock(ArgList const& a) const {
+  return (a.CommandIs("done"));
+}
+
+/** Set all loops to their initial values and determine # iterations
+  * \return 0 if all loops were set up, 1 if an error occurred.
+  */
+int ControlBlock_For::Start(DataSetList const& DSL) {
+  int MaxIterations = -1;
+  for (Marray::iterator MH = Vars_.begin(); MH != Vars_.end(); ++MH)
+  {
+    int Niterations = ((*MH)->BeginFor(DSL));
+    if (Niterations == ForLoop::LOOP_ERROR) return 1;
+    // Check number of values
+    if (Niterations != ForLoop::NITERATIONS_UNKNOWN)
+    {
+      if (MaxIterations == -1)
+        MaxIterations = Niterations;
+      else {
+        if (Niterations != MaxIterations)
+          mprintf("Warning: # iterations %i != previous # iterations %i\n",
+                  Niterations, MaxIterations);
+        MaxIterations = std::min(Niterations, MaxIterations);
+      }
+      mprintf("\tLoop over '%s' will execute for %i iterations.\n",
+              (*MH)->VarName().c_str(), Niterations);
+    } else
+      mprintf("\tLoop over '%s' has unknown # iterations.\n", (*MH)->VarName().c_str());
+  }
+  if (Vars_.size() > 1)
+    mprintf("\tLoop will execute for %i iterations.\n", MaxIterations);
+  if (MaxIterations < 1) {
+    mprintf("Warning: Loop has less than 1 iteration.\n");
+    return 0; 
+  }
+
+  return 0;
+}
+
+/** For each mask check if done, then update variables, then increment. */
+ControlBlock::DoneType ControlBlock_For::CheckDone(DataSetList& DSL) {
+  // NOTE: DataSetList is not const ref so dataSetBlocks loop can create sets
+  DoneType retval = NOT_DONE;
+  for (Marray::iterator MH = Vars_.begin(); MH != Vars_.end(); ++MH) {
+    // Exit as soon as one is done, but check all so that
+    // all loops are properly incremented if necessary.
+    if ( (*MH)->EndFor(DSL) ) retval = DONE;
+  }
+
+  return retval;
+}
diff --git a/src/ControlBlock_For.h b/src/ControlBlock_For.h
new file mode 100644
index 0000000000..44527caedf
--- /dev/null
+++ b/src/ControlBlock_For.h
@@ -0,0 +1,26 @@
+#ifndef INC_CONTROLBLOCK_FOR_H
+#define INC_CONTROLBLOCK_FOR_H
+#include "ControlBlock.h"
+class ForLoop;
+/// Hold one or more 'for' loops of various types 
+class ControlBlock_For : public ControlBlock {
+  public:
+    ControlBlock_For() {}
+    ~ControlBlock_For();
+    void Help() const;
+    void Help(ArgList&) const;
+    DispatchObject* Alloc() const { return (DispatchObject*)new ControlBlock_For(); }
+
+    int SetupBlock(CpptrajState&, ArgList&);
+    bool EndBlock(ArgList const&) const;
+    void AddCommand(ArgList const& c) { commands_.push_back(c); }
+    const_iterator begin() const { return commands_.begin(); }
+    const_iterator end()   const { return commands_.end();   }
+    int Start(DataSetList const&);
+    DoneType CheckDone(DataSetList&);
+  private:
+    typedef std::vector<ForLoop*> Marray;
+    Marray Vars_; ///< Hold all for loops for this block
+    ArgArray commands_;
+};
+#endif
diff --git a/src/DataFile.cpp b/src/DataFile.cpp
index 8a729f30c3..e832416ea6 100644
--- a/src/DataFile.cpp
+++ b/src/DataFile.cpp
@@ -2,6 +2,7 @@
 #include "DataFile.h"
 #include "CpptrajStdio.h"
 #include "StringRoutines.h" // DigitWidth, integerToString
+#include "ArgList.h"
 #ifdef TIMER
 # include "Timer.h"
 #endif
@@ -239,6 +240,12 @@ int DataFile::ReadDataOfType(FileName const& fnameIn, DataFormatType typeIn,
 }
 
 // -----------------------------------------------------------------------------
+
+int DataFile::SetupDatafile(FileName const& f, int d) {
+  ArgList a;
+  return SetupDatafile(f, a, d);
+}
+
 // DataFile::SetupDatafile()
 int DataFile::SetupDatafile(FileName const& fnameIn, ArgList& argIn, int debugIn) {
   return SetupDatafile(fnameIn, argIn, UNKNOWN_DATA, debugIn);
@@ -281,6 +288,11 @@ int DataFile::SetupStdout(ArgList& argIn, int debugIn) {
   return 0;
 }
 
+int DataFile::SetupStdout(int d) {
+  ArgList tmp;
+  return SetupStdout(tmp, d);
+}
+
 // DataFile::AddDataSet()
 int DataFile::AddDataSet(DataSet* dataIn) {
   if (dataIn == 0) return 1;
@@ -302,7 +314,12 @@ int DataFile::AddDataSet(DataSet* dataIn) {
         delete dataio_;
         dataio_ = 0;
       }
-      if (dataio_ == 0) return Error("Error: Data file allocation failed.\n");
+      if (dataio_ == 0) {
+        mprinterr("Error: Set '%s' is not valid for '%s' file type.\n",
+                  dataIn->legend(), DataFilename().full());
+        mprinterr("Error: No valid file type could be found.\n");
+        return Error("Error: Data file allocation failed.\n");
+      }
       mprintf("\tChanged DataFile '%s' type to %s for set %s\n", filename_.base(),
               FileTypes::FormatDescription(DF_AllocArray, dfType_),
               dataIn->legend());
diff --git a/src/DataFile.h b/src/DataFile.h
index 368842a462..0615488d1d 100644
--- a/src/DataFile.h
+++ b/src/DataFile.h
@@ -1,7 +1,9 @@
 #ifndef INC_DATAFILE_H
 #define INC_DATAFILE_H
-#include "DataIO.h"
 #include "FileTypes.h"
+#include "DataSetList.h"
+class FileName;
+class DataIO;
 /// Write DataSets to a file with specific format.
 class DataFile {
     /// Allocator and description for file types. 
@@ -46,16 +48,16 @@ class DataFile {
     int ReadDataIn(FileName const&, ArgList const&, DataSetList&, int, int);
     /// Read data from specific type of DataFile
     int ReadDataOfType(FileName const&, DataFormatType, DataSetList&);
+    /// Set up DataFile for writing, no args.
+    int SetupDatafile(FileName const&, int);
     /// Set up DataFile for writing with optional args.
     int SetupDatafile(FileName const&, ArgList&, int);
     /// Set up DataFile for writing with specific format.
     int SetupDatafile(FileName const&, ArgList&, DataFormatType, int);
     /// Set up DataFile for writing to STDOUT (DataIO_Std) with optional arguments
     int SetupStdout(ArgList&, int);
-    /// Set up DataFile for writing to STDOUT
-    int SetupStdout(int d) { ArgList tmp; return SetupStdout(tmp, d); }
-    /// Set up DataFile for writing, no args.
-    int SetupDatafile(FileName const& f, int d) { ArgList a; return SetupDatafile(f, a, d); }
+    /// Set up DataFile for writing to STDOUT with debug level
+    int SetupStdout(int);
     /// Add a previously set-up DataSet to DataFile.
     int AddDataSet(DataSet*);
     /// Remove a set from the DataFile.
diff --git a/src/DataFileList.cpp b/src/DataFileList.cpp
index 325235bcf5..a3b11ec7a5 100644
--- a/src/DataFileList.cpp
+++ b/src/DataFileList.cpp
@@ -3,6 +3,7 @@
 #include "CpptrajStdio.h"
 #include "PDBfile.h"
 #include "StringRoutines.h" // integerToString
+#include "ArgList.h"
 #ifdef TIMER
 # include "Timer.h"
 #endif
diff --git a/src/DataFileList.h b/src/DataFileList.h
index 84c2ce1e01..83b83302e0 100644
--- a/src/DataFileList.h
+++ b/src/DataFileList.h
@@ -1,8 +1,10 @@
 #ifndef INC_DATAFILELIST_H
 #define INC_DATAFILELIST_H
 #include "DataFile.h"
-#include "DataSet.h"
-#include "ArgList.h"
+class DataSet;
+class ArgList;
+class FileName;
+class CpptrajFile;
 /// Holds a list of output DataFiles/CpptrajFiles.
 /** The DataFileList is meant to hold all output data files defined by any
   * Actions or Analysis. This allows multiple sets to be directed to the
diff --git a/src/DataIO_Grace.cpp b/src/DataIO_Grace.cpp
index d19878175b..0b7b824aa4 100644
--- a/src/DataIO_Grace.cpp
+++ b/src/DataIO_Grace.cpp
@@ -84,8 +84,9 @@ int DataIO_Grace::ReadData(FileName const& fname,
 }
 // -----------------------------------------------------------------------------
 void DataIO_Grace::WriteHelp() {
-  mprintf("\tinvert: Flip X/Y axes.\n");
-  mprintf("\txydy  : Make consecutive sets into XYDY sets.\n");
+  mprintf("\tinvert      : Flip X/Y axes.\n"
+          "\txydy        : Make consecutive sets into XYDY sets.\n"
+          "\t<label set> : If a string dataset is specified, assume it has data point labels.\n");
 }
 
 // DataIO_Grace::processWriteArgs()
@@ -116,6 +117,26 @@ int DataIO_Grace::WriteData(FileName const& fname, DataSetList const& SetList)
   return err;
 }
 
+/** Determine if we have a single STRING DataSet. Assume these contain labels. */
+DataSet_string* DataIO_Grace::findLabelSet(DataSetList const& Sets) {
+  DataSet_string* labelSet = 0;
+  for (DataSetList::const_iterator set = Sets.begin(); set != Sets.end(); ++set)
+  {
+    if (labelSet == 0) {
+      if ( (*set)->Type() == DataSet::STRING )
+        labelSet = (DataSet_string*)(*set);
+    } else {
+      if ( (*set)->Type() == DataSet::STRING ) {
+        labelSet = 0;
+        break;
+      }
+    }
+  }
+  if (labelSet != 0)
+    mprintf("\tUsing string set '%s' for data point labels\n", labelSet->legend());
+  return labelSet;
+}
+
 // DataIO_Grace::WriteDataNormal()
 int DataIO_Grace::WriteDataNormal(CpptrajFile& file, DataSetList const& Sets) {
   // Hold all 1D data sets.
@@ -132,21 +153,7 @@ int DataIO_Grace::WriteDataNormal(CpptrajFile& file, DataSetList const& Sets) {
               "@  legend 0.2, 0.995\n@  legend char size 0.60\n",
               Sets[0]->Dim(0).Label().c_str(), "");
   // Determine if we have a single STRING DataSet. Assume these contain labels.
-  DataSet_string* labelSet = 0;
-  for (DataSetList::const_iterator set = Sets.begin(); set != Sets.end(); ++set)
-  {
-    if (labelSet == 0) {
-      if ( (*set)->Type() == DataSet::STRING )
-        labelSet = (DataSet_string*)(*set);
-    } else {
-      if ( (*set)->Type() == DataSet::STRING ) {
-        labelSet = 0;
-        break;
-      }
-    }
-  }
-  if (labelSet != 0)
-    mprintf("\tUsing string set '%s' for data point labels\n", labelSet->legend());
+  DataSet_string* labelSet = findLabelSet( Sets );
   // Loop over DataSets
   unsigned int setnum = 0;
   DataSet::SizeArray frame(1);
@@ -192,6 +199,8 @@ int DataIO_Grace::WriteDataXYDY(CpptrajFile& file, DataSetList const& Sets) {
   file.Printf("@with g0\n@  xaxis label \"%s\"\n@  yaxis label \"%s\"\n"
               "@  legend 0.2, 0.995\n@  legend char size 0.60\n",
               Sets[0]->Dim(0).Label().c_str(), "");
+  // Determine if we have a single STRING DataSet. Assume these contain labels.
+  DataSet_string* labelSet = findLabelSet( Sets );
   // Loop over DataSets
   unsigned int setnum = 0;
   DataSet::SizeArray frame(1);
@@ -216,6 +225,8 @@ int DataIO_Grace::WriteDataXYDY(CpptrajFile& file, DataSetList const& Sets) {
       file.Printf(xfmt.fmt(), ds1->Coord(0, frame[0]));
       ds1->WriteBuffer(file, frame);
       ds2->WriteBuffer(file, frame);
+      if (labelSet != 0)
+        file.Printf(" \"%s\"", (*labelSet)[frame[0]].c_str());
       file.Printf("\n");
     }
   }
diff --git a/src/DataIO_Grace.h b/src/DataIO_Grace.h
index d455f8e81f..5f30c07f35 100644
--- a/src/DataIO_Grace.h
+++ b/src/DataIO_Grace.h
@@ -1,6 +1,7 @@
 #ifndef INC_DATAIO_GRACE_H
 #define INC_DATAIO_GRACE_H
 #include "DataIO.h"
+class DataSet_string;
 /// Read/write Grace data files.
 class DataIO_Grace : public DataIO {
   public:
@@ -17,6 +18,7 @@ class DataIO_Grace : public DataIO {
     int WriteDataNormal(CpptrajFile&,DataSetList const&);
     int WriteDataXYDY(CpptrajFile&, DataSetList const&);
     int WriteDataInverted(CpptrajFile&,DataSetList const&);
+    static DataSet_string* findLabelSet( DataSetList const& );
     bool isInverted_; ///< For 1D writes invert X/Y.
     bool isXYDY_;     ///< Write consecutive sets as XYDY
 };
diff --git a/src/DataIO_Std.cpp b/src/DataIO_Std.cpp
index ecb0f8fabd..9f0158cd5d 100644
--- a/src/DataIO_Std.cpp
+++ b/src/DataIO_Std.cpp
@@ -686,6 +686,16 @@ int DataIO_Std::Read_3D(std::string const& fname,
 int DataIO_Std::Read_Vector(std::string const& fname, 
                             DataSetList& datasetlist, std::string const& dsname)
 {
+  // See if set exists
+  DataSet* ds = datasetlist.CheckForSet( dsname );
+  if (ds != 0) {
+    mprintf("\tAppending vector data to set '%s'\n", ds->legend());
+    // Set exists.
+    if (ds->Group() != DataSet::VECTOR_1D) {
+      mprinterr("Error: Cannot append vector data to non-vector set '%s'\n", ds->legend());
+      return 1;
+    }
+  }
   // Buffer file
   BufferedLine buffer;
   if (buffer.OpenFileRead( fname )) return 1;
@@ -713,21 +723,53 @@ int DataIO_Std::Read_Vector(std::string const& fname,
     mprinterr("Error: Expected 3, 6, or 9 columns of vector data, got %i.\n", ncols);
     return 1;
   }
+  bool hasOrigins;
   if (ncols >= 6) {
     nv = 6;
     mprintf("\tReading vector X Y Z and origin X Y Z values.\n");
+    hasOrigins = true;
+    // If set already exists, see if it doesnt have origins.
+    if (ds != 0 && !((DataSet_Vector*)ds)->HasOrigins()) {
+      mprintf("Warning: Existing set '%s' does not have origin data.\n", ds->legend());
+      mprintf("Warning: Existing set will be filled with zeroed origin data where none exists.\n");
+      DataSet* oldSet = datasetlist.PopSet( ds );
+      DataSet_Vector* voxyz =
+        (DataSet_Vector*)datasetlist.AddSet(DataSet::VECTOR, oldSet->Meta());
+      if (voxyz == 0) return 1;
+      // Make sure dimension info matches
+      voxyz->SetDim(Dimension::X, oldSet->Dim(Dimension::X));
+      // Add existing vector values to set with origin at 0.0.
+      for (unsigned int idx = 0; idx < oldSet->Size(); idx++)
+        voxyz->AddVxyzo( ((DataSet_Vector*)oldSet)->VXYZ(idx), Vec3(0.0) );
+      ds = (DataSet*)voxyz;
+      // Free old set memory
+      delete oldSet;
+    }
   } else {
     nv = 3;
     mprintf("\tReading vector X Y Z values.\n");
+    hasOrigins = false;
+    // If set already exists, see if it has origins.
+    if (ds != 0 && ((DataSet_Vector*)ds)->HasOrigins()) {
+      mprintf("Warning: Existing set '%s' has origin data.\n", ds->legend());
+      mprintf("Warning: Existing set will be filled with zeroed origin data where none exists.\n");
+      hasOrigins = true;
+    }
+  }
+  // Create set if it doesnt yet exist;
+  if (ds == 0) {
+    DataSet::DataType dtype = DataSet::VECTOR;
+    //if (hasOrigins)
+    //  dtype = DataSet::VEC_OXYZ;
+    //else
+    //  dtype = DataSet::VEC_XYZ;
+    ds = datasetlist.AddSet(dtype, dsname);
+    if (ds == 0) return 1;
   }
-  // Create set
-  DataSet_Vector* ds = new DataSet_Vector();
-  if (ds == 0) return 1;
-  ds->SetMeta( dsname );
   // Read vector data
   double vec[6];
   std::fill(vec, vec+6, 0.0);
-  size_t ndata = 0;
+  size_t ndata = ds->Size();
   while (linebuffer != 0) {
     if (hasIndex)
       ntokens = sscanf(linebuffer, "%*f %lf %lf %lf %lf %lf %lf",
@@ -740,10 +782,13 @@ int DataIO_Std::Read_Vector(std::string const& fname,
                 buffer.LineNumber(), nv, ntokens);
       break;
     }
-    ds->Add( ndata++, vec ); 
+    if (hasOrigins)
+      ds->Add( ndata++, vec );
+    else
+      ((DataSet_Vector*)ds)->AddVxyz( Vec3(vec) ); // TODO: Remove if DataSet_Vector is split to with/without origins
     linebuffer = buffer.Line();
   }
-  return (datasetlist.AddOrAppendSets("", DataSetList::Darray(), DataSetList::DataListType(1, ds)));
+  return 0;
 }
 
 // DataIO_Std::Read_Mat3x3()
diff --git a/src/DataIO_VecTraj.cpp b/src/DataIO_VecTraj.cpp
index a18899cdfe..b933ad97a8 100644
--- a/src/DataIO_VecTraj.cpp
+++ b/src/DataIO_VecTraj.cpp
@@ -30,12 +30,14 @@ int DataIO_VecTraj::WriteData(FileName const& fname, DataSetList const& SetList)
   if (SetList.empty()) return 1;
   // Check input data sets
   int vec_size = -1;
-  unsigned int num_no_origins = 0;
   typedef std::vector<DataSet_Vector*> Varray;
   Varray VecSets;
   VecSets.reserve( SetList.size() );
+  typedef std::vector<bool> Barray;
+  Barray VecNeedsBond;
+  VecNeedsBond.reserve( SetList.size() );
   for (DataSetList::const_iterator set = SetList.begin(); set != SetList.end(); ++set) {
-    if ((*set)->Type() != DataSet::VECTOR)
+    if ((*set)->Group() != DataSet::VECTOR_1D)
       mprintf("Warning: Set '%s' is not a vector, skipping.\n", (*set)->legend());
     else {
       DataSet_Vector const& Vec = static_cast<DataSet_Vector const&>( *(*set) );
@@ -47,16 +49,17 @@ int DataIO_VecTraj::WriteData(FileName const& fname, DataSetList const& SetList)
                   Vec.legend(), Vec.Size(), vec_size);
         return 1;
       }
-      if (!Vec.HasOrigins()) num_no_origins++;
       VecSets.push_back( (DataSet_Vector*)*set );
+      if (Vec.HasOrigins() && includeOrigin_)
+        VecNeedsBond.push_back( true );
+      else
+        VecNeedsBond.push_back( false );
     }
   }
   if (VecSets.empty()) {
     mprinterr("Error: No vector data sets.\n");
     return 1;
   }
-  if (num_no_origins == VecSets.size())
-    includeOrigin_ = false;
   // Set up pseudo topology for all vectors
   Topology pseudo;
   BondArray bonds;
@@ -65,14 +68,15 @@ int DataIO_VecTraj::WriteData(FileName const& fname, DataSetList const& SetList)
   int natom = 0;
   for (unsigned int nres = 1; nres <= VecSets.size(); nres++) {
     Residue vec_res("VEC", nres, ' ', ' ');
-    if (includeOrigin_)
+    if (VecNeedsBond[nres-1]) {
       pseudo.AddTopAtom(Atom("OXYZ", 0), vec_res);
-    pseudo.AddTopAtom(Atom("VXYZ", 0), vec_res);
-    if (includeOrigin_) {
+      pseudo.AddTopAtom(Atom("VXYZ", 0), vec_res);
       pseudo.AddBond(natom, natom+1, 0); // Bond parm index 0
       natom += 2;
-    } else
+    } else {
+      pseudo.AddTopAtom(Atom("VXYZ", 0), vec_res);
       natom++;
+    }
   }
   pseudo.CommonSetup();
   if (!parmoutName_.empty()) {
@@ -90,14 +94,21 @@ int DataIO_VecTraj::WriteData(FileName const& fname, DataSetList const& SetList)
     Frame outFrame(pseudo.Natom());
     for (int i = 0; i != vec_size; ++i) {
       outFrame.ClearAtoms();
-      for (Varray::const_iterator set = VecSets.begin(); set != VecSets.end(); ++set) {
-        DataSet_Vector const& Vec = static_cast<DataSet_Vector const&>( *(*set) );
-        if (includeOrigin_) {
+      Barray::const_iterator needsBond = VecNeedsBond.begin();
+      for (Varray::const_iterator set = VecSets.begin();
+                                  set != VecSets.end();
+                                ++set, ++needsBond)
+      {
+        if ( *needsBond ) {
+          DataSet_Vector const& Vec =
+            static_cast<DataSet_Vector const&>( *(*set) );
           Vec3 const& ovec = Vec.OXYZ(i);
           outFrame.AddVec3( ovec );
           outFrame.AddVec3( Vec[i] + ovec );
-        } else
+        } else {
+          DataSet_Vector const& Vec = static_cast<DataSet_Vector const&>( *(*set) );
           outFrame.AddVec3( Vec[i] );
+        }
       }
       if (out.WriteSingle(i, outFrame)) return 1;
     }
diff --git a/src/DataSet.cpp b/src/DataSet.cpp
index 22cc7a4c1f..c462a52007 100644
--- a/src/DataSet.cpp
+++ b/src/DataSet.cpp
@@ -29,7 +29,8 @@ const char* DataSet::Descriptions_[] = {
   "pH REMD (explicit)",         // PH_EXPL
   "pH REMD (implicit)",         // PH_IMPL
   "parameters",                 // PARAMETERS
-  "tensor"                      // TENSOR
+  "tensor",                     // TENSOR
+  "string variable"             // STRINGVAR
 };
 
 // CONSTRUCTOR
diff --git a/src/DataSet.h b/src/DataSet.h
index f4c3714792..152141823d 100644
--- a/src/DataSet.h
+++ b/src/DataSet.h
@@ -28,11 +28,11 @@ class DataSet {
       UNKNOWN_DATA=0, DOUBLE, FLOAT, INTEGER, STRING, MATRIX_DBL, MATRIX_FLT, 
       COORDS, VECTOR, MODES, GRID_FLT, GRID_DBL, REMLOG, XYMESH, TRAJ, REF_FRAME,
       MAT3X3, TOPOLOGY, CMATRIX, CMATRIX_NOMEM, CMATRIX_DISK, PH, PH_EXPL, PH_IMPL,
-      PARAMETERS, TENSOR
+      PARAMETERS, TENSOR, STRINGVAR
     };
     /// Group DataSet belongs to.
     enum DataGroup {
-      GENERIC=0, SCALAR_1D, MATRIX_2D, GRID_3D, COORDINATES, CLUSTERMATRIX, PHREMD
+      GENERIC=0, SCALAR_1D, MATRIX_2D, GRID_3D, COORDINATES, CLUSTERMATRIX, PHREMD, VECTOR_1D
     };
 
     DataSet();
@@ -45,6 +45,8 @@ class DataSet {
     // ----------===== Inheritable functions =====----------
     /// \return the number of data elements stored in the DataSet.
     virtual size_t Size() const = 0;
+    /// \return SizeArray containing sizes in each dimension TODO pure virtual
+    virtual SizeArray DimSizes() const { return SizeArray(); }
     /// Print DataSet information //TODO return string instead?
     virtual void Info() const = 0;
     /// Write data to file given start indices. FIXME Buffer? Should this function take number of elements as well?
@@ -52,8 +54,10 @@ class DataSet {
     /// \return value of coordinate for specified dimension d and position p.
     /** NOTE: It is assumed this can ALWAYS be represented as double precision. */
     virtual double Coord(unsigned int d, size_t p) const { return dim_[d].Coord(p); }
-    /// Allocate data given numbers of elements.
+    /// Reserve memory for given number(s) of elements. TODO rename?
     virtual int Allocate(SizeArray const&) = 0;
+    /// Actually allocate memory for given number(s) of elements TODO pure virtual?
+    virtual int MemAlloc(SizeArray const&) { return 1; }
     /// Add element to data set.
     /** A pointer to the data is passed in as void - it is up to the
       * inheriting class to cast it. The X value for the data is passed
@@ -66,6 +70,8 @@ class DataSet {
     virtual int Append(DataSet*) = 0;
     /// \return Size of data set in memory (in bytes).
     virtual size_t MemUsageInBytes() const = 0;
+    /// Copy a block to position in this set from given set OF SAME TYPE using specified position and size TODO pure virtual
+    virtual void CopyBlock(size_t, const DataSet*, size_t, size_t) {}
 #   ifdef MPI
     /// Piece this DataSet together from multiple threads.
     virtual int Sync(size_t, std::vector<int> const&, Parallel::Comm const&) = 0;
diff --git a/src/DataSetList.cpp b/src/DataSetList.cpp
index b1a225ceef..d0f99e9c30 100644
--- a/src/DataSetList.cpp
+++ b/src/DataSetList.cpp
@@ -2,6 +2,7 @@
 #include "CpptrajStdio.h"
 #include "StringRoutines.h" // DigitWidth
 #include "Constants.h" // For AddOrAppendSets
+#include "ArgList.h"
 // Data types go here
 #include "DataSet_double.h"
 #include "DataSet_float.h"
@@ -31,6 +32,7 @@
 #include "DataSet_PHREMD_Implicit.h"
 #include "DataSet_Parameters.h"
 #include "DataSet_Tensor.h"
+#include "DataSet_StringVar.h"
 
 bool DataSetList::useDiskCache_ = false;
 
@@ -78,6 +80,7 @@ DataSet* DataSetList::NewSet(DataSet::DataType typeIn) {
     case DataSet::PH_IMPL       : ds = DataSet_PHREMD_Implicit::Alloc(); break;
     case DataSet::PARAMETERS    : ds = DataSet_Parameters::Alloc(); break;
     case DataSet::TENSOR        : ds = DataSet_Tensor::Alloc(); break;
+    case DataSet::STRINGVAR     : ds = DataSet_StringVar::Alloc(); break;
     // Sanity check
     default:
       mprinterr("Internal Error: No allocator for DataSet type '%s'\n",
@@ -454,6 +457,10 @@ DataSet* DataSetList::AddSet(DataSet::DataType inType, MetaData const& metaIn)
 # ifdef TIMER
   time_setup_.Start();
 # endif
+  //mprintf("DEBUG: Adding and setting up data set '%s'\n", meta.PrintName().c_str());
+  //if (meta.TimeSeries() == MetaData::UNKNOWN_TS)
+  //  mprintf("DEBUG: UNKNOWN_TS\n");
+  //mprintf("DEBUG: ndim= %i\n", DS->Ndim());
   // If 1 dim set and time series status not set, set to true.
   if (meta.TimeSeries() == MetaData::UNKNOWN_TS && DS->Ndim() == 1) {
     meta.SetTimeSeries( MetaData::IS_TS );
@@ -713,6 +720,17 @@ void DataSetList::ListDataOnly() const {
   mprintf("\nDATASETS (%zu total):\n", temp.size());
   PrintList( temp );
 }
+
+void DataSetList::ListStringVar() const {
+  for (DataListType::const_iterator ds = DataList_.begin(); ds != DataList_.end(); ++ds)
+  {
+    if ( (*ds)->Type() == DataSet::STRINGVAR) {
+      DataSet_StringVar const& var = static_cast<DataSet_StringVar const&>( *(*ds) );
+      mprintf("\t%s = %s\n", var.legend(), var.Value().c_str());
+    }
+  }
+}
+
 #ifdef MPI
 // DataSetList::SynchronizeData()
 /** Synchronize timeseries data from child ranks to master. */
@@ -782,6 +800,121 @@ int DataSetList::SynchronizeData(Parallel::Comm const& commIn) {
   return 0;
 }
 #endif
+// -----------------------------------------------------------------------------
+
+int DataSetList::UpdateStringVar(std::string const& varnameIn, std::string const& newValue)
+const
+{
+  DataSet* ds = FindSetOfType( varnameIn, DataSet::STRINGVAR );
+  if (ds == 0) {
+    mprinterr("Error: No string variable named '%s'\n", varnameIn.c_str());
+    return 1;
+  }
+  DataSet_StringVar& var = static_cast<DataSet_StringVar&>( *ds );
+  var.assign( newValue );
+  return 0;
+}
+
+/** Get a value from specified DataSet as a string. */
+std::string DataSetList::GetVariable(std::string const& varnameIn) const {
+  DataSet* ds = CheckForSet( varnameIn );
+  if (ds == 0) return std::string();
+  std::string val;
+  if (ds->Size() > 0) {
+    if (ds->Type() == DataSet::STRINGVAR) {
+      val = ((DataSet_StringVar*)ds)->Value();
+    } else if (ds->Type() == DataSet::STRING) {
+      val = (*((DataSet_string*)ds))[0];
+    } else if (ds->Group() == DataSet::SCALAR_1D) { 
+      val = doubleToString( ((DataSet_1D*)ds)->Dval(0) );
+    } else {
+      mprinterr("Internal Error: DataSetList::GetVariable(): Invalid set type: '%s'\n",
+                ds->legend());
+      return std::string();
+    }
+  }
+  
+  return val;
+}
+
+/** Replace all variables (beginning with $) in string with their values.
+  * \param varname Final string containing values.
+  * \param varnameIn Initial string containing variables to replace.
+  */
+int DataSetList::ReplaceVariables(std::string& varname, std::string const& varnameIn)
+const
+{
+  int nReplaced = 0;
+  varname = varnameIn;
+  size_t pos = varname.find("$");
+  while (pos != std::string::npos) {
+    // Argument is/contains a variable. Find first non-alphanumeric char
+    size_t len = 1;
+    for (size_t pos1 = pos+1; pos1 < varname.size(); pos1++, len++)
+      if (!isalnum(varname[pos1])) break;
+    std::string var_in_arg = varname.substr(pos+1, len-1);
+    // String variables will never have aspect/index etc. See if string
+    // variable with this name exists.
+    DataSet* ds = 0;
+    //mprintf("DEBUG: Check for string var: '%s'\n", var_in_arg.c_str());
+    for (const_iterator it = begin(); it != end(); ++it)
+    {
+      if ( (*it)->Type() == DataSet::STRINGVAR && (*it)->Matches_Exact(MetaData(var_in_arg)) ) {
+        ds = *it;
+        break;
+      }
+    }
+    if (ds == 0) {
+      // String variable not found; see if this is a DataSet.
+      for (size_t pos1 = pos+len; pos1 < varname.size(); pos1++, len++)
+      {
+        if (!isalnum(varname[pos1]) &&
+            varname[pos1] != '[' &&
+            varname[pos1] != ':' &&
+            varname[pos1] != ']' &&
+            varname[pos1] != '_' &&
+            varname[pos1] != '-' &&
+            varname[pos1] != '%')
+          break;
+      }
+      var_in_arg = varname.substr(pos+1, len-1);
+      ds = CheckForSet( var_in_arg );
+    }
+    if (ds == 0) {
+      mprinterr("Error: Unrecognized variable in command: %s\n", var_in_arg.c_str());
+      return -1;
+    } else {
+      if (ds->Type() != DataSet::STRINGVAR &&
+          ds->Type() != DataSet::STRING && 
+          ds->Group() != DataSet::SCALAR_1D)
+      {
+        mprinterr("Error: Only strings and 1D data sets supported for variable replacement.\n");
+        return -1;
+      }
+      if (ds->Size() < 1) {
+        mprinterr("Error: Set is empty.\n");
+        return -1;
+      }
+      if (ds->Size() > 1)
+        mprintf("Warning: Only using first value.\n");
+      std::string value;
+      if (ds->Type() == DataSet::STRINGVAR)
+        value = (*((DataSet_StringVar*)ds)).Value(); 
+      else if (ds->Type() == DataSet::STRING)
+        value = (*((DataSet_string*)ds))[0];
+      else
+        value = doubleToString(((DataSet_1D*)ds)->Dval(0));
+      if (debug_ > 0)
+        mprintf("DEBUG: Replaced variable '$%s' with value '%s' from DataSet '%s'\n",
+                var_in_arg.c_str(), value.c_str(), ds->legend());
+      varname.replace(pos, var_in_arg.size()+1, value);
+      nReplaced++;
+    }
+    pos = varname.find("$");
+  } // END loop over this argument
+  return nReplaced;
+}
+
 // -----------------------------------------------------------------------------
 const char* DataSetList::RefArgs = "reference | ref <name> | refindex <#>";
 
diff --git a/src/DataSetList.h b/src/DataSetList.h
index b1189bef19..c04d096194 100644
--- a/src/DataSetList.h
+++ b/src/DataSetList.h
@@ -116,6 +116,8 @@ class DataSetList {
     void List() const;
     /// List all non-Topology/Reference data sets.
     void ListDataOnly() const;
+    /// List all string variables
+    void ListStringVar() const;
 #   ifdef MPI
     /// Indicate whether sets added to the list need to be synced
     void SetNewSetsNeedSync(bool b) { newSetsNeedSync_ = b; }
@@ -123,6 +125,13 @@ class DataSetList {
     int SynchronizeData(Parallel::Comm const&);
 #   endif
 
+    /// Update value in given string variable with new value
+    int UpdateStringVar(std::string const&, std::string const&) const;
+    /// \return Value corresponding to given data set as a string
+    std::string GetVariable(std::string const&) const;
+    /// \return number of variables replaced with their values in given string.
+    int ReplaceVariables(std::string&, std::string const&) const;
+
     // REF_COORDS functions ----------------------
     /// reference arg help text
     static const char* RefArgs;
diff --git a/src/DataSet_1D.h b/src/DataSet_1D.h
index 4d9aaddf03..1e5c2a6447 100644
--- a/src/DataSet_1D.h
+++ b/src/DataSet_1D.h
@@ -11,6 +11,8 @@ class DataSet_1D : public DataSet {
     DataSet_1D() {}
     DataSet_1D(DataSet::DataType tIn, TextFormat const& fIn) : DataSet(tIn, SCALAR_1D, fIn, 1) {}
     virtual ~DataSet_1D() {}
+    // ----- DataSet functions -------------------
+    SizeArray DimSizes() const { return SizeArray(1, Size()); }
     // ---- DataSet_1D functions -----------------
     /// \return data from set at position as double precision.
     virtual double Dval(size_t) const = 0;
diff --git a/src/DataSet_Coords_REF.cpp b/src/DataSet_Coords_REF.cpp
index 844c630d7e..4c1623ab81 100644
--- a/src/DataSet_Coords_REF.cpp
+++ b/src/DataSet_Coords_REF.cpp
@@ -1,6 +1,7 @@
 #include "DataSet_Coords_REF.h"
 #include "CpptrajStdio.h"
 #include "Trajin_Single.h"
+#include "ArgList.h"
 
 void DataSet_Coords_REF::Info() const {
   //if (!tag_.empty())
diff --git a/src/DataSet_Mesh.cpp b/src/DataSet_Mesh.cpp
index 28494a59f5..5acc58221f 100644
--- a/src/DataSet_Mesh.cpp
+++ b/src/DataSet_Mesh.cpp
@@ -1,4 +1,5 @@
 #include <cmath> // regression
+#include <algorithm> // copy
 #include "DataSet_Mesh.h"
 #include "CpptrajStdio.h"
 #include "Constants.h" // regression
@@ -28,6 +29,25 @@ int DataSet_Mesh::Allocate( SizeArray const& sizeIn ) {
   return 0;
 }
 
+/** Allocate space in arrays. */
+int DataSet_Mesh::MemAlloc( SizeArray const& sizeIn ) {
+  if (!sizeIn.empty()) {
+    mesh_x_.resize( sizeIn[0] );
+    mesh_y_.resize( sizeIn[0] );
+  }
+  return 0;
+}
+
+// DataSet_Mesh::CopyBlock()
+void DataSet_Mesh::CopyBlock(size_t startIdx, DataSet const* dptrIn, size_t pos, size_t nelts)
+{
+  DataSet_Mesh const& setIn = static_cast<DataSet_Mesh const&>( *dptrIn );
+  const double* ptr = (&(setIn.mesh_x_[0])+pos);
+  std::copy( ptr, ptr + nelts, &(mesh_x_[0]) + startIdx );
+                ptr = (&(setIn.mesh_y_[0])+pos);
+  std::copy( ptr, ptr + nelts, &(mesh_y_[0]) + startIdx );
+}
+
 /** Insert data vIn at frame. */
 void DataSet_Mesh::Add(size_t frame, const void* vIn) {
   if (frame > mesh_x_.size()) {
diff --git a/src/DataSet_Mesh.h b/src/DataSet_Mesh.h
index ce94ec4fef..6f3b8f9c76 100644
--- a/src/DataSet_Mesh.h
+++ b/src/DataSet_Mesh.h
@@ -25,6 +25,8 @@ class DataSet_Mesh : public DataSet_1D {
     int Append(DataSet*);
     double Coord(unsigned int d, size_t p) const { return mesh_x_[p]; }
     size_t MemUsageInBytes() const { return ((mesh_x_.size() + mesh_y_.size()) * sizeof(double)) + cspline_.DataSize(); }
+    int MemAlloc(SizeArray const&);
+    void CopyBlock(size_t, const DataSet*, size_t, size_t);
     // ----- DataSet_1D functions ----------------
     double Dval(size_t idx)  const { return mesh_y_[idx];       }
     double Xcrd(size_t idx)  const { return mesh_x_[idx];       }
diff --git a/src/DataSet_StringVar.cpp b/src/DataSet_StringVar.cpp
new file mode 100644
index 0000000000..5e1ffcebc3
--- /dev/null
+++ b/src/DataSet_StringVar.cpp
@@ -0,0 +1,16 @@
+#include "DataSet_StringVar.h"
+#include "CpptrajStdio.h"
+
+/// CONSTRUCTOR
+DataSet_StringVar::DataSet_StringVar() :
+  DataSet(STRINGVAR, GENERIC, TextFormat(), 0)
+{ }
+
+size_t DataSet_StringVar::MemUsageInBytes() const {
+  return sizeof(std::string) + (var_.size() * sizeof(char));
+}
+
+void DataSet_StringVar::Add(size_t n, const void* ptr) {
+  const char* cptr = (const char*)ptr;
+  var_ = std::string(cptr);
+}
diff --git a/src/DataSet_StringVar.h b/src/DataSet_StringVar.h
new file mode 100644
index 0000000000..2e8738f65c
--- /dev/null
+++ b/src/DataSet_StringVar.h
@@ -0,0 +1,30 @@
+#ifndef INC_DATASET_STRINGVAR_H
+#define INC_DATASET_STRINGVAR_H
+#include "DataSet.h"
+#include <string>
+/// Hold a single string variable 
+class DataSet_StringVar : public DataSet {
+  public:
+    DataSet_StringVar();
+    static DataSet* Alloc() { return (DataSet*)new DataSet_StringVar(); }
+    // ----- DataSet functions -------------------
+    size_t Size()                                    const { return 1; }
+    void Info()                                      const { return; }
+    int Allocate(SizeArray const&)                         { return 0; }
+    void Add(size_t, const void*);
+    void WriteBuffer(CpptrajFile&, SizeArray const&) const { return; }
+    int Append(DataSet*)                                   { return 1; }
+    size_t MemUsageInBytes() const;
+#   ifdef MPI
+    int Sync(size_t, std::vector<int> const&, Parallel::Comm const&) { return 1; }
+#   endif
+    // -------------------------------------------
+
+    void append(std::string const& s) { var_.append(s); }
+    void assign(std::string const& s) { var_.assign(s); }
+
+    std::string const& Value() const { return var_; }
+  private:
+    std::string var_; ///< String variable
+};
+#endif
diff --git a/src/DataSet_Vector.cpp b/src/DataSet_Vector.cpp
index 152c9abd00..694649981a 100644
--- a/src/DataSet_Vector.cpp
+++ b/src/DataSet_Vector.cpp
@@ -1,6 +1,7 @@
 #include <cstdlib> // abs, intel 11 compilers choke on std::abs
 #include <cmath> // sqrt
 #include "DataSet_Vector.h"
+#include "DataSet_1D.h"
 #include "Constants.h" // For spherical harmonics norm.
 #include "Corr.h"
 
@@ -9,9 +10,10 @@ const ComplexArray DataSet_Vector::COMPLEXBLANK = ComplexArray(0);
 
 // CONSTRUCTOR
 DataSet_Vector::DataSet_Vector() :
-  DataSet(VECTOR, GENERIC, TextFormat(TextFormat::DOUBLE, 8, 4, 6), 1),
+  DataSet(VECTOR, VECTOR_1D, TextFormat(TextFormat::DOUBLE, 8, 4, 6), 1),
   order_(0) {}
 
+/** \return Vector memory usage in bytes. */
 size_t DataSet_Vector::MemUsageInBytes() const {
   size_t mySize = (vectors_.size() * Vec3::DataSize()) +
                   (origins_.size() * Vec3::DataSize()) +
@@ -22,7 +24,6 @@ size_t DataSet_Vector::MemUsageInBytes() const {
     mySize += (SH->DataSize());
   return mySize;
 }
-         
 
 // DataSet_Vector::Allocate()
 int DataSet_Vector::Allocate(SizeArray const& Nin) {
@@ -33,6 +34,26 @@ int DataSet_Vector::Allocate(SizeArray const& Nin) {
   return 0;
 }
 
+// DataSet_Vector::MemAlloc
+int DataSet_Vector::MemAlloc(SizeArray const& Nin) {
+  vectors_.resize( Nin[0] );
+  if (HasOrigins())
+    origins_.resize( Nin[0] );
+  return 0;
+}
+
+// DataSet_Vector::CopyBlock()
+void DataSet_Vector::CopyBlock(size_t startIdx, DataSet const* dptrIn, size_t pos, size_t nelts)
+{
+  DataSet_Vector const& setIn = static_cast<DataSet_Vector const&>( *dptrIn );
+  Varray::const_iterator ptr = setIn.begin() + pos;
+  std::copy(ptr, ptr + nelts, vectors_.begin() + startIdx);
+  if (HasOrigins()) {
+    ptr = setIn.origins_.begin() + pos;
+    std::copy( ptr, ptr + nelts, origins_.begin() + startIdx );
+  }
+}
+
 // DataSet_Vector::WriteBuffer()
 void DataSet_Vector::WriteBuffer(CpptrajFile &cbuffer, SizeArray const& pIn) const {
   if (pIn[0] >= vectors_.size()) {
@@ -45,6 +66,7 @@ void DataSet_Vector::WriteBuffer(CpptrajFile &cbuffer, SizeArray const& pIn) con
   }
 }
 
+// DataSet_Vector::Append()
 int DataSet_Vector::Append(DataSet* dsIn) {
   if (dsIn->Empty()) return 0;
   if (dsIn->Type() != VECTOR) return 1;
diff --git a/src/DataSet_Vector.h b/src/DataSet_Vector.h
index ae05b7ba15..8ac5b6c8b6 100644
--- a/src/DataSet_Vector.h
+++ b/src/DataSet_Vector.h
@@ -1,10 +1,10 @@
 #ifndef INC_DATASET_VECTOR_H
 #define INC_DATASET_VECTOR_H
 #include "DataSet.h"
-#include "DataSet_1D.h" // FIXME remove after Correlation gone
 #include "Vec3.h"
 #include "ComplexArray.h"
 #include "SymbolExporting.h"
+class DataSet_1D;
 class DataSet_Vector : public DataSet {
     static const ComplexArray COMPLEXBLANK;
   public:
@@ -19,6 +19,8 @@ class DataSet_Vector : public DataSet {
 #   endif
     void Info()                         const { return;                 }
     int Allocate(SizeArray const&);
+    int MemAlloc(SizeArray const&);
+    void CopyBlock(size_t, DataSet const*, size_t, size_t);
     inline void Add(size_t, const void*);
     void WriteBuffer(CpptrajFile&,SizeArray const&) const;
     int Append( DataSet* );
@@ -27,30 +29,32 @@ class DataSet_Vector : public DataSet {
     void reset();
     void Resize(size_t s)               { vectors_.resize( s );    }
     void Resize(size_t s, Vec3 const& v){ vectors_.resize(s, v);   }
-    //typedef Varray::iterator iterator;
-    //iterator begin()                    { return vectors_.begin(); }
-    //iterator end()                      { return vectors_.end();   }
+
+    // Vector functions
     const Vec3& operator[](int i) const { return vectors_[i];      }
     Vec3&       operator[](int i)       { return vectors_[i];      }
     const Vec3& VXYZ(int i)       const { return vectors_[i];      }
+    void AddVxyz(Vec3 const& v)         { vectors_.push_back( v ); }
+    typedef Varray::const_iterator const_iterator;
+    const_iterator begin()       const { return vectors_.begin(); }
+    const_iterator end()         const { return vectors_.end();   }
+    const Vec3&    Back()        const { return vectors_.back();  }
+
+    // Origin functions
     const Vec3& OXYZ(int i)       const {
       if (origins_.empty())
         return ZERO;
       return origins_[i];
     }
     bool HasOrigins()             const { return !origins_.empty(); }
-    void ReserveVecs(size_t n)          { vectors_.reserve( n );   }
-    void AddVxyz(Vec3 const& v)         { vectors_.push_back( v ); }
-    void AddVxyz(Vec3 const& v, Vec3 const& c) {
+    void AddVxyzo(Vec3 const& v, Vec3 const& c) {
       vectors_.push_back( v );
       origins_.push_back( c );
     }
-    typedef Varray::const_iterator const_iterator;
-    const_iterator begin()       const { return vectors_.begin(); }
-    const_iterator end()         const { return vectors_.end();   }
-    const Vec3&    Back()        const { return vectors_.back();  }
+
     /// Calculate auto/cross-correlation //TODO Move to Corr.cpp
     int CalcVectorCorr(DataSet_Vector const&, DataSet_1D&, int) const;
+
     /// Calculate spherical harmonics arrays for given Legendre order
     int CalcSphericalHarmonics(int);
     /// \return Spherical harmonics array for given m (-order_ <= m <= order_)
diff --git a/src/DataSet_double.cpp b/src/DataSet_double.cpp
index cd74114eec..7f0d65173b 100644
--- a/src/DataSet_double.cpp
+++ b/src/DataSet_double.cpp
@@ -1,3 +1,4 @@
+#include <algorithm> // copy
 #include "DataSet_double.h"
 
 // DataSet_double::Allocate()
@@ -18,6 +19,21 @@ void DataSet_double::Add(size_t frame, const void* vIn) {
   Data_.push_back( *((double*)vIn) );
 }
 
+/** Allocate space in Data_ array. */
+int DataSet_double::MemAlloc( SizeArray const& sizeIn ) {
+  if (!sizeIn.empty())
+    Data_.resize( sizeIn[0] );
+  return 0;
+}
+
+// DataSet_double::CopyBlock()
+void DataSet_double::CopyBlock(size_t startIdx, DataSet const* dptrIn, size_t pos, size_t nelts)
+{
+  DataSet_double const& setIn = static_cast<DataSet_double const&>( *dptrIn );
+  const double* ptr = (&(setIn.Data_[0])+pos);
+  std::copy( ptr, ptr + nelts, &(Data_[0]) + startIdx );
+}
+
 // DataSet_double::WriteBuffer()
 /** Write data at frame to CharBuffer. If no data for frame write 0.0.
   */
diff --git a/src/DataSet_double.h b/src/DataSet_double.h
index 4f29c47d56..4232245fb5 100644
--- a/src/DataSet_double.h
+++ b/src/DataSet_double.h
@@ -31,6 +31,8 @@ class DataSet_double : public DataSet_1D {
     void WriteBuffer(CpptrajFile&, SizeArray const&) const;
     int Append(DataSet*);
     size_t MemUsageInBytes() const { return Data_.size() * sizeof(double); }
+    int MemAlloc(SizeArray const&);
+    void CopyBlock(size_t, const DataSet*, size_t, size_t);
     // ----- DataSet_1D functions ----------------
     double Dval(size_t idx)        const { return Data_[idx];         }
     double Xcrd(size_t idx)        const { return Dim(0).Coord(idx);  }
diff --git a/src/DataSet_float.cpp b/src/DataSet_float.cpp
index 69acfb8ecb..4ff1ee7ba4 100644
--- a/src/DataSet_float.cpp
+++ b/src/DataSet_float.cpp
@@ -8,6 +8,21 @@ int DataSet_float::Allocate( SizeArray const& sizeIn ) {
   return 0;
 }
 
+/** Allocate space in Data_ array. */
+int DataSet_float::MemAlloc( SizeArray const& sizeIn ) {
+  if (!sizeIn.empty())
+    Data_.resize( sizeIn[0] );
+  return 0;
+}
+
+// DataSet_float::CopyBlock()
+void DataSet_float::CopyBlock(size_t startIdx, DataSet const* dptrIn, size_t pos, size_t nelts)
+{
+  DataSet_float const& setIn = static_cast<DataSet_float const&>( *dptrIn );
+  const float* ptr = (&(setIn.Data_[0])+pos);
+  std::copy( ptr, ptr + nelts, &(Data_[0]) + startIdx );
+}
+
 // DataSet_float::Add()
 /** Insert data vIn at frame. */
 void DataSet_float::Add(size_t frame, const void* vIn) {
diff --git a/src/DataSet_float.h b/src/DataSet_float.h
index 3c56d407bd..7bed6b349d 100644
--- a/src/DataSet_float.h
+++ b/src/DataSet_float.h
@@ -25,6 +25,8 @@ class DataSet_float : public DataSet_1D {
     void WriteBuffer(CpptrajFile&, SizeArray const&) const;
     int Append(DataSet*);
     size_t MemUsageInBytes() const { return Data_.size() * sizeof(float); }
+    int MemAlloc(SizeArray const&);
+    void CopyBlock(size_t, const DataSet*, size_t, size_t);
     // ----- DataSet_1D functions ----------------
     double Dval(size_t idx)        const { return (double)Data_[idx]; }
     double Xcrd(size_t idx)        const { return Dim(0).Coord(idx);  }
diff --git a/src/DataSet_integer_mem.cpp b/src/DataSet_integer_mem.cpp
index 81f93aebe5..bac4eeca8e 100644
--- a/src/DataSet_integer_mem.cpp
+++ b/src/DataSet_integer_mem.cpp
@@ -9,6 +9,21 @@ int DataSet_integer_mem::Allocate( SizeArray const& sizeIn ) {
   return 0;
 }
 
+/** Allocate space in Data_ array. */
+int DataSet_integer_mem::MemAlloc( SizeArray const& sizeIn ) {
+  if (!sizeIn.empty())
+    Data_.resize( sizeIn[0] );
+  return 0;
+}
+
+// DataSet_integer_mem::CopyBlock()
+void DataSet_integer_mem::CopyBlock(size_t startIdx, DataSet const* dptrIn, size_t pos, size_t nelts)
+{
+  DataSet_integer_mem const& setIn = static_cast<DataSet_integer_mem const&>( *dptrIn );
+  const int* ptr = (&(setIn.Data_[0])+pos);
+  std::copy( ptr, ptr + nelts, &(Data_[0]) + startIdx );
+}
+
 // DataSet_integer_mem::Add()
 /** Insert data vIn at frame. */
 void DataSet_integer_mem::Add(size_t frame, const void* vIn) {
diff --git a/src/DataSet_integer_mem.h b/src/DataSet_integer_mem.h
index 58ad304086..24412971a2 100644
--- a/src/DataSet_integer_mem.h
+++ b/src/DataSet_integer_mem.h
@@ -32,6 +32,8 @@ class DataSet_integer_mem : public DataSet_integer {
     void WriteBuffer(CpptrajFile&, SizeArray const&) const;
     int Append(DataSet*);
     size_t MemUsageInBytes() const { return Data_.size() * sizeof(int); }
+    int MemAlloc(SizeArray const&);
+    void CopyBlock(size_t, const DataSet*, size_t, size_t);
     // -------------------------------------------
     //typedef std::vector<int>::iterator iterator;
     //iterator begin()                  { return Data_.begin();      }
diff --git a/src/EnsembleIn_Multi.cpp b/src/EnsembleIn_Multi.cpp
index e0e4c9c4f1..b5e7a30779 100644
--- a/src/EnsembleIn_Multi.cpp
+++ b/src/EnsembleIn_Multi.cpp
@@ -3,6 +3,7 @@
 #include "CpptrajStdio.h"
 #include "DataFile.h" // TODO remove
 #include "StringRoutines.h" // integerToString TODO remove
+#include "ArgList.h"
 
 // EnsembleIn_Multi::SetupEnsembleRead()
 int EnsembleIn_Multi::SetupEnsembleRead(FileName const& tnameIn, ArgList& argIn, Topology *tparmIn)
diff --git a/src/EnsembleIn_Single.cpp b/src/EnsembleIn_Single.cpp
index 08e3aa947d..363b500140 100644
--- a/src/EnsembleIn_Single.cpp
+++ b/src/EnsembleIn_Single.cpp
@@ -5,6 +5,7 @@
 #include "FrameArray.h"
 #include "TrajectoryFile.h"
 #include "CpptrajStdio.h"
+#include "ArgList.h"
 
 // CONSTRUCTOR
 EnsembleIn_Single::EnsembleIn_Single() : eio_(0), ensembleSize_(0) {}
diff --git a/src/EnsembleOutList.cpp b/src/EnsembleOutList.cpp
index d3699b2c1f..371c707ccd 100644
--- a/src/EnsembleOutList.cpp
+++ b/src/EnsembleOutList.cpp
@@ -3,6 +3,7 @@
 #include "CpptrajStdio.h"
 #include "EnsembleOut_Single.h"
 #include "EnsembleOut_Multi.h"
+#include "ArgList.h"
 
 /// CONSTRUCTOR
 EnsembleOutList::EnsembleOutList() : debug_(0) {}
diff --git a/src/EnsembleOut_Multi.cpp b/src/EnsembleOut_Multi.cpp
index 8411305285..2e1f2733a4 100644
--- a/src/EnsembleOut_Multi.cpp
+++ b/src/EnsembleOut_Multi.cpp
@@ -3,6 +3,7 @@
 #include "Topology.h"
 #include "CpptrajStdio.h"
 #include "StringRoutines.h" // AppendNumber
+#include "ArgList.h"
 #ifdef MPI
 # include "Parallel.h"
 #endif
diff --git a/src/EnsembleOut_Single.cpp b/src/EnsembleOut_Single.cpp
index f467fd97df..88f1e6d5b9 100644
--- a/src/EnsembleOut_Single.cpp
+++ b/src/EnsembleOut_Single.cpp
@@ -3,6 +3,7 @@
 #include "TrajectoryIO.h"
 #include "Topology.h"
 #include "CpptrajStdio.h"
+#include "ArgList.h"
 
 // CONSTRUCTOR
 EnsembleOut_Single::EnsembleOut_Single() : eio_(0), ensembleSize_(0) {}
diff --git a/src/Exec_DataSetCmd.cpp b/src/Exec_DataSetCmd.cpp
index c0564c1679..9c5f9fbae5 100644
--- a/src/Exec_DataSetCmd.cpp
+++ b/src/Exec_DataSetCmd.cpp
@@ -285,7 +285,7 @@ Exec::RetType Exec_DataSetCmd::VectorCoord(CpptrajState& State, ArgList& argIn)
   while (!dsl1.empty()) {
     for (DataSetList::const_iterator it = dsl1.begin(); it != dsl1.end(); ++it)
     {
-      if ( (*it)->Type() != DataSet::VECTOR) {
+      if ( (*it)->Group() != DataSet::VECTOR_1D) {
         mprintf("Warning: '%s' 'vectorcoord' only works with vector data sets.\n", (*it)->legend());
       } else if ( (*it)->Size() < 1) {
         mprintf("Warning: '%s' is empty.\n", (*it)->legend());
@@ -820,7 +820,7 @@ Exec::RetType Exec_DataSetCmd::ChangeModeType(CpptrajState const& State, ArgList
           mprintf("Warning: '%s': Expected scalar 1D data set type for mode '%s'\n",
                   (*ds)->legend(), MetaData::ModeString(dmode));
         else if ( dmode == MetaData::M_VECTOR &&
-                  (*ds)->Type() != DataSet::VECTOR )
+                  (*ds)->Group() != DataSet::VECTOR_1D )
           mprintf("Warning: '%s': Expected vector data set type for mode '%s'\n",
                   (*ds)->legend(), MetaData::ModeString(dmode));
         else if ( dmode == MetaData::M_MATRIX &&
diff --git a/src/Exec_Help.cpp b/src/Exec_Help.cpp
index f44531a323..3c8befead8 100644
--- a/src/Exec_Help.cpp
+++ b/src/Exec_Help.cpp
@@ -10,7 +10,7 @@ void Exec_Help::Help() const {
           "\t    <command category> |\n"
           "\t    Form[ats] [{read|write}] |\n"
           "\t    Form[ats] [{trajin|trajout|readdata|writedata|parm|parmwrite} [<fmt key>]] |\n"
-          "\t    Mask\n"
+          "\t    Mask | Math\n"
           "\t   } ]\n"
           "\tCommand Categories: Gen[eral] Sys[tem] Coor[ds] Traj[ectory] Top[ology]\n"
           "\t                    Act[ion] Ana[lysis] Con[trol]\n"
@@ -18,7 +18,8 @@ void Exec_Help::Help() const {
           "  <cmd>              : Print help for command <cmd>.\n"
           "  <command category> : Print all commands in specified category.\n"
           "  Form[ats]          : Help for file formats.\n"
-          "  Mask               : Help for mask syntax.\n");
+          "  Mask               : Help for mask syntax.\n"
+          "  Math               : Help for math operations/functions.\n");
 }
 
 /** Print help for file formats. */
@@ -128,6 +129,36 @@ int Exec_Help::Masks(ArgList& argIn) const {
   return 1;
 }
 
+int Exec_Help::Math(ArgList& argIn) const {
+  mprintf("    Available Math Operations\n"
+          "\tSymbol    Operation\n"
+          "\t  -     : Minus, negate\n"
+          "\t  +     : Plus\n"
+          "\t  /     : Divide\n"
+          "\t  *     : Multiply\n"
+          "\t  ^     : Power\n"
+          "\t  =     : Assign\n"
+          "    Available functions\n"
+          "\tForm      Function\n"
+          "\tsqrt()  : Square root\n"
+          "\texp()   : Exponential\n"
+          "\tln()    : Natural logarithm\n"
+          "\tabs()   : Absolute value\n"
+          "\tsin()   : Sine\n"
+          "\tcos()   : Cosine\n"
+          "\ttan()   : Tangent\n"
+          "    Data set functions\n"
+          "\tsum()   : Summation\n"
+          "\tavg()   : Average\n"
+          "\tstdev() : Standard deviation\n"
+          "\tmin()   : Minimum\n"
+          "\tmax()   : Maximum\n"
+          "    Constants\n"
+          "\tPI      : Pi\n"
+         );
+  return 1;
+}
+
 /** \return 1 if a help topic was found, 0 otherwise. */
 int Exec_Help::Topics(ArgList& argIn) const {
   // By convention, Topics will start with uppercase letters and
@@ -137,6 +168,8 @@ int Exec_Help::Topics(ArgList& argIn) const {
       return Formats(argIn);
     else if (argIn[0].compare(0,4,"Mask")==0)
       return Masks(argIn);
+    else if (argIn[0].compare(0,4,"Math")==0)
+      return Math(argIn);
     else if (argIn.CommandIs("All")) {
       Command::ListCommands( NONE );
       return 1;
diff --git a/src/Exec_Help.h b/src/Exec_Help.h
index 66e7113313..b494b391d0 100644
--- a/src/Exec_Help.h
+++ b/src/Exec_Help.h
@@ -11,6 +11,7 @@ class Exec_Help : public Exec {
   private:
     int Formats(ArgList&) const;
     int Masks(ArgList&) const;
+    int Math(ArgList&) const;
     int Topics(ArgList&) const;
 };
 #endif
diff --git a/src/Exec_Set.cpp b/src/Exec_Set.cpp
new file mode 100644
index 0000000000..ab33068c55
--- /dev/null
+++ b/src/Exec_Set.cpp
@@ -0,0 +1,141 @@
+#include "Exec_Set.h"
+#include "CpptrajStdio.h"
+#include "StringRoutines.h"
+#include "DataSet_StringVar.h"
+
+void Exec_Set::Help() const {
+  mprintf("\t{ <variable> <OP> <value> |\n"
+          "\t  <variable> <OP> {atoms|residues|molecules} inmask <mask>\n"
+          "\t    [%s]\n"
+          "\t  <variable> <OP> trajinframes }\n",
+          DataSetList::TopIdxArgs);
+  mprintf("  Set (<OP> = '=') or append (<OP> = '+=') a script variable.\n"
+          "  - Set script variable <variable> to value <value>.\n"
+          "  - Set script variable to the number of atoms/residues/molecules in\n"
+          "     the given atom mask.\n"
+          "  - Set script variable to the current number of frames that will\n"
+          "     be read from all previous 'trajin' statements.\n");
+}
+
+/** Set up variable with value. In this case allow any amount of whitespace,
+  * so re-tokenize the original argument line (minus the command).
+  */
+Exec::RetType Exec_Set::Execute(CpptrajState& State, ArgList& argIn)
+{
+  ArgList remaining = argIn.RemainingArgs();
+  size_t pos0 = remaining.ArgLineStr().find_first_of("=");
+  if (pos0 == std::string::npos) {
+    mprinterr("Error: Expected <var>=<value>\n");
+    return CpptrajState::ERR;
+  }
+  size_t pos1 = pos0;
+  bool append = false;
+  if (pos0 > 0 && remaining.ArgLineStr()[pos0-1] == '+') {
+    pos0--;
+    append = true;
+  }
+  std::string variable = NoWhitespace( remaining.ArgLineStr().substr(0, pos0) );
+  if (variable.empty()) {
+    mprinterr("Error: No variable name.\n");
+    return CpptrajState::ERR;
+  }
+  ArgList equals( NoLeadingWhitespace(remaining.ArgLineStr().substr(pos1+1)) );
+  std::string value;
+  if (equals.Contains("inmask")) {
+    AtomMask mask( equals.GetStringKey("inmask") );
+    Topology* top = State.DSL().GetTopByIndex( equals );
+    if (top == 0) return CpptrajState::ERR;
+    if (top->SetupIntegerMask( mask )) return CpptrajState::ERR;
+    if (equals.hasKey("atoms"))
+      value = integerToString( mask.Nselected() );
+    else if (equals.hasKey("residues")) {
+      int curRes = -1;
+      int nres = 0;
+      for (AtomMask::const_iterator at = mask.begin(); at != mask.end(); ++at) {
+        int res = (*top)[*at].ResNum();
+        if (res != curRes) {
+          nres++;
+          curRes = res;
+        }
+      }
+      value = integerToString( nres );
+    } else if (equals.hasKey("molecules")) {
+      int curMol = -1;
+      int nmol = 0;
+      for (AtomMask::const_iterator at = mask.begin(); at != mask.end(); ++at) {
+        int mol = (*top)[*at].MolNum();
+        if (mol != curMol) {
+          nmol++;
+          curMol = mol;
+        }
+      }
+      value = integerToString( nmol );
+    } else {
+      mprinterr("Error: Expected 'atoms', 'residues', or 'molecules'.\n");
+      return CpptrajState::ERR;
+    }
+  } else if (equals.hasKey("trajinframes")) {
+    value = integerToString(State.InputTrajList().MaxFrames());
+  } else
+    value = equals.ArgLineStr();
+  if (append) {
+    AppendVariable( State, variable, value );
+    mprintf("\tVariable '%s' appended with '%s'\n", variable.c_str(), value.c_str());
+  } else {
+    UpdateVariable( State, variable, value );
+    mprintf("\tVariable '%s' set to '%s'\n", variable.c_str(), value.c_str());
+  }
+  for (int iarg = 0; iarg < argIn.Nargs(); iarg++)
+    argIn.MarkArg( iarg );
+  return CpptrajState::OK;
+}
+
+/** Create new variable set with given value. */
+int Exec_Set::AddVariable(CpptrajState& State, std::string const& varname,
+                              std::string const& value)
+{
+  DataSet* ds = State.DSL().AddSet( DataSet::STRINGVAR, MetaData(varname) );
+  if (ds == 0) return 1;
+  DataSet_StringVar& var = static_cast<DataSet_StringVar&>( *ds );
+  var.assign( value );
+
+  return 0;
+}
+
+/** Add variable/value if it doesnt exist, otherwise append value. */
+int Exec_Set::AppendVariable(CpptrajState& State, std::string const& varname,
+                              std::string const& value)
+{
+  DataSet* ds = State.DSL().CheckForSet( varname );
+  if (ds == 0) {
+    // Create new
+    return AddVariable(State, varname, value);
+  }
+  // Set exists; append
+  if (ds->Type() != DataSet::STRINGVAR) {
+    mprinterr("Error: 'set +=' can only be done for string variable sets.\n");
+    return 1;
+  }
+  DataSet_StringVar& var = static_cast<DataSet_StringVar&>( *ds );
+  var.append( value );
+  return 0;
+}
+
+/** Add variable/value if it doesnt exist, otherwise set value. */
+int Exec_Set::UpdateVariable(CpptrajState& State, std::string const& varname,
+                             std::string const& value)
+{
+  DataSet* ds = State.DSL().CheckForSet( varname );
+  if (ds == 0) {
+    // Create new
+    return AddVariable(State, varname, value);
+  }
+  // Set exists; replace current value
+  if (ds->Type() != DataSet::STRINGVAR) {
+    mprinterr("Error: 'set +=' can only be done for string variable sets.\n");
+    return 1;
+  }
+  DataSet_StringVar& var = static_cast<DataSet_StringVar&>( *ds );
+  var.assign( value );
+  return 0;
+}
diff --git a/src/Exec_Set.h b/src/Exec_Set.h
new file mode 100644
index 0000000000..1498356cd0
--- /dev/null
+++ b/src/Exec_Set.h
@@ -0,0 +1,16 @@
+#ifndef INC_EXEC_SET_H
+#define INC_EXEC_SET_H
+#include "Exec.h"
+/// Used to set script variables
+class Exec_Set : public Exec {
+  public:
+    Exec_Set() : Exec(CONTROL) {}
+    void Help() const;
+    DispatchObject* Alloc() const { return (DispatchObject*)new Exec_Set(); }
+    RetType Execute(CpptrajState&, ArgList&);
+  private:
+    static int AddVariable(CpptrajState&, std::string const&, std::string const&);
+    static int AppendVariable(CpptrajState&, std::string const&, std::string const&);
+    static int UpdateVariable(CpptrajState&, std::string const&, std::string const&);
+};
+#endif
diff --git a/src/Exec_Show.cpp b/src/Exec_Show.cpp
new file mode 100644
index 0000000000..88133dfc30
--- /dev/null
+++ b/src/Exec_Show.cpp
@@ -0,0 +1,33 @@
+#include "Exec_Show.h"
+#include "CpptrajStdio.h"
+#include "DataSet_StringVar.h"
+
+void Exec_Show::Help() const {
+  mprintf("\t[<var1> ...]\n"
+          "  If no variable names specified, show all current script variables and\n"
+          "  their values. Otherwise, show the values of the specified script\n"
+          "  variables.\n");
+}
+
+Exec::RetType Exec_Show::Execute(CpptrajState& State, ArgList& argIn)
+{
+  std::string varname = argIn.GetStringNext();
+  if (varname.empty()) {
+    State.DSL().ListStringVar();
+  } else {
+    while (!varname.empty()) {
+      DataSetList Svars = State.DSL().GetMultipleSets( varname );
+      if (Svars.empty()) {
+        return CpptrajState::ERR;
+      }
+      for (DataSetList::const_iterator ds = Svars.begin(); ds != Svars.end(); ++ds) {
+        if ( (*ds)->Type() == DataSet::STRINGVAR ) {
+          DataSet_StringVar const& var = static_cast<DataSet_StringVar const&>( *(*ds) );
+          mprintf("\t%s = '%s'\n", var.legend(), var.Value().c_str());
+        }
+      }
+      varname = argIn.GetStringNext();
+    }
+  }
+  return CpptrajState::OK;
+}
diff --git a/src/Exec_Show.h b/src/Exec_Show.h
new file mode 100644
index 0000000000..5bb2973d15
--- /dev/null
+++ b/src/Exec_Show.h
@@ -0,0 +1,12 @@
+#ifndef INC_EXEC_SHOW_H
+#define INC_EXEC_SHOW_H
+#include "Exec.h"
+/// Used to print current script variables to stdout
+class Exec_Show : public Exec {
+  public:
+    Exec_Show() : Exec(CONTROL) {}
+    void Help() const;
+    DispatchObject* Alloc() const { return (DispatchObject*)new Exec_Show(); }
+    RetType Execute(CpptrajState&, ArgList&);
+};
+#endif
diff --git a/src/FileTypes.cpp b/src/FileTypes.cpp
index 1c63573f93..f9e21fe1cd 100644
--- a/src/FileTypes.cpp
+++ b/src/FileTypes.cpp
@@ -3,6 +3,8 @@
 #include <cstring> // strlen
 #include "FileTypes.h"
 #include "CpptrajStdio.h"
+#include "ArgList.h"
+
 // FileTypes::GetFormatFromArg()
 FileTypes::FileFormatType FileTypes::GetFormatFromArg(KeyPtr begin, ArgList& argIn,
                                                       FileFormatType def)
diff --git a/src/FileTypes.h b/src/FileTypes.h
index 4b38e2232a..8d0d8a21da 100644
--- a/src/FileTypes.h
+++ b/src/FileTypes.h
@@ -1,7 +1,8 @@
 #ifndef INC_FILETYPES_H
 #define INC_FILETYPES_H
+#include <string>
 #include "BaseIOtype.h"
-#include "ArgList.h"
+class ArgList;
 /** This static class is used to create arrays for allocatable file classes
   * like DataFiles and Trajectories.
   */
diff --git a/src/ForLoop.cpp b/src/ForLoop.cpp
new file mode 100644
index 0000000000..c74223c464
--- /dev/null
+++ b/src/ForLoop.cpp
@@ -0,0 +1,25 @@
+#include "ForLoop.h"
+#include "DataSetList.h"
+#include "CpptrajStdio.h"
+#include "DataSet.h"
+
+int ForLoop::SetupLoopVar(DataSetList& DSL, std::string const& varname)
+{
+  loopvar_ = DSL.CheckForSet( varname );
+  if (loopvar_ != 0) {
+    if (loopvar_->Type() != DataSet::STRINGVAR) {
+      mprinterr("Error: Set '%s' exists but is not a string variable, cannot be used for loop.\n",
+                varname.c_str());
+      return 1;
+    }
+  } else {
+    loopvar_ = DSL.AddSet( DataSet::STRINGVAR, varname );
+    if (loopvar_ == 0) return 1;
+  }
+  //mprintf("DEBUG: Loop variable: '%s'\n", loopvar_->legend());
+  return 0;
+}
+
+std::string const& ForLoop::VarName() const {
+  return loopvar_->Meta().Name();
+}
diff --git a/src/ForLoop.h b/src/ForLoop.h
new file mode 100644
index 0000000000..b9d747b3f4
--- /dev/null
+++ b/src/ForLoop.h
@@ -0,0 +1,44 @@
+#ifndef INC_FORLOOP_H
+#define INC_FORLOOP_H
+#include <string>
+class CpptrajState;
+class ArgList;
+class DataSetList;
+class DataSet;
+/// Abstract base class for all for loops
+class ForLoop {
+  public:
+    ForLoop() : loopvar_(0) {}
+    virtual ~ForLoop() {}
+
+    /// Set up the loop, ensure syntax is correct
+    virtual int SetupFor(CpptrajState&, ArgList&)  = 0;
+    /// Start the loop
+    /** \return Number of iterations in loop, or NITERATIONS_UNKNOWN. */
+    virtual int BeginFor(DataSetList const&) = 0;
+    /// \return True if loop is done, otherwise increment the loop
+    virtual bool EndFor(DataSetList&) = 0;
+
+    /// Return value when number of iterations is not known
+    static const int NITERATIONS_UNKNOWN = -1;
+    /// Return value when an error has occurred
+    static const int LOOP_ERROR = -2;
+
+    /// \return For loop description TODO make virtual fn?
+    std::string const& Description() const { return description_; }
+    /// \return For loop variable name
+    std::string const& VarName() const;
+    /// \return true if For loop is set up and has a variable
+    bool IsSetup() const { return (loopvar_ != 0); }
+  protected:
+    /// Set loop description. Should be called inside SetupFor.
+    void SetDescription(std::string const& descIn) { description_ = descIn; }
+    /// Set up the loop variable with given name. Should be called inside SetupFor
+    int SetupLoopVar(DataSetList&, std::string const&);
+
+    //ForType VarType()            const { return varType_; }
+  private:
+    std::string description_; ///< For loop long description
+    DataSet* loopvar_;        ///< Variable over which loop is iterating.
+};
+#endif
diff --git a/src/ForLoop_dataSetBlocks.cpp b/src/ForLoop_dataSetBlocks.cpp
new file mode 100644
index 0000000000..fe846706c2
--- /dev/null
+++ b/src/ForLoop_dataSetBlocks.cpp
@@ -0,0 +1,163 @@
+#include "ForLoop_dataSetBlocks.h"
+#include "CpptrajStdio.h"
+#include "ArgList.h"
+#include "CpptrajState.h"
+#include "DataSet.h"
+#include "StringRoutines.h"
+#ifdef MPI
+# include "Parallel.h"
+#endif
+
+/// CONSTRUCTOR
+ForLoop_dataSetBlocks::ForLoop_dataSetBlocks() :
+  sourceSet_(0),
+  currentSet_(0),
+  blocksize_(0),
+  blockoffset_(0),
+  idx_(0),
+  mode_(BLOCKS)
+{}
+
+void ForLoop_dataSetBlocks::helpText() {
+  mprintf("\t<var> datasetblocks <set> blocksize <#> [blockoffset <#>]\n"
+          "\t[cumulative [firstblock <#>]]\n"
+          "  Loop over blocks of a dataset. The blocks can be either\n"
+          "  fixed or cumulative.\n");
+}
+
+int ForLoop_dataSetBlocks::SetupFor(CpptrajState& State, ArgList& argIn)
+{
+  // <var> datasetblocks <set> blocksize <#> [blockoffset <#>] [cumulative [firstblock <#>]]
+# ifdef MPI
+  if (Parallel::World().Size() > 1) {
+    mprinterr("Error: 'datasetblocks' loop cannot be used in parallel.\n");
+    return 1;
+  }
+# endif
+  if (argIn.hasKey("cumulative"))
+    mode_ = CUMULATIVE;
+  else
+    mode_ = BLOCKS;
+  sourceSetName_ = argIn.GetStringKey("datasetblocks");
+  if (sourceSetName_.empty()) {
+    mprinterr("Error: No data set name given.\n");
+    return 1;
+  }
+  blocksize_ = argIn.getKeyInt("blocksize", 0);
+  if (blocksize_ < 1) {
+    mprinterr("Error: No blocksize or invalid blocksize: %li\n", blocksize_);
+    return 1;
+  }
+  blockoffset_ = argIn.getKeyInt("blockoffset", 0);
+  if (mode_ == BLOCKS) {
+    if (blockoffset_ == 0) {
+      mprintf("Warning: 'blockoffset' not specified, using 'blocksize'.\n");
+      blockoffset_ = blocksize_;
+    }
+  } else if (mode_ == CUMULATIVE) {
+    if (blockoffset_ != 0) {
+      mprinterr("Error: 'blockoffset' cannot be specified with 'cumulative'\n");
+      return 1;
+    }
+    blockoffset_ = blocksize_;
+    blocksize_ = argIn.getKeyInt("firstblock", blocksize_);
+  }
+  idx_ = argIn.getKeyInt("blockstart", 0);
+  // Set up loop variable
+  if (SetupLoopVar( State.DSL(), argIn.GetStringNext() )) return 1;
+  // Description
+  std::string description("(" + VarName() + " datasetblocks " + sourceSetName_ + ")");
+  SetDescription( description );
+  return 0;
+}
+
+int ForLoop_dataSetBlocks::BeginFor(DataSetList const& DSL) {
+  sourceSet_ = DSL.GetDataSet( sourceSetName_ );
+  if (sourceSet_ == 0) {
+    mprinterr("Error: No data set found with name '%s'\n", sourceSetName_.c_str());
+    return 1;
+  }
+  if (sourceSet_->Group() != DataSet::SCALAR_1D &&
+      sourceSet_->Group() != DataSet::VECTOR_1D)
+  {
+    mprinterr("Error: Set '%s' is not 1D scalar or vector.\n", sourceSet_->legend());
+    return 1;
+  }
+  if (sourceSet_->Size() < 1) {
+    mprinterr("Error: Set '%s' is empty.\n", sourceSet_->legend());
+    return 1;
+  }
+  // Determine # iterations
+  long int total_size = (long int)sourceSet_->Size() - idx_;
+  long int niterations = 0;
+  if (mode_ == CUMULATIVE) {
+    niterations = 1;
+    total_size -= blocksize_;
+    if (total_size < 0) total_size = 0;
+  }
+  niterations += ( total_size / labs(blockoffset_) );
+  if ( (total_size % labs(blockoffset_)) > 0 )
+    ++niterations;
+  return niterations;
+}
+
+bool ForLoop_dataSetBlocks::EndFor(DataSetList& DSL) {
+  // Determine stop of the current block.
+  long int block_end = idx_ + blocksize_;
+  long int dsidx = 0;
+  std::string aspect = "";
+  // Check if done.
+  switch (mode_) {
+    case BLOCKS:
+      // Check if done by seeing if the current start value is outside the data set.
+      if (idx_ < 0 || idx_ >= (long int)sourceSet_->Size()) return true;
+      dsidx = idx_ + 1;
+      aspect = "block";
+      break;
+    case CUMULATIVE:
+      // Check if done by seeing if current end value is outside the data set.
+      //if (block_end < 0) {
+      //  if ( block_end < blockoffset_ ) return true;
+      //} else if (block_end > (long int)sourceSet_->size()) {
+        //mprintf("DEBUG: Block end %li set size %zu\n", block_end, sourceSet_->Size());
+        if ( block_end >= (long int)sourceSet_->Size() + blockoffset_ ) return true;
+        // Ensure block end is not too high
+        if (block_end > (long int)sourceSet_->Size())
+          block_end = (long int)sourceSet_->Size();
+        dsidx = block_end;
+        aspect = "cumul";
+      break;
+  }
+  //mprintf("DEBUG: Block %li to %li\n", idx_, block_end);
+  // Create the subset
+  currentSet_ = DSL.AddSet(sourceSet_->Type(), MetaData(VarName(), aspect, dsidx));
+  if (currentSet_ == 0) {
+    mprinterr("Error: Could not create dataSetBlocks subset.\n");
+    return true;
+  }
+  // Update the set legend
+  currentSet_->SetLegend(sourceSet_->Meta().Name() + "_" +
+                         integerToString(idx_+1) + "-" +
+                         integerToString(block_end));
+  // Update the set name in loop variable
+  DSL.UpdateStringVar( VarName(), currentSet_->Meta().PrintName() );
+  // Allocate memory
+  DataSet::SizeArray dsSize(1, blocksize_);
+  if ( currentSet_->MemAlloc( dsSize ) ) {
+    mprinterr("Internal Error: Could not allocate dataSetBlocks subset; not yet supported.\n");
+    return true;
+  }
+  // Copy block
+  currentSet_->CopyBlock(0, sourceSet_, idx_, blocksize_);
+  switch (mode_) {
+    case BLOCKS:
+      // Increment the start
+      idx_ += blockoffset_;
+      break;
+    case CUMULATIVE:
+      // Increment the size
+      blocksize_ += blockoffset_;
+      break;
+  }
+  return false;
+}
diff --git a/src/ForLoop_dataSetBlocks.h b/src/ForLoop_dataSetBlocks.h
new file mode 100644
index 0000000000..4770e6e3a3
--- /dev/null
+++ b/src/ForLoop_dataSetBlocks.h
@@ -0,0 +1,27 @@
+#ifndef INC_FORLOOP_DATASETBLOCKS_H
+#define INC_FORLOOP_DATASETBLOCKS_H
+#include "ForLoop.h"
+/// For loop, data set blocks
+class ForLoop_dataSetBlocks : public ForLoop {
+  public:
+    ForLoop_dataSetBlocks();
+
+    static void helpText();
+
+    int SetupFor(CpptrajState&, ArgList&);
+    int BeginFor(DataSetList const&);
+    // NOTE: Not a const ref so dataSetBlocks loop can create sets
+    bool EndFor(DataSetList&);
+    
+  private:
+    enum ModeType { BLOCKS=0, CUMULATIVE };
+
+    DataSet* sourceSet_;   ///< Set to loop over
+    DataSet* currentSet_;  ///< Current subset
+    std::string sourceSetName_; 
+    long int blocksize_;   ///< Size of blocks
+    long int blockoffset_; ///< Block offset
+    long int idx_;         ///< Current index into sourceSet_
+    ModeType mode_;        ///< Current mode
+};
+#endif
diff --git a/src/ForLoop_integer.cpp b/src/ForLoop_integer.cpp
new file mode 100644
index 0000000000..e42bd5b527
--- /dev/null
+++ b/src/ForLoop_integer.cpp
@@ -0,0 +1,270 @@
+#include "ForLoop_integer.h"
+#include "CpptrajStdio.h"
+#include "ArgList.h"
+#include "StringRoutines.h"
+#include "CpptrajState.h"
+#include "DataSetList.h"
+
+const char* ForLoop_integer::OpStr_[NO_OP] = {"+=", "-=", "<", ">", "<=", ">=" };
+
+ForLoop_integer::ForLoop_integer() :
+  endOp_(NO_OP),
+  incOp_(NO_OP),
+  start_(0),
+  end_(0),
+  inc_(0),
+  currentVal_(0),
+  endArgPresent_(false)
+{}
+
+void ForLoop_integer::helpText() {
+  mprintf("\t<var>=<start>;[<var><end OP><end>;]<var><increment OP>[<value>]\n"
+          "    Available 'end OP'       : '<' '>' '<=' '>='\n"
+          "    Available 'increment OP' : '++', '--', '+=', '-='\n"
+          "  Loop over an integer value.\n");
+}
+
+/** Setup integer for loop. */
+int ForLoop_integer::SetupFor(CpptrajState& State, ArgList& argIn) {
+  // [<var>=<start>;[<var><OP><end>;]<var><OP>[<value>]]
+  //SetType( INTEGER );
+  // Sanity check
+  if (argIn.Nargs() != 1) {
+    mprinterr("Internal Error: Too many arguments for integer for loop.\n");
+    return 1;
+  }
+  ArgList varArg( argIn.GetStringNext(), ";" );
+  //varArg.PrintDebug(); // DEBUG
+  if (varArg.Nargs() < 2 || varArg.Nargs() > 3) {
+    mprinterr("Error: Malformed 'for' loop variable.\n"
+              "Error: Expected '[<var>=<start>;[<var><OP><end>;]<var><OP>[<value>]]'\n"
+              "Error: Got '%s'\n", argIn[0].c_str());
+    return 1;
+  }
+  // First argument: <var>=<start>
+  ArgList startArg( varArg[0], "=" );
+  if (startArg.Nargs() != 2) {
+    mprinterr("Error: Malformed 'start' argument.\n"
+              "Error: Expected <var>=<start>, got '%s'\n", varArg[0].c_str());
+    return 1;
+  }
+  if (SetupLoopVar( State.DSL(),startArg[0] )) return 1;
+  //mprintf("DEBUG: Start argument: '%s' = '%s'\n", VarName().c_str(), startArg[1].c_str());
+  if ( startArg[1][0] == '$' ) {
+    // Variable name 
+    startVarName_ = RemoveLeadingChars(startArg[1], 1);
+  } else if (!validInteger(startArg[1])) {
+    // Not Integer or variable
+    mprinterr("Error: Start argument must be an integer or variable name.\n");
+    return 1;
+  } else
+    start_ = convertToInteger(startArg[1]);
+  // Second argument: <var><OP><end>
+  size_t pos0 = VarName().size();
+  size_t pos1 = pos0 + 1;
+  endOp_ = NO_OP;
+  int iargIdx = 1;
+  if (varArg.Nargs() == 3) {
+    iargIdx = 2;
+    if ( varArg[1][pos0] == '<' ) {
+      if ( varArg[1][pos0+1] == '=' ) {
+        endOp_ = LT_EQUALS;
+        pos1 = pos0 + 2;
+      } else
+        endOp_ = LESS_THAN;
+    } else if ( varArg[1][pos0] == '>' ) {
+      if ( varArg[1][pos0+1] == '=' ) {
+        endOp_ = GT_EQUALS;
+        pos1 = pos0 + 2;
+      } else
+        endOp_ = GREATER_THAN;
+    }
+    if (endOp_ == NO_OP) {
+      mprinterr("Error: Unrecognized end op: '%s'\n",
+                varArg[1].substr(pos0, pos1-pos0).c_str());
+      return 1;
+    }
+    std::string endStr = varArg[1].substr(pos1);
+    //mprintf("DEBUG: endStr= '%s'\n", endStr.c_str());
+    if ( endStr[0] == '$' ) {
+      // Variable name
+      endVarName_ = RemoveLeadingChars(endStr, 1);
+    } else if (!validInteger(endStr)) {
+      // Not Integer of variable
+      mprinterr("Error: End argument must be an integer or variable name.\n");
+      return 1;
+    } else
+      end_ = convertToInteger(endStr);
+  }
+  // Third argument: <var><OP>[<value>]
+  pos1 = pos0 + 2;
+  incOp_ = NO_OP;
+  bool needValue = false;
+  if ( varArg[iargIdx][pos0] == '+' ) {
+    if (varArg[iargIdx][pos0+1] == '+') {
+      incOp_ = INCREMENT;
+      inc_ = 1;
+    } else if (varArg[iargIdx][pos0+1] == '=') {
+      incOp_ = INCREMENT;
+      needValue = true;
+    }
+  } else if ( varArg[iargIdx][pos0] == '-' ) {
+    if (varArg[iargIdx][pos0+1] == '-' ) {
+      incOp_ = DECREMENT;
+      inc_ = 1;
+    } else if (varArg[iargIdx][pos0+1] == '=') {
+      incOp_ = DECREMENT;
+      needValue = true;
+    }
+  }
+  if (incOp_ == NO_OP) {
+    mprinterr("Error: Unrecognized increment op: '%s'\n",
+              varArg[iargIdx].substr(pos0, pos1-pos0).c_str());
+    return 1;
+  }
+  if (needValue) {
+    std::string incStr = varArg[iargIdx].substr(pos1);
+    if (!validInteger(incStr)) {
+      mprinterr("Error: increment value is not a valid integer.\n");
+      return 1;
+    }
+    inc_ = convertToInteger(incStr);
+    if (inc_ < 1) {
+      mprinterr("Error: Extra '-' detected in increment.\n");
+      return 1;
+    }
+  }
+  // Description
+  std::string sval;
+  if (startVarName_.empty())
+    sval = integerToString(start_);
+  else
+    sval = startVarName_;
+  std::string description("(" + VarName() + "=" + sval + "; ");
+  std::string eval;
+  if (iargIdx == 2) {
+    // End argument present
+    endArgPresent_ = true;
+    if (endVarName_.empty())
+      eval = integerToString(end_);
+    else
+      eval = endVarName_;
+    description.append(VarName() + std::string(OpStr_[endOp_]) + eval + "; ");
+  } else
+    endArgPresent_ = false;
+  description.append( VarName() + std::string(OpStr_[incOp_]) +
+                       integerToString(inc_) + ")" );
+  SetDescription( description );
+  // If decrementing just negate value
+  if (incOp_ == DECREMENT)
+    inc_ = -inc_;
+  // DEBUG
+  //mprintf("DEBUG: start=%i endOp=%i end=%i incOp=%i val=%i startArg=%s endArg=%s\n",
+  //        start_, (int)endOp_, end_, (int)incOp_, inc_,
+  //        startArg_.c_str(), endArg_.c_str());
+
+  return 0;
+}
+
+/** Calculate the number of times the loop will execute. Also check
+  * that start and end values are sane.
+  */
+int ForLoop_integer::calcNumIterations() const {
+  if (!endArgPresent_) return NITERATIONS_UNKNOWN;
+  // Check end > start for increment, start > end for decrement
+  int maxval, minval;
+  if (incOp_ == INCREMENT) {
+    // When incrementing, start must be less than end, so only valid end
+    // ops are < and <=.
+    if (endOp_ != LESS_THAN && endOp_ != LT_EQUALS) {
+      mprinterr("Error: For increment, only valid end ops are < and <=.\n");
+      return LOOP_ERROR;
+    }
+    int offset = 0;
+    if (endOp_ == LT_EQUALS) offset = inc_;
+    if ( start_ >= end_ + offset )
+    {
+      mprintf("Warning: start (%i) and end (%i) values result in no iterations.\n",
+                start_, end_ + offset);
+      return 0;
+    }
+    minval = start_;
+    maxval = end_ + offset;
+  } else {
+    // When decrementing, end must be less than start, so only valid end
+    // ops are > and >=.
+    if (endOp_ != GREATER_THAN && endOp_ != GT_EQUALS) {
+      mprinterr("Error: For decrement, only valid end ops are > and >=.\n");
+      return LOOP_ERROR;
+    }
+    int offset = 0;
+    if (endOp_ == GT_EQUALS) offset = inc_;
+    if ( (endOp_ == GREATER_THAN && end_ >= start_) ||
+         (endOp_ == GT_EQUALS    && end_ > start_) )
+    {
+      mprintf("Warning: end (%i) and start (%i) values result in no iterations.\n",
+                end_, start_);
+      return 0;
+    }
+    minval = end_ + offset;
+    maxval = start_;
+  }
+  // Figure out number of iterations
+  int Niterations = (maxval - minval) / inc_;
+  // Sanity check
+  if (Niterations < 0) return LOOP_ERROR;
+  if (((maxval-minval) % inc_) > 0) Niterations++;
+  return Niterations;
+}
+
+/** Set start value and determine number of iterations. */
+int ForLoop_integer::BeginFor(DataSetList const& DSL) {
+  if (!startVarName_.empty()) {
+    std::string sval = DSL.GetVariable( startVarName_ );
+    if (sval.empty()) {
+      mprinterr("Error: Start variable '%s' does not exist.\n", startVarName_.c_str());
+      return LOOP_ERROR;
+    }
+    if (!validInteger(sval)) {
+      mprinterr("Error: Variable '%s' does not contain a valid integer (%s)\n",
+                startVarName_.c_str(), sval.c_str());
+      return LOOP_ERROR;
+    }
+    start_ = convertToInteger(sval);
+  }
+  currentVal_ = start_;
+  // Determine end arg if necessary
+  if (endArgPresent_ && !endVarName_.empty()) {
+    std::string eval = DSL.GetVariable( endVarName_ );
+    if (eval.empty()) {
+      mprinterr("Error: End variable '%s' does not exist.\n", endVarName_.c_str());
+      return LOOP_ERROR;
+    }
+    if (!validInteger(eval)) {
+      mprinterr("Error: Variable '%s' does not contain a valid integer (%s)\n",
+                endVarName_.c_str(), eval.c_str());
+      return LOOP_ERROR;
+    }
+    end_ = convertToInteger(eval);
+  }
+  return calcNumIterations();
+}
+
+/** Check if integer for loop is done, increment if not. */
+bool ForLoop_integer::EndFor(DataSetList& DSL) {
+  bool retval = false;
+  if (endOp_ == LESS_THAN) {
+    if (currentVal_ >= end_) retval = true;
+  } else if (endOp_ == GREATER_THAN) {
+    if (currentVal_ <= end_) retval = true;
+  } else if (endOp_ == LT_EQUALS) {
+    if ( currentVal_ > end_ ) retval = true;
+  } else if (endOp_ == GT_EQUALS) {
+    if ( currentVal_ < end_ ) retval = true;
+  }
+  // Get variable value and update CurrentVars
+  DSL.UpdateStringVar( VarName(), integerToString( currentVal_ ) );
+  // Increment
+  currentVal_ += inc_;
+  return retval;
+}
diff --git a/src/ForLoop_integer.h b/src/ForLoop_integer.h
new file mode 100644
index 0000000000..981bf2caf9
--- /dev/null
+++ b/src/ForLoop_integer.h
@@ -0,0 +1,31 @@
+#ifndef INC_FORLOOP_INTEGER_H
+#define INC_FORLOOP_INTEGER_H
+#include "ForLoop.h"
+/// Basic for loops over integer value
+class ForLoop_integer : public ForLoop {
+  public:
+    ForLoop_integer();
+
+    static void helpText();
+
+    int SetupFor(CpptrajState&, ArgList&);
+    int BeginFor(DataSetList const&);
+    bool EndFor(DataSetList&);
+
+    enum OpType { INCREMENT=0, DECREMENT, LESS_THAN, GREATER_THAN, LT_EQUALS, GT_EQUALS, NO_OP };
+  private:
+    static const char* OpStr_[NO_OP];
+
+    int calcNumIterations() const;
+
+    std::string startVarName_;   ///< Variable containing initial value
+    std::string endVarName_;     ///< Variable containing the end value
+    OpType endOp_;               ///< (INTEGER only) end operator
+    OpType incOp_;               ///< (INTEGER only) increment operator
+    int start_;                  ///< (INTEGER only) initial value
+    int end_;                    ///< (INTEGER only) end value
+    int inc_;                    ///< (INTEGER only) increment value
+    int currentVal_;             ///< (INTEGER only) current value
+    bool endArgPresent_;         ///< True if an end argument was specified
+};
+#endif
diff --git a/src/ForLoop_list.cpp b/src/ForLoop_list.cpp
new file mode 100644
index 0000000000..8fdf583c4c
--- /dev/null
+++ b/src/ForLoop_list.cpp
@@ -0,0 +1,76 @@
+#include "ForLoop_list.h"
+#include "CpptrajStdio.h"
+#include "ArgList.h"
+#include "FileName.h"
+#include "DataSetList.h"
+#include "CpptrajState.h"
+
+void ForLoop_list::helpText() {
+  mprintf("\t<var> in <list>\n"
+          "  Loop over values in comma-separated list. Values can be file names\n"
+          "  containing wildcard characters ('*' or '?').\n");
+}
+
+int ForLoop_list::SetupFor(CpptrajState& State, ArgList& argIn) {
+  // <var> in <string0>[,<string1>...]
+  //MH.varType_ = ftype;
+  // Comma-separated list of strings.
+  std::string listArg = argIn.GetStringKey("in");
+  if (listArg.empty()) {
+    mprinterr("Error: 'for in': missing ' in <comma-separated list of strings>'.\n");
+    return 1;
+  }
+  ArgList list(listArg, ",");
+  if (list.Nargs() < 1) {
+    mprinterr("Error: Could not parse '%s' for 'for in'\n", listArg.c_str());
+    return 1;
+  }
+  // Variable name.
+  if (SetupLoopVar( State.DSL(), argIn.GetStringNext() )) return 1;
+  // Go through list of strings
+  for (int il = 0; il != list.Nargs(); il++) {
+    Names_.push_back( list[il] );
+  }
+  // Description
+  std::string description( "(" + VarName() + " in " + listArg + ")" );
+  SetDescription( description );
+  return 0;
+}
+
+int ForLoop_list::BeginFor(DataSetList const& CurrentVars) {
+  // Go through list of strings
+  List_.clear();
+  for (Sarray::const_iterator it = Names_.begin(); it != Names_.end(); ++it)
+  {
+    // Try variable replacement
+    std::string listEntry;
+    CurrentVars.ReplaceVariables(listEntry, *it);
+    // Check if file name expansion should occur
+    if (listEntry.find_first_of("*?") != std::string::npos) {
+      File::NameArray files = File::ExpandToFilenames( listEntry );
+      // DEBUG
+      //for (File::NameArray::const_iterator fn = files.begin(); fn != files.end(); ++fn)
+      //  mprintf("DEBUG: '%s'\n", fn->full());
+      // Allow wildcard expansion to fail with a warning.
+      if (!files.empty() && files.front().Full().compare( listEntry ) == 0) {
+        mprintf("Warning: '%s' selects no files.\n", it->c_str());
+      } else {
+        for (File::NameArray::const_iterator fn = files.begin(); fn != files.end(); ++fn)
+          List_.push_back( fn->Full() );
+      }
+    } else
+      List_.push_back( listEntry );
+  }
+
+  sdx_ = List_.begin();
+  return (int)List_.size();
+}
+
+bool ForLoop_list::EndFor(DataSetList& DSL) {
+  if (sdx_ == List_.end()) return true;
+  // Get variable value
+  DSL.UpdateStringVar( VarName(), *(sdx_) );
+  // Increment
+  ++(sdx_);
+  return false;
+}
diff --git a/src/ForLoop_list.h b/src/ForLoop_list.h
new file mode 100644
index 0000000000..eefb4afb6f
--- /dev/null
+++ b/src/ForLoop_list.h
@@ -0,0 +1,21 @@
+#ifndef INC_FORLOOP_LIST_H
+#define INC_FORLOOP_LIST_H
+#include <vector>
+#include <string>
+#include "ForLoop.h"
+class ForLoop_list : public ForLoop {
+  public:
+    ForLoop_list() {}
+
+    static void helpText();
+
+    int SetupFor(CpptrajState&, ArgList&);
+    int BeginFor(DataSetList const&);
+    bool EndFor(DataSetList&);
+  private:
+    typedef std::vector<std::string> Sarray;
+    Sarray Names_;               ///< List of strings, potentially need expansion/replacement
+    Sarray List_;                ///< (LIST only) List of strings to iterate over.
+    Sarray::const_iterator sdx_; ///< (LIST only) Iterator to current list item.
+};
+#endif
diff --git a/src/ForLoop_mask.cpp b/src/ForLoop_mask.cpp
new file mode 100644
index 0000000000..b7e2756a5f
--- /dev/null
+++ b/src/ForLoop_mask.cpp
@@ -0,0 +1,104 @@
+#include "ForLoop_mask.h"
+#include "CpptrajStdio.h"
+#include "ArgList.h"
+#include "CpptrajState.h"
+#include "StringRoutines.h"
+#include "DataSetList.h"
+
+void ForLoop_mask::helpText() {
+  mprintf("\t{atoms|residues|molecules|molfirstres|mollastres}\n"
+          "\t  <var> inmask <mask> [%s]\n", DataSetList::TopIdxArgs);
+  mprintf("  Loop over elements selected by specified mask expression.\n");
+}
+
+int ForLoop_mask::SetupFor(CpptrajState& State, ArgList& argIn) {
+  static const char* TypeStr[NTYPES] = { "ATOMS ", "RESIDUES ", "MOLECULES ",
+                                   "MOL_FIRST_RES ", "MOL_LAST_RES " };
+  // {atoms|residues|molecules} <var> inmask <mask> [TOP KEYWORDS]
+  Topology* currentTop = 0;
+  mtype_ = NTYPES;
+  if      (argIn.hasKey("atoms")) mtype_ = ATOMS;
+  else if (argIn.hasKey("residues")) mtype_ = RESIDUES;
+  else if (argIn.hasKey("molecules")) mtype_ = MOLECULES;
+  else if (argIn.hasKey("molfirstres")) mtype_ = MOLFIRSTRES;
+  else if (argIn.hasKey("mollastres")) mtype_ = MOLLASTRES;
+  if (mtype_ == NTYPES) {
+    mprinterr("Error: No recognized type for mask 'for' loop.\n");
+    return 1;
+  }
+  //if (argIn[iarg+2] != "inmask") {
+  //  mprinterr("Error: Expected 'inmask', got %s\n", argIn[iarg+2].c_str());
+  //  return 1;
+  //}
+  if (!argIn.Contains("inmask")) {
+    mprinterr("Error: mask for loop does not contain 'inmask' keyword.\n");
+    return 1;
+  }
+  AtomMask currentMask;
+  if (currentMask.SetMaskString( argIn.GetStringKey("inmask") )) return 1;
+  Topology* top = State.DSL().GetTopByIndex( argIn );
+  if (top != 0) currentTop = top;
+  if (currentTop == 0) return 1;
+  // Get the variable name
+  if (SetupLoopVar( State.DSL(), argIn.GetStringNext() )) return 1;
+  // Set up mask
+  if (currentTop->SetupIntegerMask( currentMask )) return 1;
+  currentMask.MaskInfo();
+  if (currentMask.None()) return 1;
+  // Set up indices
+  if (mtype_ == ATOMS)
+    Idxs_ = currentMask.Selected();
+  else if (mtype_ == RESIDUES) {
+    int curRes = -1;
+    for (AtomMask::const_iterator at = currentMask.begin(); at != currentMask.end(); ++at) {
+      int res = (*currentTop)[*at].ResNum();
+      if (res != curRes) {
+        Idxs_.push_back( res );
+        curRes = res;
+      }
+    }
+  } else if (mtype_ == MOLECULES ||
+             mtype_ == MOLFIRSTRES ||
+             mtype_ == MOLLASTRES)
+  {
+    int curMol = -1;
+    for (AtomMask::const_iterator at = currentMask.begin(); at != currentMask.end(); ++at) {
+      int mol = (*currentTop)[*at].MolNum();
+      if (mol != curMol) {
+        if (mtype_ == MOLECULES)
+          Idxs_.push_back( mol );
+        else {
+          int res;
+          if (mtype_ == MOLFIRSTRES)
+            res = (*currentTop)[ currentTop->Mol( mol ).BeginAtom() ].ResNum();
+          else // MOLLASTRES
+            res = (*currentTop)[ currentTop->Mol( mol ).EndAtom()-1 ].ResNum();
+          Idxs_.push_back( res );
+        }
+        curMol = mol;
+      }
+    }
+  }
+  std::string description("(" + std::string(TypeStr[mtype_]) +
+                          VarName() + " inmask " + currentMask.MaskExpression() + ")");
+  SetDescription( description );
+  return 0;
+}
+
+int ForLoop_mask::BeginFor(DataSetList const& DSL) {
+  idx_ = Idxs_.begin();
+  return (int)Idxs_.size();
+}
+
+bool ForLoop_mask::EndFor(DataSetList& DSL) {
+  static const char* prefix[NTYPES] = {"@", ":", "^", ":", ":"};
+  if (idx_ == Idxs_.end()) return true;
+  // Get variable value
+  std::string maskStr = prefix[mtype_] + integerToString(*(idx_) + 1);
+  //mprintf("DEBUG: ControlBlock_For: %s\n", maskStr.c_str());
+  // Update CurrentVars
+  DSL.UpdateStringVar( VarName(), maskStr );
+  // Increment
+  ++(idx_);
+  return false;
+}
diff --git a/src/ForLoop_mask.h b/src/ForLoop_mask.h
new file mode 100644
index 0000000000..3cc8c6221d
--- /dev/null
+++ b/src/ForLoop_mask.h
@@ -0,0 +1,23 @@
+#ifndef INC_FORLOOP_MASK_H
+#define INC_FORLOOP_MASK_H
+#include <vector>
+#include "ForLoop.h"
+/// For loop over mask expression
+class ForLoop_mask : public ForLoop {
+    enum MaskType {ATOMS=0, RESIDUES, MOLECULES, MOLFIRSTRES, MOLLASTRES, NTYPES};
+  public:
+    ForLoop_mask() : mtype_(NTYPES) {}
+
+    static void helpText();
+
+    int SetupFor(CpptrajState&, ArgList&);
+    int BeginFor(DataSetList const&);
+    bool EndFor(DataSetList&);
+  private:
+    typedef std::vector<int> Iarray;
+
+    Iarray Idxs_;                ///< (MASK only) Selected atom/residue/molecule indices
+    Iarray::const_iterator idx_; ///< (MASK only) Current atom/residue/molecule index
+    MaskType mtype_;             ///< Hold specific mask type
+};
+#endif
diff --git a/src/ForLoop_overSets.cpp b/src/ForLoop_overSets.cpp
new file mode 100644
index 0000000000..dca927747c
--- /dev/null
+++ b/src/ForLoop_overSets.cpp
@@ -0,0 +1,65 @@
+#include "ForLoop_overSets.h"
+#include "CpptrajStdio.h"
+#include "ArgList.h"
+#include "DataSetList.h"
+#include "CpptrajState.h"
+
+void ForLoop_overSets::helpText() {
+  mprintf("\t<var> oversets <list>\n"
+          "  Loop over data sets selected by values in comma-separated list.\n"
+          "  Names may contain wildcard characters ('*' or '?').\n");
+}
+
+int ForLoop_overSets::SetupFor(CpptrajState& State, ArgList& argIn) {
+  // <var> oversets <string0>[,<string1>...]
+  //MH.varType_ = ftype;
+  // Comma-separated list of data set names.
+  std::string listArg = argIn.GetStringKey("oversets");
+  if (listArg.empty()) {
+    mprinterr("Error: 'for oversets': missing ' oversets <comma-separated list of names>'.\n");
+    return 1;
+  }
+  ArgList list(listArg, ",");
+  if (list.Nargs() < 1) {
+    mprinterr("Error: Could not parse '%s' for 'for oversets'\n", listArg.c_str());
+    return 1;
+  }
+  // Variable name.
+  if (SetupLoopVar( State.DSL(), argIn.GetStringNext() )) return 1;
+  // Go through list of names 
+  for (int il = 0; il != list.Nargs(); il++) {
+    Names_.push_back( list[il] );
+  }
+  // Description
+  std::string description( "(" + VarName() + " oversets " + listArg + ")" );
+  SetDescription( description );
+  return 0;
+}
+
+int ForLoop_overSets::BeginFor(DataSetList const& CurrentVars) {
+  // Go through list of names
+  List_.clear();
+  for (Sarray::const_iterator it = Names_.begin(); it != Names_.end(); ++it)
+  {
+    std::string listEntry;
+    CurrentVars.ReplaceVariables(listEntry, *it);
+    DataSetList dsl = CurrentVars.SelectSets( listEntry );
+    if (dsl.empty()) {
+      mprintf("Warning: '%s' selects no sets.\n", it->c_str());
+    } else {
+      for (DataSetList::const_iterator ds = dsl.begin(); ds != dsl.end(); ++ds)
+        List_.push_back( (*ds)->Meta().PrintName() );
+    }
+  }
+  sdx_ = List_.begin();
+  return (int)List_.size();
+}
+
+bool ForLoop_overSets::EndFor(DataSetList& DSL) {
+  if (sdx_ == List_.end()) return true;
+  // Get variable value
+  DSL.UpdateStringVar( VarName(), *(sdx_) );
+  // Increment
+  ++(sdx_);
+  return false;
+}
diff --git a/src/ForLoop_overSets.h b/src/ForLoop_overSets.h
new file mode 100644
index 0000000000..c3076b92da
--- /dev/null
+++ b/src/ForLoop_overSets.h
@@ -0,0 +1,21 @@
+#ifndef INC_FORLOOP_OVERSETS_H
+#define INC_FORLOOP_OVERSETS_H
+#include <vector>
+#include <string>
+#include "ForLoop.h"
+class ForLoop_overSets : public ForLoop {
+  public:
+    ForLoop_overSets() {}
+
+    static void helpText();
+
+    int SetupFor(CpptrajState&, ArgList&);
+    int BeginFor(DataSetList const&);
+    bool EndFor(DataSetList&);
+  private:
+    typedef std::vector<std::string> Sarray;
+    Sarray Names_;               ///< List of non-expanded names
+    Sarray List_;                ///< List of data set names to iterate over.
+    Sarray::const_iterator sdx_; ///< Iterator to current list item.
+};
+#endif
diff --git a/src/GridAction.cpp b/src/GridAction.cpp
index 75b2e99909..670a4858ed 100644
--- a/src/GridAction.cpp
+++ b/src/GridAction.cpp
@@ -1,5 +1,6 @@
 #include "GridAction.h"
 #include "CpptrajStdio.h"
+#include "ArgList.h"
 
 // GridAction::HelpText
 const char* GridAction::HelpText =
diff --git a/src/OutputTrajCommon.cpp b/src/OutputTrajCommon.cpp
index c43462dfd8..db1df14e56 100644
--- a/src/OutputTrajCommon.cpp
+++ b/src/OutputTrajCommon.cpp
@@ -3,6 +3,7 @@
 #include "Topology.h"
 #include "CpptrajStdio.h"
 #include "StringRoutines.h" // fileExists
+#include "ArgList.h"
 
 // CONSTRUCTOR
 OutputTrajCommon::OutputTrajCommon() :
diff --git a/src/RPNcalc.cpp b/src/RPNcalc.cpp
index 4243070f9e..9fe5d3b061 100644
--- a/src/RPNcalc.cpp
+++ b/src/RPNcalc.cpp
@@ -3,12 +3,15 @@
 #include <locale>
 #include <stack>
 #include "RPNcalc.h"
+#include "DataSetList.h"
 #include "DataSet_Vector.h"
 #include "DataSet_double.h"
 #include "DataSet_MatrixDbl.h"
 #include "DataSet_GridFlt.h"
 #include "CpptrajStdio.h"
 #include "Constants.h" // PI
+#include "StringRoutines.h"
+#include "ArgList.h"
 
 // CONSTRUCTOR
 RPNcalc::RPNcalc() : fmt_(TextFormat::DOUBLE), formatSet_(false) {}
@@ -50,23 +53,52 @@ int RPNcalc::ProcessOptions(ArgList& argIn) {
   return 0;
 }
 
+const RPNcalc::FnIdType RPNcalc::FnIdArray_[] = {
+  { FN_SQRT,  5, "sqrt("  },
+  { FN_EXP,   4, "exp("   },
+  { FN_LN,    3, "ln("    },
+  { FN_ABS,   4, "abs("   },
+  { FN_SIN,   4, "sin("   },
+  { FN_COS,   4, "cos("   },
+  { FN_TAN,   4, "tan("   },
+  { FN_SUM,   4, "sum("   },
+  { FN_AVG,   4, "avg("   },
+  { FN_STDEV, 6, "stdev(" },
+  { FN_MIN,   4, "min("   },
+  { FN_MAX,   4, "max("   },
+  { NONE,     0, 0        }
+};
+
+RPNcalc::FnIdPtr RPNcalc::IdFunction(std::string const& expression, size_t pos)
+{
+  FnIdPtr fnid = FnIdArray_;
+  for (; fnid->nChar_ != 0; ++fnid)
+  {
+    if (expression.compare(pos, fnid->nChar_, fnid->fnName_) == 0)
+    {
+      return fnid;
+    }
+  }
+  return fnid;
+}
+
 /** Convert infix expression to RPN in tokens_ array. This uses a
   * shunting-yard algorithm which has been slightly modified to
   * recognize unary right-associative operators.
   */
-int RPNcalc::ProcessExpression(std::string const& expression) {
+int RPNcalc::ProcessExpression(std::string const& expressionIn) {
   std::locale loc;
-  if (expression.empty()) return 1;
-  if (debug_ > 0) mprintf("Parsing expression: '%s'\n", expression.c_str());
+  if (expressionIn.empty()) return 1;
+  // Remove all whitespace
+  std::string expression = NoWhitespace(expressionIn);
+  if (debug_ > 0) mprintf("DEBUG: Parsing expression: '%s'\n", expression.c_str());
   tokens_.clear();
   std::stack<Token> op_stack;
   std::string::const_iterator ptr = expression.begin();
   bool lastTokenWasOperator = true;
   while ( ptr != expression.end() )
   {
-    //mprintf("DEBUG: Start of loop, char is '%c'\n", *ptr);
-    // Skip whitespace
-    if (isspace(*ptr, loc)) { ++ptr; continue; }
+    if (debug_ > 2) mprintf("DEBUG: Start of loop, char is '%c'\n", *ptr);
 
     // NUMBER ------------------------------------
     if (*ptr == '.' || isdigit(*ptr, loc))
@@ -149,79 +181,17 @@ int RPNcalc::ProcessExpression(std::string const& expression) {
     else if ( isalpha(*ptr, loc) )
     { // Look for Function name
       size_t pos = ptr - expression.begin();
-      if (expression.compare(pos, 4, "sqrt")==0)
-      {
-        op_stack.push( Token(FN_SQRT) );
-        ptr += 4;
-        lastTokenWasOperator = true;
-      }
-      else if (expression.compare(pos, 3, "exp")==0)
-      {
-        op_stack.push( Token(FN_EXP) );
-        ptr += 3;
-        lastTokenWasOperator = true;
-      }
-      else if (expression.compare(pos, 2, "ln")==0)
-      {
-        op_stack.push( Token(FN_LN) );
-        ptr += 2;
-        lastTokenWasOperator = true;
-      }
-      else if (expression.compare(pos, 3, "abs")==0)
-      {
-        op_stack.push( Token(FN_ABS) );
-        ptr += 3;
-        lastTokenWasOperator = true;
-      }
-      else if (expression.compare(pos, 3, "sin")==0)
-      {
-        op_stack.push( Token(FN_SIN) );
-        ptr += 3;
-        lastTokenWasOperator = true;
-      }
-      else if (expression.compare(pos, 3, "cos")==0)
-      {
-        op_stack.push( Token(FN_COS) );
-        ptr += 3;
-        lastTokenWasOperator = true;
-      }
-      else if (expression.compare(pos, 3, "tan")==0)
+      FnIdPtr fnid = IdFunction(expression, pos);
+      if (fnid->fnType_ != NONE)
       {
-        op_stack.push( Token(FN_TAN) );
-        ptr += 3;
+        if (debug_ > 0) mprintf("DEBUG: Function found: '%s'\n", fnid->fnName_);
+        op_stack.push( Token(fnid->fnType_) );
+        // Advance pointer to left parenthese
+        ptr = ptr + (fnid->nChar_) - 1;
         lastTokenWasOperator = true;
       }
-      else if (expression.compare(pos, 3, "sum")==0)
-      {
-        op_stack.push( Token(FN_SUM) );
-        ptr += 3;
-        lastTokenWasOperator = true;
-      }
-      else if (expression.compare(pos, 3, "avg")==0)
-      {
-        op_stack.push( Token(FN_AVG) );
-        ptr += 3;
-        lastTokenWasOperator = true;
-      }
-      else if (expression.compare(pos, 5, "stdev")==0)
-      {
-        op_stack.push( Token(FN_STDEV) );
-        ptr += 5;
-        lastTokenWasOperator = true;
-      }
-      else if (expression.compare(pos, 3, "min")==0)
-      {
-        op_stack.push( Token(FN_MIN) );
-        ptr += 3;
-        lastTokenWasOperator = true;
-      } 
-      else if (expression.compare(pos, 3, "max")==0)
-      {
-        op_stack.push( Token(FN_MAX) );
-        ptr += 3;
-        lastTokenWasOperator = true;
-      } 
       // -----------------------------------------
+      // Look for constants
       else if (expression.compare(pos, 2, "PI")==0)
       {
         tokens_.push_back( Token( Constants::PI ) );
@@ -235,7 +205,7 @@ int RPNcalc::ProcessExpression(std::string const& expression) {
         bool has_colon = false; // For index
         enum BracketState { NONE, OPEN, CLOSED };
         BracketState bracket = NONE;
-        while (ptr != expression.end() && !isspace(*ptr,loc))
+        while (ptr != expression.end())
         {
           if (bracket != OPEN && isOpChar(*ptr)) break;
           //mprintf("DEBUG: Var '%c'\n", *ptr);
@@ -506,29 +476,63 @@ int RPNcalc::TokenLoop(DataSetList& DSL) const {
           mprinterr("Internal Error: Assigning to wrong data set!\n");
           return 1;
         }
-        // Check if set already exists.
+        //mprintf("DEBUG: DS= %x  output= %x\n", Dval[1].DS(), output);
+        // Check if set already exists in master DataSetList.
         DataSet* mainDS = DSL.CheckForSet(tokens_.front().Name());
         if (mainDS != 0) {
           // Overwriting. TODO Only allow if dimensions match?
-          mprintf("Warning: Overwriting existing set '%s'\n", mainDS->legend());
+          // First check if the set we will be overwriting is itself!
+          if (Dval[0].IsDataSet()) {
+            if (Dval[0].DS()->Matches_Exact( mainDS->Meta() )) {
+              mprintf("Warning: Attempting to assign '%s' to itself.\n",
+                      mainDS->Meta().PrintName().c_str());
+              return 0;
+            }
+          }
+          mprintf("Warning: Overwriting existing set '%s'\n", mainDS->Meta().PrintName().c_str());
           DSL.RemoveSet( mainDS );
         }
         if (Dval[0].IsDataSet()) {
           output = Dval[0].DS();
-          if (debug_>0)
+          if (debug_ > 0)
             mprintf("DEBUG: output set is '%s'\n", output->legend());
           bool outputIsLocal = (LocalList.PopSet( output ) != 0);
-          if (!outputIsLocal)
-            mprintf("Warning: Data set copy not yet implemented. Renaming set '%s' to '%s'\n",
-                    output->Meta().PrintName().c_str(), tokens_.front().Name().c_str());
-          if (debug_>0)
-            mprintf("DEBUG: Assigning '%s' to '%s'\n", Dval[0].DS()->legend(),
-                    tokens_.front().Name().c_str());
-          // Reset DataSet info.
-          output->SetMeta( tokens_.front().Name() );
-          if (outputIsLocal) {
+          if (!outputIsLocal) {
+            // The output set is in the master DataSetList. First see if we
+            // can create a copy of it.
+            MetaData md( output->Meta() );
+            md.SetName( tokens_.front().Name() );
+            DataSet* currentSet = DSL.AddSet( output->Type(), md );
+            if (currentSet == 0) {
+              mprinterr("Error: Could not allocate set '%s'\n", md.PrintName().c_str());
+              return 1;
+            }
+            if ( currentSet->MemAlloc(output->DimSizes()) ) {
+              mprintf("Warning: Copy of set '%s' not yet implemented. Renaming to '%s'\n",
+                      output->Meta().PrintName().c_str(), tokens_.front().Name().c_str());
+              DSL.RemoveSet( currentSet );
+              // Reset existing DataSet info.
+              output->SetMeta( tokens_.front().Name() );
+            } else {
+              mprintf("\tCopying set '%s' to '%s'\n",
+                      output->Meta().PrintName().c_str(),
+                      currentSet->Meta().PrintName().c_str());
+              currentSet->CopyBlock(0, output, 0, output->Size());
+              for (size_t dim = 0; dim != output->Ndim(); dim++)
+                currentSet->SetDim(dim, output->Dim(dim));
+              output = currentSet;
+            }
+            //mprintf("Warning: Data set copy not yet implemented. Renaming set '%s' to '%s'\n",
+            //        output->Meta().PrintName().c_str(), tokens_.front().Name().c_str());
+          } else {
+            // Output set is only in LocalList; rename and add to master DataSetList
+            if (debug_ > 0)
+              mprintf("DEBUG: Assigning '%s' to '%s'\n", Dval[0].DS()->legend(),
+                      tokens_.front().Name().c_str());
+            // Reset DataSet info.
+            output->SetMeta( tokens_.front().Name() );
             if (DSL.AddSet( output )) return 1;
-          } 
+          }
         } else {
           output = DSL.AddSet(DataSet::DOUBLE, tokens_.front().Name(), "CALC");
           if (output == 0) return 1;
@@ -683,7 +687,7 @@ int RPNcalc::TokenLoop(DataSetList& DSL) const {
               for (unsigned int n = 0; n != D1.Size(); n++)
                 D0.AddElement( DoOperation(D1.Dval(n), D2.Dval(n), T->Type()) );
             }
-            else if (ds1->Type() == DataSet::VECTOR && ds2->Type() == DataSet::VECTOR)
+            else if (ds1->Group() == DataSet::VECTOR_1D && ds2->Group() == DataSet::VECTOR_1D)
             {
               // Both DataSets are vector time series. If ds1 size != ds2 size, ds1 or ds2
               // may be of size 1.
@@ -700,6 +704,12 @@ int RPNcalc::TokenLoop(DataSetList& DSL) const {
                   return 1;
                 }
               }
+              //if (ds1->Type() == DataSet::VEC_OXYZ)
+              //  mprintf("Warning: '%s' contains vector origins; not used in math ops.\n",
+              //          ds1->legend());
+              //if (ds2->Type() == DataSet::VEC_OXYZ)
+              //  mprintf("Warning: '%s' contains vector origins; not used in math ops.\n",
+              //          ds2->legend());
               tempDS = LocalList.AddSet(DataSet::VECTOR, MetaData("TEMP", T-tokens_.begin()));
               DataSet_Vector& V0 = static_cast<DataSet_Vector&>(*tempDS);
               V0.Allocate( DataSet::SizeArray(1, Max) );
@@ -819,8 +829,11 @@ int RPNcalc::TokenLoop(DataSetList& DSL) const {
                 for (unsigned int n = 0; n != D1.Size(); n++)
                   D0.AddElement( DoOperation(d2, D1.Dval(n), T->Type()) );
               }
-              else if ( ds1->Type() == DataSet::VECTOR )
+              else if ( ds1->Group() == DataSet::VECTOR_1D )
               {
+                //if (ds1->Type() == DataSet::VEC_OXYZ)
+                //  mprintf("Warning: '%s' contains vector origins; not used in math ops.\n",
+                //          ds1->legend());
                 tempDS = LocalList.AddSet(DataSet::VECTOR, MetaData("TEMP", T-tokens_.begin()));
                 DataSet_Vector& V0 = static_cast<DataSet_Vector&>(*tempDS);
                 V0.Allocate( DataSet::SizeArray(1, ds1->Size()) );
@@ -889,12 +902,18 @@ int RPNcalc::TokenLoop(DataSetList& DSL) const {
     return 1;
   }
   if (output == 0) {
-    mprintf("Result: ");
+    mprintf("    Result: ");
     mprintf(fmt_.fmt(), Stack.top().Value());
     mprintf("\n");
   } else {
     if (formatSet_) output->SetupFormat() = fmt_;
-    mprintf("Result stored in '%s'\n", output->legend());
+    mprintf("    Result stored in '%s'", output->Meta().PrintName().c_str());
+    if (output->Group() == DataSet::SCALAR_1D && output->Size() == 1)
+    {
+      mprintf(": ");
+      mprintf(fmt_.fmt(), ((DataSet_1D*)output)->Dval(0));
+    }
+    mprintf("\n");
   }
   return 0;
 }
diff --git a/src/RPNcalc.h b/src/RPNcalc.h
index a818c9c3c6..b57bd147ee 100644
--- a/src/RPNcalc.h
+++ b/src/RPNcalc.h
@@ -1,6 +1,10 @@
 #ifndef INC_RPNCALC_H
 #define INC_RPNCALC_H
-#include "DataSetList.h"
+#include <vector>
+#include "TextFormat.h"
+class DataSetList;
+class DataSet;
+class ArgList;
 /// Reverse Polish notation calculator
 class RPNcalc {
   public:
@@ -49,6 +53,17 @@ class RPNcalc {
       int resultIsScalar_;
       const char* description_;
     };
+    /// Hold info for recognizing functions
+    struct FnIdType {
+      TokenType fnType_;   ///< Function token type
+      int nChar_;          ///< Number of characters in function name including left parentheses
+      const char* fnName_; ///< Function name including left parentheses
+    };
+    typedef const FnIdType* FnIdPtr;
+    /// Array containing info for recognizing functions
+    static const FnIdType FnIdArray_[];
+    /// Identify function in given expression at given position
+    static FnIdPtr IdFunction(std::string const&, size_t);
 
     static inline double DoOperation(double, double, TokenType);
     int TokenLoop(DataSetList& DSL) const;
diff --git a/src/ReferenceAction.cpp b/src/ReferenceAction.cpp
index 8c5b64295f..b997306613 100644
--- a/src/ReferenceAction.cpp
+++ b/src/ReferenceAction.cpp
@@ -3,6 +3,7 @@
 #include "CpptrajStdio.h"
 #include "DataSet_Coords_TRJ.h"
 #include "ReferenceFrame.h"
+#include "ArgList.h"
 
 ReferenceAction::ReferenceAction() :
   refMode_( FIRST ),
diff --git a/src/StringRoutines.cpp b/src/StringRoutines.cpp
index 487d30ddc3..04cbb5fd11 100644
--- a/src/StringRoutines.cpp
+++ b/src/StringRoutines.cpp
@@ -178,6 +178,14 @@ std::string NoWhitespace(std::string const& line) {
   return out;
 }
 
+/// \return Given string with N leading characters removed.
+std::string RemoveLeadingChars(std::string const& strIn, int NtoRemove)
+{
+  if (strIn.empty()) return std::string();
+  std::string out = strIn.substr(NtoRemove, std::string::npos);
+  return out;
+}
+
 // integerToString()
 std::string integerToString(int i) {
   std::ostringstream oss;
diff --git a/src/StringRoutines.h b/src/StringRoutines.h
index c58e4337f0..f6aad4449f 100644
--- a/src/StringRoutines.h
+++ b/src/StringRoutines.h
@@ -28,6 +28,8 @@ std::string NoLeadingWhitespace(std::string const&);
 void RemoveAllWhitespace(std::string&);
 /// \return string with all whitespace removed.
 std::string NoWhitespace(std::string const&);
+/// \return String with the specified number of leading characters removed.
+std::string RemoveLeadingChars(std::string const&, int);
 /// Convert string to integer.
 int convertToInteger(std::string const &);
 /// Convert string to double.
diff --git a/src/TrajIOarray.cpp b/src/TrajIOarray.cpp
index ffb079d208..262405d5da 100644
--- a/src/TrajIOarray.cpp
+++ b/src/TrajIOarray.cpp
@@ -3,6 +3,7 @@
 #include "StringRoutines.h" // integerToString, validInteger
 #include "CpptrajStdio.h"
 #include "TrajectoryFile.h"
+#include "ArgList.h"
 
 TrajIOarray::~TrajIOarray() { ClearIOarray(); }
 
diff --git a/src/TrajinList.cpp b/src/TrajinList.cpp
index 999b89d71d..de242c87ab 100644
--- a/src/TrajinList.cpp
+++ b/src/TrajinList.cpp
@@ -7,6 +7,7 @@
 #include "EnsembleIn_Single.h"
 #include "EnsembleIn_Multi.h"
 #include "StringRoutines.h" // ExpandToFilenames
+#include "ArgList.h"
 
 TrajinList::TrajinList() : debug_(0), maxframes_(0), ensembleSize_(-1) {}
 
diff --git a/src/Trajin_Single.cpp b/src/Trajin_Single.cpp
index 39c4cc4df7..de6b1cbd3e 100644
--- a/src/Trajin_Single.cpp
+++ b/src/Trajin_Single.cpp
@@ -3,6 +3,7 @@
 #include "TrajectoryIO.h"
 #include "TrajectoryFile.h"
 #include "CpptrajStdio.h"
+#include "ArgList.h"
 
 // CONSTRUCTOR
 Trajin_Single::Trajin_Single() : trajio_(0), velio_(0), frcio_(0) {}
diff --git a/src/TrajoutList.cpp b/src/TrajoutList.cpp
index 2ec9e8e8b8..b003616f55 100644
--- a/src/TrajoutList.cpp
+++ b/src/TrajoutList.cpp
@@ -2,6 +2,7 @@
 #include "Trajout_Single.h"
 #include "Topology.h"
 #include "CpptrajStdio.h"
+#include "ArgList.h"
 // FIXME for pytraj compatibility
 #include "DataSetList.h"
 
diff --git a/src/Trajout_Single.cpp b/src/Trajout_Single.cpp
index b97658b8d4..d845a9ff9f 100644
--- a/src/Trajout_Single.cpp
+++ b/src/Trajout_Single.cpp
@@ -3,6 +3,7 @@
 #include "Topology.h"
 #include "CpptrajStdio.h"
 #include "StringRoutines.h" // AppendNumber
+#include "ArgList.h"
 
 // DESTRUCTOR
 Trajout_Single::~Trajout_Single() {
diff --git a/src/VariableArray.cpp b/src/VariableArray.cpp
deleted file mode 100644
index 799bad4339..0000000000
--- a/src/VariableArray.cpp
+++ /dev/null
@@ -1,108 +0,0 @@
-#include "VariableArray.h"
-#include "CpptrajStdio.h"
-#include "DataSet_string.h"
-#include "DataSet_1D.h"
-#include "StringRoutines.h"
-
-/** Add variable/value to array if it doesnt exist, otherwise set value. */
-void VariableArray::UpdateVariable(std::string const& varname, std::string const& value)
-{
-  Varray::iterator it = CurrentVars_.begin();
-  for (; it != CurrentVars_.end(); ++it)
-    if (it->first == varname)
-      break;
-  if (it == CurrentVars_.end())
-    CurrentVars_.push_back( Vpair(varname, value) );
-  else
-    it->second = value;
-}
-
-/** Add variable/value to array if it doesnt exist, otherwise append value. */
-void VariableArray::AppendVariable(std::string const& varname, std::string const& value)
-{
-  Varray::iterator it = CurrentVars_.begin();
-  for (; it != CurrentVars_.end(); ++it)
-    if (it->first == varname)
-      break;
-  if (it == CurrentVars_.end())
-    CurrentVars_.push_back( Vpair(varname, value) );
-  else
-    it->second += value;
-}
-
-/** Replace all variables in given ArgList with their values. */
-ArgList VariableArray::ReplaceVariables(ArgList const& argIn, DataSetList const& DSL, int debug)
-{
-  if (debug > 0) mprintf("DEBUG: Before variable replacement:  [%s]\n", argIn.ArgLine());
-  ArgList modCmd = argIn;
-  for (int n = 0; n < modCmd.Nargs(); n++) {
-    size_t pos = modCmd[n].find("$");
-    while (pos != std::string::npos) {
-      // Argument is/contains a variable. Find first non-alphanumeric char
-      size_t len = 1;
-      for (size_t pos1 = pos+1; pos1 < modCmd[n].size(); pos1++, len++)
-        if (!isalnum(modCmd[n][pos1])) break;
-      std::string var_in_arg = modCmd[n].substr(pos, len);
-      // See if variable occurs in CurrentVars_
-      Varray::const_iterator vp = CurrentVars_.begin();
-      for (; vp != CurrentVars_.end(); ++vp)
-        if (vp->first == var_in_arg) break;
-      // If found replace with value from CurrentVars_
-      if (vp != CurrentVars_.end()) {
-        if (debug > 0)
-          mprintf("DEBUG: Replaced variable '%s' with value '%s'\n",
-                  var_in_arg.c_str(), vp->second.c_str());
-        std::string arg = modCmd[n];
-        arg.replace(pos, vp->first.size(), vp->second);
-        modCmd.ChangeArg(n, arg);
-      } else {
-        // Not found in CurrentVars_; see if this is a DataSet.
-        for (size_t pos1 = pos+len; pos1 < modCmd[n].size(); pos1++, len++)
-          if (!isalnum(modCmd[n][pos1]) &&
-              modCmd[n][pos1] != '[' &&
-              modCmd[n][pos1] != ':' &&
-              modCmd[n][pos1] != ']' &&
-              modCmd[n][pos1] != '_' &&
-              modCmd[n][pos1] != '-' &&
-              modCmd[n][pos1] != '%')
-            break;
-        var_in_arg = modCmd[n].substr(pos+1, len-1);
-        DataSet* ds = DSL.GetDataSet( var_in_arg );
-        if (ds == 0) {
-          mprinterr("Error: Unrecognized variable in command: %s\n", var_in_arg.c_str());
-          return ArgList();
-        } else {
-          if (ds->Type() != DataSet::STRING && ds->Group() != DataSet::SCALAR_1D) {
-            mprinterr("Error: Only 1D data sets supported.\n");
-            return ArgList();
-          }
-          if (ds->Size() < 1) {
-            mprinterr("Error: Set is empty.\n");
-            return ArgList();
-          }
-          if (ds->Size() > 1)
-            mprintf("Warning: Only using first value.\n");
-          std::string value;
-          if (ds->Type() == DataSet::STRING)
-            value = (*((DataSet_string*)ds))[0];
-          else
-            value = doubleToString(((DataSet_1D*)ds)->Dval(0));
-          if (debug > 0)
-            mprintf("DEBUG: Replaced variable '$%s' with value '%s' from DataSet '%s'\n",
-                    var_in_arg.c_str(), value.c_str(), ds->legend());
-          std::string arg = modCmd[n];
-          arg.replace(pos, var_in_arg.size()+1, value);
-          modCmd.ChangeArg(n, arg);
-        }
-      }
-      pos = modCmd[n].find("$");
-    } // END loop over this argument
-  }
-  return modCmd;
-}
-
-void VariableArray::PrintVariables() const {
-  for (Varray::const_iterator vp = CurrentVars_.begin(); vp != CurrentVars_.end(); ++vp)
-    mprintf(" %s=%s", vp->first.c_str(), vp->second.c_str());
-  mprintf("\n");
-}
diff --git a/src/VariableArray.h b/src/VariableArray.h
deleted file mode 100644
index 51e171f4f5..0000000000
--- a/src/VariableArray.h
+++ /dev/null
@@ -1,28 +0,0 @@
-#ifndef INC_VARIABLEARRAY_H
-#define INC_VARIABLEARRAY_H
-#include "DataSetList.h"
-/// Hold script variables and their values.
-class VariableArray {
-    /// Hold variable and corresponding value.
-    typedef std::pair<std::string, std::string> Vpair;
-    /// Hold list of variables and corresponding values.
-    typedef std::vector<Vpair> Varray;
-  public:
-    /// CONSTRUCTOR
-    VariableArray() {}
-    /// Add/update variable with given value.
-    void UpdateVariable(std::string const&, std::string const&);
-    /// Add/append variable with given value.
-    void AppendVariable(std::string const&, std::string const&);
-    /// Replace all variables in given ArgList with their values.
-    ArgList ReplaceVariables(ArgList const&, DataSetList const&, int);
-    /// Print all variable/value pairs to stdout
-    void PrintVariables() const;
-
-    typedef Varray::const_iterator const_iterator;
-    const_iterator begin() const { return CurrentVars_.begin(); }
-    const_iterator end()   const { return CurrentVars_.end(); }
-  private:
-    Varray CurrentVars_; ///< Hold all current variables
-};
-#endif
diff --git a/src/Version.h b/src/Version.h
index 549bb90411..3c004fe453 100644
--- a/src/Version.h
+++ b/src/Version.h
@@ -12,7 +12,7 @@
  * Whenever a number that precedes <revision> is incremented, all subsequent
  * numbers should be reset to 0.
  */
-#define CPPTRAJ_INTERNAL_VERSION "V4.25.2"
+#define CPPTRAJ_INTERNAL_VERSION "V4.25.3"
 /// PYTRAJ relies on this
 #define CPPTRAJ_VERSION_STRING CPPTRAJ_INTERNAL_VERSION
 #endif
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index b44607dee0..d88419aa13 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -1,133 +1,133 @@
-Action.o : Action.cpp Action.h ActionState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action.o : Action.cpp Action.h ActionState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
 ActionFrameCounter.o : ActionFrameCounter.cpp ActionFrameCounter.h ArgList.h CpptrajStdio.h
-ActionList.o : ActionList.cpp Action.h ActionList.h ActionState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_Align.o : Action_Align.cpp Action.h ActionState.h Action_Align.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_Angle.o : Action_Angle.cpp Action.h ActionState.h Action_Angle.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Vec3.h
-Action_AreaPerMol.o : Action_AreaPerMol.cpp Action.h ActionState.h Action_AreaPerMol.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_AtomMap.o : Action_AtomMap.cpp Action.h ActionState.h Action_AtomMap.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h StructureMapper.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_AtomicCorr.o : Action_AtomicCorr.cpp Action.h ActionState.h Action_AtomicCorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_AtomicFluct.o : Action_AtomicFluct.cpp Action.h ActionFrameCounter.h ActionState.h Action_AtomicFluct.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_AutoImage.o : Action_AutoImage.cpp Action.h ActionState.h Action_AutoImage.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_Average.o : Action_Average.cpp Action.h ActionFrameCounter.h ActionState.h Action_Average.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Vec3.h
-Action_Bounds.o : Action_Bounds.cpp Action.h ActionState.h Action_Bounds.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_Box.o : Action_Box.cpp Action.h ActionState.h Action_Box.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_Center.o : Action_Center.cpp Action.h ActionState.h Action_Center.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_Channel.o : Action_Channel.cpp Action.h ActionState.h Action_Channel.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_CheckChirality.o : Action_CheckChirality.cpp Action.h ActionState.h Action_CheckChirality.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Vec3.h
-Action_CheckStructure.o : Action_CheckStructure.cpp Action.h ActionState.h Action_CheckStructure.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_integer.h DataSet_string.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_Closest.o : Action_Closest.cpp Action.h ActionState.h Action_Closest.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.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_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageRoutines.h ImageTypes.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h ParmIO.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_ClusterDihedral.o : Action_ClusterDihedral.cpp Action.h ActionState.h Action_ClusterDihedral.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Vec3.h
-Action_Contacts.o : Action_Contacts.cpp Action.h ActionState.h Action_Contacts.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_CreateCrd.o : Action_CreateCrd.cpp Action.h ActionState.h Action_CreateCrd.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_CreateReservoir.o : Action_CreateReservoir.cpp Action.h ActionState.h Action_CreateReservoir.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 NetcdfFile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_DNAionTracker.o : Action_DNAionTracker.cpp Action.h ActionState.h Action_DNAionTracker.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_DSSP.o : Action_DSSP.cpp Action.h ActionState.h Action_DSSP.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_Density.o : Action_Density.cpp Action.h ActionState.h Action_Density.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_Diffusion.o : Action_Diffusion.cpp Action.h ActionState.h Action_Diffusion.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_Dihedral.o : Action_Dihedral.cpp Action.h ActionState.h Action_Dihedral.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Vec3.h
-Action_DihedralRMS.o : Action_DihedralRMS.cpp Action.h ActionState.h Action_DihedralRMS.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Vec3.h
-Action_Dipole.o : Action_Dipole.cpp Action.h ActionState.h Action_Dipole.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridAction.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_DistRmsd.o : Action_DistRmsd.cpp Action.h ActionState.h Action_DistRmsd.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_Distance.o : Action_Distance.cpp Action.h ActionState.h Action_Distance.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_Energy.o : Action_Energy.cpp Action.h ActionState.h Action_Energy.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h Energy.h Ewald.h Ewald_ParticleMesh.h Ewald_Regular.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h helpme_standalone.h
-Action_Esander.o : Action_Esander.cpp Action.h ActionState.h Action_Esander.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h Energy_Sander.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_FilterByData.o : Action_FilterByData.cpp Action.h ActionState.h Action_FilterByData.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_FixAtomOrder.o : Action_FixAtomOrder.cpp Action.h ActionState.h Action_FixAtomOrder.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.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 ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h ParmIO.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_FixImagedBonds.o : Action_FixImagedBonds.cpp Action.h ActionState.h Action_FixImagedBonds.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_GIST.o : Action_GIST.cpp Action.h ActionState.h Action_GIST.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridDbl.h DataSet_GridFlt.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h ImagedAction.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_Grid.o : Action_Grid.cpp Action.h ActionState.h Action_Grid.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridAction.h GridBin.h MaskArray.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_GridFreeEnergy.o : Action_GridFreeEnergy.cpp Action.h ActionState.h Action_GridFreeEnergy.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridAction.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_HydrogenBond.o : Action_HydrogenBond.cpp Action.h ActionState.h Action_HydrogenBond.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Vec3.h
-Action_Image.o : Action_Image.cpp Action.h ActionState.h Action_Image.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_InfraredSpectrum.o : Action_InfraredSpectrum.cpp Action.h ActionState.h Action_InfraredSpectrum.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_Jcoupling.o : Action_Jcoupling.cpp Action.h ActionState.h Action_Jcoupling.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Vec3.h
-Action_LESsplit.o : Action_LESsplit.cpp Action.h ActionFrameCounter.h ActionState.h Action_LESsplit.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Vec3.h
-Action_LIE.o : Action_LIE.cpp Action.h ActionState.h Action_LIE.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_LipidOrder.o : Action_LipidOrder.cpp Action.h ActionState.h Action_LipidOrder.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_MakeStructure.o : Action_MakeStructure.cpp Action.h ActionState.h Action_MakeStructure.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Vec3.h
-Action_Mask.o : Action_Mask.cpp Action.h ActionFrameCounter.h ActionState.h Action_Mask.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Vec3.h
-Action_Matrix.o : Action_Matrix.cpp Action.h ActionFrameCounter.h ActionState.h Action_Matrix.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_MinImage.o : Action_MinImage.cpp Action.h ActionState.h Action_MinImage.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_Molsurf.o : Action_Molsurf.cpp Action.h ActionState.h Action_Molsurf.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h molsurf.h
-Action_MultiDihedral.o : Action_MultiDihedral.cpp Action.h ActionState.h Action_MultiDihedral.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DihedralSearch.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Vec3.h
-Action_MultiVector.o : Action_MultiVector.cpp Action.h ActionState.h Action_MultiVector.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_NAstruct.o : Action_NAstruct.cpp Action.h ActionState.h Action_NAstruct.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h AxisType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_float.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_NMRrst.o : Action_NMRrst.cpp Action.h ActionState.h Action_NMRrst.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h ViewRst.h
-Action_NativeContacts.o : Action_NativeContacts.cpp Action.h ActionState.h Action_NativeContacts.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_OrderParameter.o : Action_OrderParameter.cpp Action.h ActionState.h Action_OrderParameter.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_Outtraj.o : Action_Outtraj.cpp Action.h ActionFrameCounter.h ActionState.h Action_Outtraj.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Vec3.h
-Action_PairDist.o : Action_PairDist.cpp Action.h ActionState.h Action_PairDist.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_Pairwise.o : Action_Pairwise.cpp Action.h ActionFrameCounter.h ActionState.h Action_Pairwise.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Vec3.h
-Action_Principal.o : Action_Principal.cpp Action.h ActionState.h Action_Principal.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_Projection.o : Action_Projection.cpp Action.h ActionFrameCounter.h ActionState.h Action_Projection.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_Pucker.o : Action_Pucker.cpp Action.h ActionState.h Action_Pucker.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Vec3.h
-Action_Radgyr.o : Action_Radgyr.cpp Action.h ActionState.h Action_Radgyr.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_Radial.o : Action_Radial.cpp Action.h ActionState.h Action_Radial.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_RandomizeIons.o : Action_RandomizeIons.cpp Action.h ActionState.h Action_RandomizeIons.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_Remap.o : Action_Remap.cpp Action.h ActionState.h Action_Remap.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.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 ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h ParmIO.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_ReplicateCell.o : Action_ReplicateCell.cpp Action.h ActionFrameCounter.h ActionState.h Action_ReplicateCell.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.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 OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.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 TypeNameHolder.h Vec3.h
-Action_Rmsd.o : Action_Rmsd.cpp Action.h ActionState.h Action_Rmsd.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_Rotate.o : Action_Rotate.cpp Action.h ActionState.h Action_Rotate.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_RunningAvg.o : Action_RunningAvg.cpp Action.h ActionState.h Action_RunningAvg.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_STFC_Diffusion.o : Action_STFC_Diffusion.cpp Action.h ActionState.h Action_STFC_Diffusion.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_Scale.o : Action_Scale.cpp Action.h ActionState.h Action_Scale.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_SetVelocity.o : Action_SetVelocity.cpp Action.h ActionState.h Action_SetVelocity.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_Spam.o : Action_Spam.cpp Action.h ActionState.h Action_Spam.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_double.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h ImagedAction.h KDE.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_Strip.o : Action_Strip.cpp Action.h ActionState.h Action_Strip.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.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 ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h ParmIO.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_Surf.o : Action_Surf.cpp Action.h ActionState.h Action_Surf.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_SymmetricRmsd.o : Action_SymmetricRmsd.cpp Action.h ActionState.h Action_SymmetricRmsd.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_Temperature.o : Action_Temperature.cpp Action.h ActionState.h Action_Temperature.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_Time.o : Action_Time.cpp Action.h ActionState.h Action_Time.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_Translate.o : Action_Translate.cpp Action.h ActionState.h Action_Translate.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_Unstrip.o : Action_Unstrip.cpp Action.h ActionState.h Action_Unstrip.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_Unwrap.o : Action_Unwrap.cpp Action.h ActionState.h Action_Unwrap.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_Vector.o : Action_Vector.cpp Action.h ActionState.h Action_Vector.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_VelocityAutoCorr.o : Action_VelocityAutoCorr.cpp Action.h ActionState.h Action_VelocityAutoCorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_Volmap.o : Action_Volmap.cpp Action.h ActionState.h Action_Volmap.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_Volume.o : Action_Volume.cpp Action.h ActionState.h Action_Volume.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_Watershell.o : Action_Watershell.cpp Action.h ActionState.h Action_Watershell.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Action_XtalSymm.o : Action_XtalSymm.cpp Action.h ActionState.h Action_XtalSymm.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SpaceGroup.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-AnalysisList.o : AnalysisList.cpp ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Analysis_AmdBias.o : Analysis_AmdBias.cpp ActionState.h Analysis.h AnalysisState.h Analysis_AmdBias.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Analysis_AutoCorr.o : Analysis_AutoCorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_AutoCorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Analysis_Average.o : Analysis_Average.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Average.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Analysis_Clustering.o : Analysis_Clustering.cpp ActionFrameCounter.h ActionState.h Analysis.h AnalysisState.h Analysis_Clustering.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h ClusterDist.h ClusterList.h ClusterMatrix.h ClusterNode.h ClusterSieve.h Cluster_DBSCAN.h Cluster_DPeaks.h Cluster_HierAgglo.h Cluster_Kmeans.h Cluster_ReadInfo.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Vec3.h
-Analysis_ConstantPHStats.o : Analysis_ConstantPHStats.cpp ActionState.h Analysis.h AnalysisState.h Analysis_ConstantPHStats.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Analysis_Corr.o : Analysis_Corr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Corr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Analysis_CrankShaft.o : Analysis_CrankShaft.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CrankShaft.h Analysis_Statistics.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Analysis_CrdFluct.o : Analysis_CrdFluct.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CrdFluct.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Analysis_CrossCorr.o : Analysis_CrossCorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CrossCorr.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Analysis_CurveFit.o : Analysis_CurveFit.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CurveFit.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h CurveFit.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Analysis_Divergence.o : Analysis_Divergence.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Divergence.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Analysis_FFT.o : Analysis_FFT.cpp ActionState.h Analysis.h AnalysisState.h Analysis_FFT.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Analysis_HausdorffDistance.o : Analysis_HausdorffDistance.cpp ActionState.h Analysis.h AnalysisState.h Analysis_HausdorffDistance.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Analysis_Hist.o : Analysis_Hist.cpp ActionFrameCounter.h ActionState.h Analysis.h AnalysisState.h Analysis_Hist.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.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 ParameterHolders.h ParameterSet.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 TypeNameHolder.h Vec3.h
-Analysis_IRED.o : Analysis_IRED.cpp ActionState.h Analysis.h AnalysisState.h Analysis_IRED.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Analysis_Integrate.o : Analysis_Integrate.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Integrate.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Analysis_KDE.o : Analysis_KDE.cpp ActionState.h Analysis.h AnalysisState.h Analysis_KDE.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Analysis_Lifetime.o : Analysis_Lifetime.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Lifetime.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Analysis_LowestCurve.o : Analysis_LowestCurve.cpp ActionState.h Analysis.h AnalysisState.h Analysis_LowestCurve.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Analysis_Matrix.o : Analysis_Matrix.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Matrix.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Analysis_MeltCurve.o : Analysis_MeltCurve.cpp ActionState.h Analysis.h AnalysisState.h Analysis_MeltCurve.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Analysis_Modes.o : Analysis_Modes.cpp ActionFrameCounter.h ActionState.h Analysis.h AnalysisState.h Analysis_Modes.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Vec3.h
-Analysis_MultiHist.o : Analysis_MultiHist.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Hist.h Analysis_KDE.h Analysis_MultiHist.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TypeNameHolder.h Vec3.h
-Analysis_Multicurve.o : Analysis_Multicurve.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CurveFit.h Analysis_Multicurve.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Analysis_Overlap.o : Analysis_Overlap.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Overlap.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Analysis_PhiPsi.o : Analysis_PhiPsi.cpp ActionState.h Analysis.h AnalysisState.h Analysis_PhiPsi.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Analysis_Regression.o : Analysis_Regression.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Regression.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Analysis_RemLog.o : Analysis_RemLog.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Lifetime.h Analysis_RemLog.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_RemLog.h DataSet_integer.h DataSet_integer_mem.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Analysis_Rms2d.o : Analysis_Rms2d.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Rms2d.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TypeNameHolder.h Vec3.h
-Analysis_RmsAvgCorr.o : Analysis_RmsAvgCorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_RmsAvgCorr.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Analysis_Rotdif.o : Analysis_Rotdif.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Rotdif.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h CurveFit.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_Mesh.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h PubFFT.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SimplexMin.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Analysis_RunningAvg.o : Analysis_RunningAvg.cpp ActionState.h Analysis.h AnalysisState.h Analysis_RunningAvg.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Analysis_Slope.o : Analysis_Slope.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Slope.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Analysis_Spline.o : Analysis_Spline.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Spline.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Analysis_State.o : Analysis_State.cpp ActionState.h Analysis.h AnalysisState.h Analysis_State.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Analysis_Statistics.o : Analysis_Statistics.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Statistics.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Analysis_TI.o : Analysis_TI.cpp ActionState.h Analysis.h AnalysisState.h Analysis_TI.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Analysis_Timecorr.o : Analysis_Timecorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Timecorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Analysis_VectorMath.o : Analysis_VectorMath.cpp ActionState.h Analysis.h AnalysisState.h Analysis_VectorMath.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Analysis_Wavelet.o : Analysis_Wavelet.cpp ActionFrameCounter.h ActionState.h Analysis.h AnalysisState.h Analysis_Wavelet.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.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 ParameterHolders.h ParameterSet.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 TypeNameHolder.h Vec3.h
+ActionList.o : ActionList.cpp Action.h ActionList.h ActionState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_Align.o : Action_Align.cpp Action.h ActionState.h Action_Align.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_Angle.o : Action_Angle.cpp Action.h ActionState.h Action_Angle.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Vec3.h
+Action_AreaPerMol.o : Action_AreaPerMol.cpp Action.h ActionState.h Action_AreaPerMol.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_AtomMap.o : Action_AtomMap.cpp Action.h ActionState.h Action_AtomMap.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h StructureMapper.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_AtomicCorr.o : Action_AtomicCorr.cpp Action.h ActionState.h Action_AtomicCorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_AtomicFluct.o : Action_AtomicFluct.cpp Action.h ActionFrameCounter.h ActionState.h Action_AtomicFluct.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_AutoImage.o : Action_AutoImage.cpp Action.h ActionState.h Action_AutoImage.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageRoutines.h ImageTypes.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_Average.o : Action_Average.cpp Action.h ActionFrameCounter.h ActionState.h Action_Average.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Vec3.h
+Action_Bounds.o : Action_Bounds.cpp Action.h ActionState.h Action_Bounds.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_Box.o : Action_Box.cpp Action.h ActionState.h Action_Box.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_Center.o : Action_Center.cpp Action.h ActionState.h Action_Center.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_Channel.o : Action_Channel.cpp Action.h ActionState.h Action_Channel.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_CheckChirality.o : Action_CheckChirality.cpp Action.h ActionState.h Action_CheckChirality.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Vec3.h
+Action_CheckStructure.o : Action_CheckStructure.cpp Action.h ActionState.h Action_CheckStructure.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_integer.h DataSet_string.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_Closest.o : Action_Closest.cpp Action.h ActionState.h Action_Closest.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageRoutines.h ImageTypes.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h ParmIO.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_ClusterDihedral.o : Action_ClusterDihedral.cpp Action.h ActionState.h Action_ClusterDihedral.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Vec3.h
+Action_Contacts.o : Action_Contacts.cpp Action.h ActionState.h Action_Contacts.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_CreateCrd.o : Action_CreateCrd.cpp Action.h ActionState.h Action_CreateCrd.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_CreateReservoir.o : Action_CreateReservoir.cpp Action.h ActionState.h Action_CreateReservoir.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h NetcdfFile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_DNAionTracker.o : Action_DNAionTracker.cpp Action.h ActionState.h Action_DNAionTracker.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_DSSP.o : Action_DSSP.cpp Action.h ActionState.h Action_DSSP.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_Density.o : Action_Density.cpp Action.h ActionState.h Action_Density.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_Diffusion.o : Action_Diffusion.cpp Action.h ActionState.h Action_Diffusion.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_Dihedral.o : Action_Dihedral.cpp Action.h ActionState.h Action_Dihedral.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Vec3.h
+Action_DihedralRMS.o : Action_DihedralRMS.cpp Action.h ActionState.h Action_DihedralRMS.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Vec3.h
+Action_Dipole.o : Action_Dipole.cpp Action.h ActionState.h Action_Dipole.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridAction.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_DistRmsd.o : Action_DistRmsd.cpp Action.h ActionState.h Action_DistRmsd.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_Distance.o : Action_Distance.cpp Action.h ActionState.h Action_Distance.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_Energy.o : Action_Energy.cpp Action.h ActionState.h Action_Energy.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h Energy.h Ewald.h Ewald_ParticleMesh.h Ewald_Regular.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h helpme_standalone.h
+Action_Esander.o : Action_Esander.cpp Action.h ActionState.h Action_Esander.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h Energy_Sander.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_FilterByData.o : Action_FilterByData.cpp Action.h ActionState.h Action_FilterByData.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_FixAtomOrder.o : Action_FixAtomOrder.cpp Action.h ActionState.h Action_FixAtomOrder.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h ParmIO.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_FixImagedBonds.o : Action_FixImagedBonds.cpp Action.h ActionState.h Action_FixImagedBonds.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_GIST.o : Action_GIST.cpp Action.h ActionState.h Action_GIST.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridDbl.h DataSet_GridFlt.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h ImagedAction.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h cuda_kernels/GistCudaSetup.cuh
+Action_Grid.o : Action_Grid.cpp Action.h ActionState.h Action_Grid.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridAction.h GridBin.h MaskArray.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_GridFreeEnergy.o : Action_GridFreeEnergy.cpp Action.h ActionState.h Action_GridFreeEnergy.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridAction.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_HydrogenBond.o : Action_HydrogenBond.cpp Action.h ActionState.h Action_HydrogenBond.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Vec3.h
+Action_Image.o : Action_Image.cpp Action.h ActionState.h Action_Image.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h ImageRoutines.h ImageTypes.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_InfraredSpectrum.o : Action_InfraredSpectrum.cpp Action.h ActionState.h Action_InfraredSpectrum.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_Jcoupling.o : Action_Jcoupling.cpp Action.h ActionState.h Action_Jcoupling.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Vec3.h
+Action_LESsplit.o : Action_LESsplit.cpp Action.h ActionFrameCounter.h ActionState.h Action_LESsplit.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Vec3.h
+Action_LIE.o : Action_LIE.cpp Action.h ActionState.h Action_LIE.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_LipidOrder.o : Action_LipidOrder.cpp Action.h ActionState.h Action_LipidOrder.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_MakeStructure.o : Action_MakeStructure.cpp Action.h ActionState.h Action_MakeStructure.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Vec3.h
+Action_Mask.o : Action_Mask.cpp Action.h ActionFrameCounter.h ActionState.h Action_Mask.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Vec3.h
+Action_Matrix.o : Action_Matrix.cpp Action.h ActionFrameCounter.h ActionState.h Action_Matrix.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Vector.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_MinImage.o : Action_MinImage.cpp Action.h ActionState.h Action_MinImage.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_Molsurf.o : Action_Molsurf.cpp Action.h ActionState.h Action_Molsurf.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h molsurf.h
+Action_MultiDihedral.o : Action_MultiDihedral.cpp Action.h ActionState.h Action_MultiDihedral.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DihedralSearch.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Vec3.h
+Action_MultiVector.o : Action_MultiVector.cpp Action.h ActionState.h Action_MultiVector.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_NAstruct.o : Action_NAstruct.cpp Action.h ActionState.h Action_NAstruct.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h AxisType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_float.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_NMRrst.o : Action_NMRrst.cpp Action.h ActionState.h Action_NMRrst.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_float.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h ViewRst.h
+Action_NativeContacts.o : Action_NativeContacts.cpp Action.h ActionState.h Action_NativeContacts.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_integer.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_OrderParameter.o : Action_OrderParameter.cpp Action.h ActionState.h Action_OrderParameter.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_Outtraj.o : Action_Outtraj.cpp Action.h ActionFrameCounter.h ActionState.h Action_Outtraj.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Vec3.h
+Action_PairDist.o : Action_PairDist.cpp Action.h ActionState.h Action_PairDist.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_Pairwise.o : Action_Pairwise.cpp Action.h ActionFrameCounter.h ActionState.h Action_Pairwise.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Vec3.h
+Action_Principal.o : Action_Principal.cpp Action.h ActionState.h Action_Principal.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_Projection.o : Action_Projection.cpp Action.h ActionFrameCounter.h ActionState.h Action_Projection.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_Pucker.o : Action_Pucker.cpp Action.h ActionState.h Action_Pucker.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Vec3.h
+Action_Radgyr.o : Action_Radgyr.cpp Action.h ActionState.h Action_Radgyr.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_Radial.o : Action_Radial.cpp Action.h ActionState.h Action_Radial.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_RandomizeIons.o : Action_RandomizeIons.cpp Action.h ActionState.h Action_RandomizeIons.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_Remap.o : Action_Remap.cpp Action.h ActionState.h Action_Remap.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h ParmIO.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_ReplicateCell.o : Action_ReplicateCell.cpp Action.h ActionFrameCounter.h ActionState.h Action_ReplicateCell.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h 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 TypeNameHolder.h Vec3.h
+Action_Rmsd.o : Action_Rmsd.cpp Action.h ActionState.h Action_Rmsd.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_Rotate.o : Action_Rotate.cpp Action.h ActionState.h Action_Rotate.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_RunningAvg.o : Action_RunningAvg.cpp Action.h ActionState.h Action_RunningAvg.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_STFC_Diffusion.o : Action_STFC_Diffusion.cpp Action.h ActionState.h Action_STFC_Diffusion.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_Scale.o : Action_Scale.cpp Action.h ActionState.h Action_Scale.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_SetVelocity.o : Action_SetVelocity.cpp Action.h ActionState.h Action_SetVelocity.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_Spam.o : Action_Spam.cpp Action.h ActionState.h Action_Spam.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_double.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h ImagedAction.h KDE.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_Strip.o : Action_Strip.cpp Action.h ActionState.h Action_Strip.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h ParmIO.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_Surf.o : Action_Surf.cpp Action.h ActionState.h Action_Surf.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_SymmetricRmsd.o : Action_SymmetricRmsd.cpp Action.h ActionState.h Action_SymmetricRmsd.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_Temperature.o : Action_Temperature.cpp Action.h ActionState.h Action_Temperature.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_Time.o : Action_Time.cpp Action.h ActionState.h Action_Time.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_Translate.o : Action_Translate.cpp Action.h ActionState.h Action_Translate.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_Unstrip.o : Action_Unstrip.cpp Action.h ActionState.h Action_Unstrip.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_Unwrap.o : Action_Unwrap.cpp Action.h ActionState.h Action_Unwrap.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h ImageRoutines.h ImageTypes.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_Vector.o : Action_Vector.cpp Action.h ActionState.h Action_Vector.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_VelocityAutoCorr.o : Action_VelocityAutoCorr.cpp Action.h ActionState.h Action_VelocityAutoCorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_Volmap.o : Action_Volmap.cpp Action.h ActionState.h Action_Volmap.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_Volume.o : Action_Volume.cpp Action.h ActionState.h Action_Volume.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_Watershell.o : Action_Watershell.cpp Action.h ActionState.h Action_Watershell.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageRoutines.h ImageTypes.h ImagedAction.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Action_XtalSymm.o : Action_XtalSymm.cpp Action.h ActionState.h Action_XtalSymm.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SpaceGroup.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+AnalysisList.o : AnalysisList.cpp ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Analysis_AmdBias.o : Analysis_AmdBias.cpp ActionState.h Analysis.h AnalysisState.h Analysis_AmdBias.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Analysis_AutoCorr.o : Analysis_AutoCorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_AutoCorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Analysis_Average.o : Analysis_Average.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Average.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Analysis_Clustering.o : Analysis_Clustering.cpp ActionFrameCounter.h ActionState.h Analysis.h AnalysisState.h Analysis_Clustering.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h ClusterDist.h ClusterList.h ClusterMatrix.h ClusterNode.h ClusterSieve.h Cluster_DBSCAN.h Cluster_DPeaks.h Cluster_HierAgglo.h Cluster_Kmeans.h Cluster_ReadInfo.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Cmatrix.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_float.h DataSet_integer.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Vec3.h
+Analysis_ConstantPHStats.o : Analysis_ConstantPHStats.cpp ActionState.h Analysis.h AnalysisState.h Analysis_ConstantPHStats.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_pH.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Analysis_Corr.o : Analysis_Corr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Corr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Analysis_CrankShaft.o : Analysis_CrankShaft.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CrankShaft.h Analysis_Statistics.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_float.h DataSet_integer.h DataSet_string.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Analysis_CrdFluct.o : Analysis_CrdFluct.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CrdFluct.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Analysis_CrossCorr.o : Analysis_CrossCorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CrossCorr.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Analysis_CurveFit.o : Analysis_CurveFit.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CurveFit.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h CurveFit.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Analysis_Divergence.o : Analysis_Divergence.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Divergence.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Analysis_FFT.o : Analysis_FFT.cpp ActionState.h Analysis.h AnalysisState.h Analysis_FFT.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Analysis_HausdorffDistance.o : Analysis_HausdorffDistance.cpp ActionState.h Analysis.h AnalysisState.h Analysis_HausdorffDistance.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Analysis_Hist.o : Analysis_Hist.cpp ActionFrameCounter.h ActionState.h Analysis.h AnalysisState.h Analysis_Hist.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridBin.h HistBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h 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 TypeNameHolder.h Vec3.h
+Analysis_IRED.o : Analysis_IRED.cpp ActionState.h Analysis.h AnalysisState.h Analysis_IRED.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Analysis_Integrate.o : Analysis_Integrate.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Integrate.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Analysis_KDE.o : Analysis_KDE.cpp ActionState.h Analysis.h AnalysisState.h Analysis_KDE.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Analysis_Lifetime.o : Analysis_Lifetime.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Lifetime.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Analysis_LowestCurve.o : Analysis_LowestCurve.cpp ActionState.h Analysis.h AnalysisState.h Analysis_LowestCurve.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Analysis_Matrix.o : Analysis_Matrix.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Matrix.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Analysis_MeltCurve.o : Analysis_MeltCurve.cpp ActionState.h Analysis.h AnalysisState.h Analysis_MeltCurve.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Analysis_Modes.o : Analysis_Modes.cpp ActionFrameCounter.h ActionState.h Analysis.h AnalysisState.h Analysis_Modes.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Modes.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Vec3.h
+Analysis_MultiHist.o : Analysis_MultiHist.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Hist.h Analysis_KDE.h Analysis_MultiHist.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h HistBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TypeNameHolder.h Vec3.h
+Analysis_Multicurve.o : Analysis_Multicurve.cpp ActionState.h Analysis.h AnalysisState.h Analysis_CurveFit.h Analysis_Multicurve.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Analysis_Overlap.o : Analysis_Overlap.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Overlap.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Analysis_PhiPsi.o : Analysis_PhiPsi.cpp ActionState.h Analysis.h AnalysisState.h Analysis_PhiPsi.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Analysis_Regression.o : Analysis_Regression.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Regression.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Analysis_RemLog.o : Analysis_RemLog.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Lifetime.h Analysis_RemLog.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h DataSet_RemLog.h DataSet_integer.h DataSet_integer_mem.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Analysis_Rms2d.o : Analysis_Rms2d.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Rms2d.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TypeNameHolder.h Vec3.h
+Analysis_RmsAvgCorr.o : Analysis_RmsAvgCorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_RmsAvgCorr.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Analysis_Rotdif.o : Analysis_Rotdif.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Rotdif.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h CurveFit.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_Mesh.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h PubFFT.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SimplexMin.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Analysis_RunningAvg.o : Analysis_RunningAvg.cpp ActionState.h Analysis.h AnalysisState.h Analysis_RunningAvg.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Analysis_Slope.o : Analysis_Slope.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Slope.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Analysis_Spline.o : Analysis_Spline.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Spline.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Analysis_State.o : Analysis_State.cpp ActionState.h Analysis.h AnalysisState.h Analysis_State.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Analysis_Statistics.o : Analysis_Statistics.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Statistics.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_float.h DataSet_integer.h DataSet_string.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Analysis_TI.o : Analysis_TI.cpp ActionState.h Analysis.h AnalysisState.h Analysis_TI.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Analysis_Timecorr.o : Analysis_Timecorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Timecorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Analysis_VectorMath.o : Analysis_VectorMath.cpp ActionState.h Analysis.h AnalysisState.h Analysis_VectorMath.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Analysis_Wavelet.o : Analysis_Wavelet.cpp ActionFrameCounter.h ActionState.h Analysis.h AnalysisState.h Analysis_Wavelet.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h ClusterMap.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h 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 TypeNameHolder.h Vec3.h
 ArgList.o : ArgList.cpp ArgList.h CpptrajStdio.h StringRoutines.h
 Array1D.o : Array1D.cpp ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
 AssociatedData.o : AssociatedData.cpp ArgList.h AssociatedData.h CpptrajStdio.h
@@ -143,13 +143,13 @@ ByteRoutines.o : ByteRoutines.cpp
 CIFfile.o : CIFfile.cpp Atom.h BufferedLine.h CIFfile.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h SymbolExporting.h
 CharMask.o : CharMask.cpp Atom.h CharMask.h CpptrajStdio.h MaskToken.h Molecule.h NameType.h Residue.h SymbolExporting.h
 CharmmParamFile.o : CharmmParamFile.cpp ArgList.h AtomType.h BufferedLine.h CharmmParamFile.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h StringRoutines.h TypeNameHolder.h
-ClusterDist.o : ClusterDist.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h ClusterDist.h Constants.h CoordinateInfo.h CpptrajFile.h DataSet.h DataSet_1D.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Topology.h TypeNameHolder.h Vec3.h
+ClusterDist.o : ClusterDist.cpp ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h ClusterDist.h Constants.h CoordinateInfo.h CpptrajFile.h DataSet.h DataSet_1D.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Topology.h TypeNameHolder.h Vec3.h
 ClusterList.o : ClusterList.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h ClusterDist.h ClusterList.h ClusterNode.h ClusterSieve.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_Cmatrix.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Topology.h TypeNameHolder.h Vec3.h
-ClusterMap.o : ClusterMap.cpp ArgList.h AssociatedData.h ClusterMap.h Constants.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_2D.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h ProgressBar.h ProgressTimer.h Range.h TextFormat.h Timer.h
+ClusterMap.o : ClusterMap.cpp AssociatedData.h ClusterMap.h Constants.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_2D.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h ProgressBar.h ProgressTimer.h Range.h TextFormat.h Timer.h
 ClusterMatrix.o : ClusterMatrix.cpp ArrayIterator.h ClusterMatrix.h CpptrajStdio.h Matrix.h
-ClusterNode.o : ClusterNode.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h ClusterDist.h ClusterNode.h ClusterSieve.h Constants.h CoordinateInfo.h CpptrajFile.h DataSet.h DataSet_1D.h DataSet_Cmatrix.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Topology.h TypeNameHolder.h Vec3.h
+ClusterNode.o : ClusterNode.cpp ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h ClusterDist.h ClusterNode.h ClusterSieve.h Constants.h CoordinateInfo.h CpptrajFile.h DataSet.h DataSet_1D.h DataSet_Cmatrix.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Topology.h TypeNameHolder.h Vec3.h
 ClusterSieve.o : ClusterSieve.cpp ClusterSieve.h Random.h
-Cluster_DBSCAN.o : Cluster_DBSCAN.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h ClusterDist.h ClusterList.h ClusterNode.h ClusterSieve.h Cluster_DBSCAN.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataIO.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Cmatrix.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+Cluster_DBSCAN.o : Cluster_DBSCAN.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h ClusterDist.h ClusterList.h ClusterNode.h ClusterSieve.h Cluster_DBSCAN.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Cmatrix.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
 Cluster_DPeaks.o : Cluster_DPeaks.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h ClusterDist.h ClusterList.h ClusterNode.h ClusterSieve.h Cluster_DPeaks.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_Cmatrix.h DataSet_Coords.h DataSet_Mesh.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReplicaDimArray.h Residue.h Spline.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Topology.h TypeNameHolder.h Vec3.h
 Cluster_HierAgglo.o : Cluster_HierAgglo.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h ClusterDist.h ClusterList.h ClusterMatrix.h ClusterNode.h ClusterSieve.h Cluster_HierAgglo.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_Cmatrix.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
 Cluster_Kmeans.o : Cluster_Kmeans.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h ClusterDist.h ClusterList.h ClusterNode.h ClusterSieve.h Cluster_Kmeans.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_Cmatrix.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Random.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Topology.h TypeNameHolder.h Vec3.h
@@ -157,20 +157,20 @@ 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_DihedralRMS.h Action_Dipole.h Action_DistRmsd.h Action_Distance.h Action_Energy.h Action_Esander.h Action_FilterByData.h Action_FixAtomOrder.h Action_FixImagedBonds.h Action_GIST.h Action_Grid.h Action_GridFreeEnergy.h Action_HydrogenBond.h Action_Image.h Action_InfraredSpectrum.h Action_Jcoupling.h Action_LESsplit.h Action_LIE.h Action_LipidOrder.h Action_MakeStructure.h Action_Mask.h Action_Matrix.h Action_MinImage.h Action_Molsurf.h Action_MultiDihedral.h Action_MultiVector.h Action_NAstruct.h Action_NMRrst.h Action_NativeContacts.h Action_OrderParameter.h Action_Outtraj.h Action_PairDist.h Action_Pairwise.h Action_Principal.h Action_Projection.h Action_Pucker.h Action_Radgyr.h Action_Radial.h Action_RandomizeIons.h Action_Remap.h Action_ReplicateCell.h Action_Rmsd.h Action_Rotate.h Action_RunningAvg.h Action_STFC_Diffusion.h Action_Scale.h Action_SetVelocity.h Action_Spam.h Action_Strip.h Action_Surf.h Action_SymmetricRmsd.h Action_Temperature.h Action_Time.h Action_Translate.h Action_Unstrip.h Action_Unwrap.h Action_Vector.h Action_VelocityAutoCorr.h Action_Volmap.h Action_Volume.h Action_Watershell.h Action_XtalSymm.h Analysis.h AnalysisList.h AnalysisState.h Analysis_AmdBias.h Analysis_AutoCorr.h Analysis_Average.h Analysis_Clustering.h Analysis_ConstantPHStats.h Analysis_Corr.h Analysis_CrankShaft.h Analysis_CrdFluct.h Analysis_CrossCorr.h Analysis_CurveFit.h Analysis_Divergence.h Analysis_FFT.h Analysis_HausdorffDistance.h Analysis_Hist.h Analysis_IRED.h Analysis_Integrate.h Analysis_KDE.h Analysis_Lifetime.h Analysis_LowestCurve.h Analysis_Matrix.h Analysis_MeltCurve.h Analysis_Modes.h Analysis_MultiHist.h Analysis_Multicurve.h Analysis_Overlap.h Analysis_PhiPsi.h Analysis_Regression.h Analysis_RemLog.h Analysis_Rms2d.h Analysis_RmsAvgCorr.h Analysis_Rotdif.h Analysis_RunningAvg.h Analysis_Slope.h Analysis_Spline.h Analysis_State.h Analysis_Statistics.h Analysis_TI.h Analysis_Timecorr.h Analysis_VectorMath.h Analysis_Wavelet.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h AxisType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h ClusterDist.h ClusterList.h ClusterMap.h ClusterNode.h ClusterSieve.h Cmd.h CmdInput.h CmdList.h Command.h ComplexArray.h Constants.h Constraints.h 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 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 ParameterSet.h ParameterTypes.h PubFFT.h RPNcalc.h Random.h Range.h ReferenceAction.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h ReplicaInfo.h Residue.h Spline.h StructureCheck.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h 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_DihedralRMS.h Action_Dipole.h Action_DistRmsd.h Action_Distance.h Action_Energy.h Action_Esander.h Action_FilterByData.h Action_FixAtomOrder.h Action_FixImagedBonds.h Action_GIST.h Action_Grid.h Action_GridFreeEnergy.h Action_HydrogenBond.h Action_Image.h Action_InfraredSpectrum.h Action_Jcoupling.h Action_LESsplit.h Action_LIE.h Action_LipidOrder.h Action_MakeStructure.h Action_Mask.h Action_Matrix.h Action_MinImage.h Action_Molsurf.h Action_MultiDihedral.h Action_MultiVector.h Action_NAstruct.h Action_NMRrst.h Action_NativeContacts.h Action_OrderParameter.h Action_Outtraj.h Action_PairDist.h Action_Pairwise.h Action_Principal.h Action_Projection.h Action_Pucker.h Action_Radgyr.h Action_Radial.h Action_RandomizeIons.h Action_Remap.h Action_ReplicateCell.h Action_Rmsd.h Action_Rotate.h Action_RunningAvg.h Action_STFC_Diffusion.h Action_Scale.h Action_SetVelocity.h Action_Spam.h Action_Strip.h Action_Surf.h Action_SymmetricRmsd.h Action_Temperature.h Action_Time.h Action_Translate.h Action_Unstrip.h Action_Unwrap.h Action_Vector.h Action_VelocityAutoCorr.h Action_Volmap.h Action_Volume.h Action_Watershell.h Action_XtalSymm.h Analysis.h AnalysisList.h AnalysisState.h Analysis_AmdBias.h Analysis_AutoCorr.h Analysis_Average.h Analysis_Clustering.h Analysis_ConstantPHStats.h Analysis_Corr.h Analysis_CrankShaft.h Analysis_CrdFluct.h Analysis_CrossCorr.h Analysis_CurveFit.h Analysis_Divergence.h Analysis_FFT.h Analysis_HausdorffDistance.h Analysis_Hist.h Analysis_IRED.h Analysis_Integrate.h Analysis_KDE.h Analysis_Lifetime.h Analysis_LowestCurve.h Analysis_Matrix.h Analysis_MeltCurve.h Analysis_Modes.h Analysis_MultiHist.h Analysis_Multicurve.h Analysis_Overlap.h Analysis_PhiPsi.h Analysis_Regression.h Analysis_RemLog.h Analysis_Rms2d.h Analysis_RmsAvgCorr.h Analysis_Rotdif.h Analysis_RunningAvg.h Analysis_Slope.h Analysis_Spline.h Analysis_State.h Analysis_Statistics.h Analysis_TI.h Analysis_Timecorr.h Analysis_VectorMath.h Analysis_Wavelet.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h AxisType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h ClusterDist.h ClusterList.h ClusterMap.h ClusterNode.h ClusterSieve.h Cmd.h CmdInput.h CmdList.h Command.h ComplexArray.h Constants.h Constraints.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h Corr.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Cmatrix.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_RemLog.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h Deprecated.h DihedralSearch.h Dimension.h DispatchObject.h DistRoutines.h Energy.h Energy_Sander.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_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_Set.h Exec_Show.h Exec_SortEnsembleData.h Exec_SplitCoords.h Exec_System.h Exec_Top.h Exec_Traj.h Exec_UpdateParameters.h Exec_ViewRst.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h Grid.h GridAction.h GridBin.h HistBin.h Hungarian.h ImageTypes.h ImagedAction.h InputTrajCommon.h MapAtom.h MaskArray.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h NetcdfFile.h OnlineVarT.h OutputTrajCommon.h PDBfile.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h RPNcalc.h Random.h Range.h ReferenceAction.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h ReplicaInfo.h Residue.h Spline.h StructureCheck.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Vec3.h cuda_kernels/GistCudaSetup.cuh molsurf.h
 ComplexArray.o : ComplexArray.cpp ArrayIterator.h ComplexArray.h
 Constraints.o : Constraints.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h TypeNameHolder.h Vec3.h
-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 AtomType.h BaseIOtype.h Box.h Constants.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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h VariableArray.h Vec3.h
+ControlBlock_For.o : ControlBlock_For.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_dataSetBlocks.h ForLoop_integer.h ForLoop_list.h ForLoop_mask.h ForLoop_overSets.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
 CoordinateInfo.o : CoordinateInfo.cpp Box.h CoordinateInfo.h CpptrajStdio.h Matrix_3x3.h Parallel.h ReplicaDimArray.h Vec3.h
 Corr.o : Corr.cpp ArrayIterator.h ComplexArray.h Corr.h PubFFT.h
 Cph.o : Cph.cpp Cph.h NameType.h
-Cpptraj.o : Cpptraj.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h Cmd.h CmdInput.h CmdList.h Command.h Constants.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 ParameterHolders.h ParameterSet.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 TypeNameHolder.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 AtomType.h BaseIOtype.h BondSearch.h Box.h Cmd.h CmdInput.h CmdList.h Command.h Constants.h CoordinateInfo.h Cpptraj.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h 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 TypeNameHolder.h Vec3.h Version.h
 CpptrajFile.o : CpptrajFile.cpp CpptrajFile.h CpptrajStdio.h FileIO.h FileIO_Bzip2.h FileIO_Gzip.h FileIO_Mpi.h FileIO_MpiShared.h FileIO_Std.h FileName.h Parallel.h StringRoutines.h
-CpptrajState.o : CpptrajState.cpp Action.h ActionList.h ActionState.h Action_CreateCrd.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
+CpptrajState.o : CpptrajState.cpp Action.h ActionList.h ActionState.h Action_CreateCrd.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleNavigator.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
 CpptrajStdio.o : CpptrajStdio.cpp Parallel.h
 CurveFit.o : CurveFit.cpp CurveFit.h
 DataFile.o : DataFile.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h ClusterDist.h ClusterSieve.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataFile.h DataIO.h DataIO_CCP4.h DataIO_CharmmFastRep.h DataIO_CharmmOutput.h DataIO_CharmmRepLog.h DataIO_CharmmRtfPrm.h DataIO_Cmatrix.h DataIO_Cpout.h DataIO_Evecs.h DataIO_Gnuplot.h DataIO_Grace.h DataIO_Mdout.h DataIO_NC_Cmatrix.h DataIO_OpenDx.h DataIO_RemLog.h DataIO_Std.h DataIO_VecTraj.h DataIO_XVG.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Cmatrix.h DataSet_Cmatrix_MEM.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Cmatrix.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TypeNameHolder.h Vec3.h
-DataFileList.o : DataFileList.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+DataFileList.o : DataFileList.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
 DataIO.o : DataIO.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
 DataIO_CCP4.o : DataIO_CCP4.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ByteRoutines.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CCP4.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
 DataIO_CharmmFastRep.o : DataIO_CharmmFastRep.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmFastRep.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
@@ -187,97 +187,100 @@ 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 AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_OpenDx.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
 DataIO_RemLog.o : DataIO_RemLog.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_RemLog.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
 DataIO_Std.o : DataIO_Std.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h ClusterDist.h ClusterSieve.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Std.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Cmatrix.h DataSet_Cmatrix_MEM.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h GridBin.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-DataIO_VecTraj.o : DataIO_VecTraj.cpp ActionFrameCounter.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h ComplexArray.h Constants.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 ParameterHolders.h ParameterSet.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 TypeNameHolder.h Vec3.h
+DataIO_VecTraj.o : DataIO_VecTraj.cpp ActionFrameCounter.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_VecTraj.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h ParmIO.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Vec3.h
 DataIO_XVG.o : DataIO_XVG.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_XVG.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
 DataIO_Xplor.o : DataIO_Xplor.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-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
-DataSetList.o : DataSetList.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h ClusterDist.h ClusterSieve.h ComplexArray.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Cmatrix.h DataSet_Cmatrix_DISK.h DataSet_Cmatrix_MEM.h DataSet_Cmatrix_NOMEM.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_GridDbl.h DataSet_GridFlt.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_Parameters.h DataSet_RemLog.h DataSet_Tensor.h DataSet_Topology.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_disk.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h Hungarian.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Cmatrix.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h SymmetricTensor.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TypeNameHolder.h Vec3.h
-DataSet_1D.o : DataSet_1D.cpp ArgList.h ArrayIterator.h AssociatedData.h ComplexArray.h Constants.h Corr.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h PubFFT.h Range.h TextFormat.h
-DataSet_3D.o : DataSet_3D.cpp ArgList.h AssociatedData.h Box.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_3D.h Dimension.h FileIO.h FileName.h GridBin.h Matrix_3x3.h MetaData.h Parallel.h Range.h TextFormat.h Vec3.h
-DataSet_Cmatrix.o : DataSet_Cmatrix.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h ClusterDist.h ClusterSieve.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_Cmatrix.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Topology.h TypeNameHolder.h Vec3.h
-DataSet_Cmatrix_DISK.o : DataSet_Cmatrix_DISK.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h ClusterDist.h ClusterSieve.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_Cmatrix.h DataSet_Cmatrix_DISK.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Cmatrix.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Topology.h TypeNameHolder.h Vec3.h
-DataSet_Cmatrix_MEM.o : DataSet_Cmatrix_MEM.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h ClusterDist.h ClusterSieve.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_Cmatrix.h DataSet_Cmatrix_MEM.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Topology.h TypeNameHolder.h Vec3.h
-DataSet_Cmatrix_NOMEM.o : DataSet_Cmatrix_NOMEM.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h ClusterDist.h ClusterSieve.h Constants.h CoordinateInfo.h CpptrajFile.h DataSet.h DataSet_1D.h DataSet_Cmatrix.h DataSet_Cmatrix_NOMEM.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Topology.h TypeNameHolder.h Vec3.h
-DataSet_Coords.o : DataSet_Coords.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Vec3.h
-DataSet_Coords_CRD.o : DataSet_Coords_CRD.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_CRD.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Vec3.h
+DataSet.o : DataSet.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
+DataSetList.o : DataSetList.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h ClusterDist.h ClusterSieve.h ComplexArray.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Cmatrix.h DataSet_Cmatrix_DISK.h DataSet_Cmatrix_MEM.h DataSet_Cmatrix_NOMEM.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_GridDbl.h DataSet_GridFlt.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_Parameters.h DataSet_RemLog.h DataSet_StringVar.h DataSet_Tensor.h DataSet_Topology.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_disk.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h Hungarian.h InputTrajCommon.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Cmatrix.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Spline.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h SymmetricTensor.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TypeNameHolder.h Vec3.h
+DataSet_1D.o : DataSet_1D.cpp ArrayIterator.h AssociatedData.h ComplexArray.h Constants.h Corr.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h PubFFT.h Range.h TextFormat.h
+DataSet_3D.o : DataSet_3D.cpp AssociatedData.h Box.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_3D.h Dimension.h FileIO.h FileName.h GridBin.h Matrix_3x3.h MetaData.h Parallel.h Range.h TextFormat.h Vec3.h
+DataSet_Cmatrix.o : DataSet_Cmatrix.cpp ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h ClusterDist.h ClusterSieve.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_Cmatrix.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Topology.h TypeNameHolder.h Vec3.h
+DataSet_Cmatrix_DISK.o : DataSet_Cmatrix_DISK.cpp ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h ClusterDist.h ClusterSieve.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_Cmatrix.h DataSet_Cmatrix_DISK.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Cmatrix.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Topology.h TypeNameHolder.h Vec3.h
+DataSet_Cmatrix_MEM.o : DataSet_Cmatrix_MEM.cpp ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h ClusterDist.h ClusterSieve.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_Cmatrix.h DataSet_Cmatrix_MEM.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Topology.h TypeNameHolder.h Vec3.h
+DataSet_Cmatrix_NOMEM.o : DataSet_Cmatrix_NOMEM.cpp ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h ClusterDist.h ClusterSieve.h Constants.h CoordinateInfo.h CpptrajFile.h DataSet.h DataSet_1D.h DataSet_Cmatrix.h DataSet_Cmatrix_NOMEM.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Topology.h TypeNameHolder.h Vec3.h
+DataSet_Coords.o : DataSet_Coords.cpp AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Vec3.h
+DataSet_Coords_CRD.o : DataSet_Coords_CRD.cpp AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_CRD.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Vec3.h
 DataSet_Coords_REF.o : DataSet_Coords_REF.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Topology.h TrajFrameCounter.h Trajin.h Trajin_Single.h TypeNameHolder.h Vec3.h
-DataSet_Coords_TRJ.o : DataSet_Coords_TRJ.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_TRJ.h Dimension.h FileIO.h FileName.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h Trajin_Single.h TypeNameHolder.h Vec3.h
-DataSet_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
-DataSet_MatrixDbl.o : DataSet_MatrixDbl.cpp ArgList.h ArrayIterator.h AssociatedData.h CpptrajFile.h DataSet.h DataSet_2D.h DataSet_MatrixDbl.h Dimension.h FileIO.h FileName.h Matrix.h MetaData.h Parallel.h Range.h TextFormat.h
-DataSet_MatrixFlt.o : DataSet_MatrixFlt.cpp ArgList.h ArrayIterator.h AssociatedData.h CpptrajFile.h DataSet.h DataSet_2D.h DataSet_MatrixFlt.h Dimension.h FileIO.h FileName.h Matrix.h MetaData.h Parallel.h Range.h TextFormat.h
-DataSet_Mesh.o : DataSet_Mesh.cpp ArgList.h AssociatedData.h Constants.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_Mesh.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h Spline.h TextFormat.h
+DataSet_Coords_TRJ.o : DataSet_Coords_TRJ.cpp AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_TRJ.h Dimension.h FileIO.h FileName.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h Trajin_Single.h TypeNameHolder.h Vec3.h
+DataSet_GridDbl.o : DataSet_GridDbl.cpp ArrayIterator.h AssociatedData.h Box.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_3D.h DataSet_GridDbl.h Dimension.h FileIO.h FileName.h Grid.h GridBin.h Matrix_3x3.h MetaData.h Parallel.h Range.h StringRoutines.h TextFormat.h Vec3.h
+DataSet_GridFlt.o : DataSet_GridFlt.cpp ArrayIterator.h AssociatedData.h Box.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_3D.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Grid.h GridBin.h Matrix_3x3.h MetaData.h Parallel.h Range.h StringRoutines.h TextFormat.h Vec3.h
+DataSet_Mat3x3.o : DataSet_Mat3x3.cpp AssociatedData.h CpptrajFile.h DataSet.h DataSet_Mat3x3.h Dimension.h FileIO.h FileName.h Matrix_3x3.h MetaData.h Parallel.h Range.h TextFormat.h Vec3.h
+DataSet_MatrixDbl.o : DataSet_MatrixDbl.cpp ArrayIterator.h AssociatedData.h CpptrajFile.h DataSet.h DataSet_2D.h DataSet_MatrixDbl.h Dimension.h FileIO.h FileName.h Matrix.h MetaData.h Parallel.h Range.h TextFormat.h
+DataSet_MatrixFlt.o : DataSet_MatrixFlt.cpp ArrayIterator.h AssociatedData.h CpptrajFile.h DataSet.h DataSet_2D.h DataSet_MatrixFlt.h Dimension.h FileIO.h FileName.h Matrix.h MetaData.h Parallel.h Range.h TextFormat.h
+DataSet_Mesh.o : DataSet_Mesh.cpp AssociatedData.h Constants.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_Mesh.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h Spline.h TextFormat.h
 DataSet_Modes.o : DataSet_Modes.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_2D.h DataSet_MatrixDbl.h DataSet_Modes.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Vec3.h
-DataSet_PHREMD_Explicit.o : DataSet_PHREMD_Explicit.cpp ArgList.h AssociatedData.h Cph.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h Dimension.h FileIO.h FileName.h MetaData.h NameType.h Parallel.h Range.h TextFormat.h
-DataSet_PHREMD_Implicit.o : DataSet_PHREMD_Implicit.cpp ArgList.h AssociatedData.h Cph.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_PHREMD.h DataSet_PHREMD_Implicit.h Dimension.h FileIO.h FileName.h MetaData.h NameType.h Parallel.h Range.h TextFormat.h
-DataSet_Parameters.o : DataSet_Parameters.cpp ArgList.h AssociatedData.h AtomType.h Constants.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h MetaData.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h TextFormat.h TypeNameHolder.h
-DataSet_RemLog.o : DataSet_RemLog.cpp ArgList.h AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h ReplicaDimArray.h TextFormat.h
-DataSet_Tensor.o : DataSet_Tensor.cpp ArgList.h AssociatedData.h CpptrajFile.h DataSet.h DataSet_Tensor.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h SymmetricTensor.h TextFormat.h
+DataSet_PHREMD_Explicit.o : DataSet_PHREMD_Explicit.cpp AssociatedData.h Cph.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h Dimension.h FileIO.h FileName.h MetaData.h NameType.h Parallel.h Range.h TextFormat.h
+DataSet_PHREMD_Implicit.o : DataSet_PHREMD_Implicit.cpp AssociatedData.h Cph.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_PHREMD.h DataSet_PHREMD_Implicit.h Dimension.h FileIO.h FileName.h MetaData.h NameType.h Parallel.h Range.h TextFormat.h
+DataSet_Parameters.o : DataSet_Parameters.cpp AssociatedData.h AtomType.h Constants.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Parameters.h Dimension.h FileIO.h FileName.h MetaData.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h TextFormat.h TypeNameHolder.h
+DataSet_RemLog.o : DataSet_RemLog.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h ReplicaDimArray.h TextFormat.h
+DataSet_StringVar.o : DataSet_StringVar.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_StringVar.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
+DataSet_Tensor.o : DataSet_Tensor.cpp AssociatedData.h CpptrajFile.h DataSet.h DataSet_Tensor.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h SymmetricTensor.h TextFormat.h
 DataSet_Topology.o : DataSet_Topology.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Topology.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h ParmIO.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Vec3.h
-DataSet_Vector.o : DataSet_Vector.cpp ArgList.h ArrayIterator.h AssociatedData.h ComplexArray.h Constants.h Corr.h CpptrajFile.h DataSet.h DataSet_1D.h DataSet_Vector.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h PubFFT.h Range.h SymbolExporting.h TextFormat.h Vec3.h
-DataSet_double.o : DataSet_double.cpp ArgList.h AssociatedData.h CpptrajFile.h DataSet.h DataSet_1D.h DataSet_double.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
-DataSet_float.o : DataSet_float.cpp ArgList.h AssociatedData.h CpptrajFile.h DataSet.h DataSet_1D.h DataSet_float.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
-DataSet_integer_disk.o : DataSet_integer_disk.cpp ArgList.h AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_integer.h DataSet_integer_disk.h Dimension.h FileIO.h FileName.h File_TempName.h MetaData.h NC_Routines.h Parallel.h Range.h TextFormat.h
-DataSet_integer_mem.o : DataSet_integer_mem.cpp ArgList.h AssociatedData.h CpptrajFile.h DataSet.h DataSet_1D.h DataSet_integer.h DataSet_integer_mem.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
-DataSet_pH.o : DataSet_pH.cpp ArgList.h AssociatedData.h Cph.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_pH.h Dimension.h FileIO.h FileName.h MetaData.h NameType.h Parallel.h Range.h TextFormat.h
-DataSet_string.o : DataSet_string.cpp ArgList.h AssociatedData.h CpptrajFile.h DataSet.h DataSet_string.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
+DataSet_Vector.o : DataSet_Vector.cpp ArrayIterator.h AssociatedData.h ComplexArray.h Constants.h Corr.h CpptrajFile.h DataSet.h DataSet_1D.h DataSet_Vector.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h PubFFT.h Range.h SymbolExporting.h TextFormat.h Vec3.h
+DataSet_double.o : DataSet_double.cpp AssociatedData.h CpptrajFile.h DataSet.h DataSet_1D.h DataSet_double.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
+DataSet_float.o : DataSet_float.cpp AssociatedData.h CpptrajFile.h DataSet.h DataSet_1D.h DataSet_float.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
+DataSet_integer_disk.o : DataSet_integer_disk.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_integer.h DataSet_integer_disk.h Dimension.h FileIO.h FileName.h File_TempName.h MetaData.h NC_Routines.h Parallel.h Range.h TextFormat.h
+DataSet_integer_mem.o : DataSet_integer_mem.cpp AssociatedData.h CpptrajFile.h DataSet.h DataSet_1D.h DataSet_integer.h DataSet_integer_mem.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
+DataSet_pH.o : DataSet_pH.cpp AssociatedData.h Cph.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_pH.h Dimension.h FileIO.h FileName.h MetaData.h NameType.h Parallel.h Range.h TextFormat.h
+DataSet_string.o : DataSet_string.cpp AssociatedData.h CpptrajFile.h DataSet.h DataSet_string.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
 Deprecated.o : Deprecated.cpp CpptrajStdio.h Deprecated.h DispatchObject.h
 DihedralSearch.o : DihedralSearch.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DihedralSearch.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Vec3.h
 DistRoutines.o : DistRoutines.cpp Box.h DistRoutines.h Matrix_3x3.h Parallel.h Vec3.h
 Energy.o : Energy.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h Energy.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Vec3.h
 Energy_Sander.o : Energy_Sander.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h Energy_Sander.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h ParmIO.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h TypeNameHolder.h Vec3.h
 EnsembleIn.o : EnsembleIn.cpp Atom.h AtomMask.h Box.h CoordinateInfo.h CpptrajStdio.h EnsembleIn.h FileName.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h Timer.h TrajFrameCounter.h Vec3.h
-EnsembleIn_Multi.o : EnsembleIn_Multi.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryIO.h TypeNameHolder.h Vec3.h
+EnsembleIn_Multi.o : EnsembleIn_Multi.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h EnsembleIn.h EnsembleIn_Multi.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryIO.h TypeNameHolder.h Vec3.h
 EnsembleIn_Single.o : EnsembleIn_Single.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleIn.h EnsembleIn_Single.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Vec3.h
 EnsembleNavigator.o : EnsembleNavigator.cpp Atom.h AtomMask.h Box.h CoordinateInfo.h CpptrajStdio.h EnsembleIn.h EnsembleNavigator.h FileName.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h Timer.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TrajinList.h Vec3.h
-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
+EnsembleOut.o : EnsembleOut.cpp ActionFrameCounter.h BaseIOtype.h Box.h CoordinateInfo.h CpptrajStdio.h EnsembleOut.h FileName.h FileTypes.h FramePtrArray.h Matrix_3x3.h OutputTrajCommon.h Parallel.h Range.h ReplicaDimArray.h TrajectoryFile.h Vec3.h
 EnsembleOutList.o : EnsembleOutList.cpp ActionFrameCounter.h ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleOut.h EnsembleOutList.h EnsembleOut_Multi.h EnsembleOut_Single.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h TrajectoryFile.h TypeNameHolder.h Vec3.h
 EnsembleOut_Multi.o : EnsembleOut_Multi.cpp ActionFrameCounter.h ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleOut.h EnsembleOut_Multi.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Vec3.h
 EnsembleOut_Single.o : EnsembleOut_Single.cpp ActionFrameCounter.h ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h EnsembleOut.h EnsembleOut_Single.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h TypeNameHolder.h Vec3.h
 Ewald.o : Ewald.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h EnergyKernel_Adjust.h EnergyKernel_Nonbond.h Ewald.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h PairListLoop.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Spline.h StringRoutines.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Vec3.h
 Ewald_ParticleMesh.o : Ewald_ParticleMesh.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Ewald.h Ewald_ParticleMesh.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Vec3.h helpme_standalone.h
 Ewald_Regular.o : Ewald_Regular.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Ewald.h Ewald_Regular.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-Exec_Analyze.o : Exec_Analyze.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h 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 AtomType.h BaseIOtype.h Box.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_Calc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
-Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
-Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
-Exec_ClusterMap.o : Exec_ClusterMap.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ClusterMap.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
-Exec_CombineCoords.o : Exec_CombineCoords.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
-Exec_Commands.o : Exec_Commands.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
-Exec_CompareTop.o : Exec_CompareTop.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
-Exec_CrdAction.o : Exec_CrdAction.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h 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 AtomType.h BaseIOtype.h Box.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_CrdOut.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Vec3.h
-Exec_CreateSet.o : Exec_CreateSet.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
-Exec_DataFile.o : Exec_DataFile.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
-Exec_DataFilter.o : Exec_DataFilter.cpp Action.h ActionList.h ActionState.h Action_FilterByData.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
-Exec_DataSetCmd.o : Exec_DataSetCmd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Vector.h DataSet_string.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_DataSetCmd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
-Exec_GenerateAmberRst.o : Exec_GenerateAmberRst.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
-Exec_Help.o : Exec_Help.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h Cmd.h CmdList.h Command.h Constants.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 ParameterHolders.h ParameterSet.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 TypeNameHolder.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 AtomType.h BaseIOtype.h Box.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_LoadCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h TypeNameHolder.h Vec3.h
-Exec_LoadTraj.o : Exec_LoadTraj.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
-Exec_ParallelAnalysis.o : Exec_ParallelAnalysis.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
-Exec_ParmBox.o : Exec_ParmBox.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
-Exec_ParmSolvent.o : Exec_ParmSolvent.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
-Exec_ParmStrip.o : Exec_ParmStrip.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
-Exec_ParmWrite.o : Exec_ParmWrite.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.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_ParmWrite.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h 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 TypeNameHolder.h Vec3.h
-Exec_PermuteDihedrals.o : Exec_PermuteDihedrals.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Vec3.h
-Exec_Precision.o : Exec_Precision.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
-Exec_PrintData.o : Exec_PrintData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
-Exec_ReadData.o : Exec_ReadData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
-Exec_ReadEnsembleData.o : Exec_ReadEnsembleData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
-Exec_ReadInput.o : Exec_ReadInput.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h 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 AtomType.h BaseIOtype.h Box.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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
-Exec_RunAnalysis.o : Exec_RunAnalysis.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h 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 AtomType.h BaseIOtype.h Box.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_ScaleDihedralK.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
-Exec_SequenceAlign.o : Exec_SequenceAlign.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Vec3.h
-Exec_SortEnsembleData.o : Exec_SortEnsembleData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
-Exec_SplitCoords.o : Exec_SplitCoords.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
-Exec_System.o : Exec_System.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
-Exec_Top.o : Exec_Top.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.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_Top.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h 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 TypeNameHolder.h Vec3.h
-Exec_Traj.o : Exec_Traj.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
-Exec_UpdateParameters.o : Exec_UpdateParameters.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_UpdateParameters.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
-Exec_ViewRst.o : Exec_ViewRst.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h ViewRst.h
+Exec_Analyze.o : Exec_Analyze.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Analyze.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
+Exec_Calc.o : Exec_Calc.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Calc.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
+Exec_CatCrd.o : Exec_CatCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CatCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
+Exec_Change.o : Exec_Change.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Change.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
+Exec_ClusterMap.o : Exec_ClusterMap.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ClusterMap.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ClusterMap.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
+Exec_CombineCoords.o : Exec_CombineCoords.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CombineCoords.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
+Exec_Commands.o : Exec_Commands.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Commands.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
+Exec_CompareTop.o : Exec_CompareTop.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CompareTop.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
+Exec_CrdAction.o : Exec_CrdAction.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CrdAction.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
+Exec_CrdOut.o : Exec_CrdOut.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CrdOut.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Vec3.h
+Exec_CreateSet.o : Exec_CreateSet.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CreateSet.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
+Exec_DataFile.o : Exec_DataFile.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_DataFile.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
+Exec_DataFilter.o : Exec_DataFilter.cpp Action.h ActionList.h ActionState.h Action_FilterByData.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_DataFilter.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
+Exec_DataSetCmd.o : Exec_DataSetCmd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Vector.h DataSet_string.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_DataSetCmd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
+Exec_GenerateAmberRst.o : Exec_GenerateAmberRst.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_GenerateAmberRst.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
+Exec_Help.o : Exec_Help.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Help.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h 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 TypeNameHolder.h Vec3.h
+Exec_LoadCrd.o : Exec_LoadCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_LoadCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h TypeNameHolder.h Vec3.h
+Exec_LoadTraj.o : Exec_LoadTraj.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_LoadTraj.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
+Exec_ParallelAnalysis.o : Exec_ParallelAnalysis.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParallelAnalysis.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
+Exec_ParmBox.o : Exec_ParmBox.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmBox.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
+Exec_ParmSolvent.o : Exec_ParmSolvent.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmSolvent.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
+Exec_ParmStrip.o : Exec_ParmStrip.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmStrip.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
+Exec_ParmWrite.o : Exec_ParmWrite.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ParmWrite.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h 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 TypeNameHolder.h Vec3.h
+Exec_PermuteDihedrals.o : Exec_PermuteDihedrals.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h DistRoutines.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_PermuteDihedrals.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImagedAction.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h StructureCheck.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Vec3.h
+Exec_Precision.o : Exec_Precision.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Precision.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
+Exec_PrintData.o : Exec_PrintData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_PrintData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
+Exec_ReadData.o : Exec_ReadData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ReadData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
+Exec_ReadEnsembleData.o : Exec_ReadEnsembleData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ReadEnsembleData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
+Exec_ReadInput.o : Exec_ReadInput.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ReadInput.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
+Exec_RotateDihedral.o : Exec_RotateDihedral.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_RotateDihedral.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
+Exec_RunAnalysis.o : Exec_RunAnalysis.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_RunAnalysis.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
+Exec_ScaleDihedralK.o : Exec_ScaleDihedralK.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ScaleDihedralK.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
+Exec_SequenceAlign.o : Exec_SequenceAlign.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SequenceAlign.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Vec3.h
+Exec_Set.o : Exec_Set.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Set.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
+Exec_Show.o : Exec_Show.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Show.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
+Exec_SortEnsembleData.o : Exec_SortEnsembleData.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_pH.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SortEnsembleData.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
+Exec_SplitCoords.o : Exec_SplitCoords.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SplitCoords.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
+Exec_System.o : Exec_System.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_System.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
+Exec_Top.o : Exec_Top.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Top.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h 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 TypeNameHolder.h Vec3.h
+Exec_Traj.o : Exec_Traj.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Traj.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
+Exec_UpdateParameters.o : Exec_UpdateParameters.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_UpdateParameters.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
+Exec_ViewRst.o : Exec_ViewRst.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ViewRst.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h ViewRst.h
 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
@@ -286,13 +289,19 @@ FileIO_Std.o : FileIO_Std.cpp FileIO.h FileIO_Std.h
 FileName.o : FileName.cpp CpptrajStdio.h FileName.h StringRoutines.h
 FileTypes.o : FileTypes.cpp ArgList.h BaseIOtype.h CpptrajStdio.h FileTypes.h
 File_TempName.o : File_TempName.cpp CpptrajStdio.h FileName.h File_TempName.h StringRoutines.h
+ForLoop.o : ForLoop.cpp AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h ForLoop.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+ForLoop_dataSetBlocks.o : ForLoop_dataSetBlocks.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_dataSetBlocks.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
+ForLoop_integer.o : ForLoop_integer.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_integer.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
+ForLoop_list.o : ForLoop_list.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_list.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
+ForLoop_mask.o : ForLoop_mask.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_mask.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
+ForLoop_overSets.o : ForLoop_overSets.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h ForLoop.h ForLoop_overSets.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
 Frame.o : Frame.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h Residue.h SymbolExporting.h Vec3.h
 GridAction.o : GridAction.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridAction.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
 HistBin.o : HistBin.cpp Constants.h CpptrajStdio.h Dimension.h HistBin.h
 Hungarian.o : Hungarian.cpp ArrayIterator.h Constants.h CpptrajStdio.h Hungarian.h Matrix.h
 ImageRoutines.o : ImageRoutines.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h DistRoutines.h FileName.h Frame.h ImageRoutines.h ImageTypes.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h TypeNameHolder.h Vec3.h
 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
+KDE.o : KDE.cpp AssociatedData.h Constants.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_double.h Dimension.h FileIO.h FileName.h HistBin.h KDE.h MetaData.h Parallel.h Range.h TextFormat.h
 MapAtom.o : MapAtom.cpp Atom.h MapAtom.h NameType.h SymbolExporting.h
 MaskArray.o : MaskArray.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h TypeNameHolder.h Vec3.h
 MaskToken.o : MaskToken.cpp ArgList.h Atom.h Box.h CpptrajStdio.h DistRoutines.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h Residue.h StringRoutines.h SymbolExporting.h Vec3.h
@@ -322,25 +331,25 @@ Parm_Tinker.o : Parm_Tinker.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType
 ProgressBar.o : ProgressBar.cpp CpptrajStdio.h ProgressBar.h
 ProgressTimer.o : ProgressTimer.cpp CpptrajStdio.h ProgressTimer.h Timer.h
 PubFFT.o : PubFFT.cpp ArrayIterator.h ComplexArray.h CpptrajStdio.h PubFFT.h
-RPNcalc.o : RPNcalc.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_Vector.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
+RPNcalc.o : RPNcalc.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_Vector.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Vec3.h
 Random.o : Random.cpp CpptrajStdio.h Random.h
 Range.o : Range.cpp ArgList.h CpptrajStdio.h Range.h
-ReadLine.o : ReadLine.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdInput.h CmdList.h Command.h Constants.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReadLine.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h 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 AtomType.h BaseIOtype.h Box.h Cmd.h CmdInput.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReadLine.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
 ReferenceAction.o : ReferenceAction.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h Dimension.h FileIO.h FileName.h Frame.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TypeNameHolder.h Vec3.h
 RemdReservoirNC.o : RemdReservoirNC.cpp Atom.h AtomMask.h Box.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h Parallel.h RemdReservoirNC.h ReplicaDimArray.h Residue.h SymbolExporting.h Vec3.h
 Residue.o : Residue.cpp NameType.h Residue.h
 SDFfile.o : SDFfile.cpp Atom.h CpptrajFile.h FileIO.h FileName.h NameType.h Parallel.h SDFfile.h StringRoutines.h SymbolExporting.h
-SimplexMin.o : SimplexMin.cpp ArgList.h AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Random.h Range.h SimplexMin.h TextFormat.h
+SimplexMin.o : SimplexMin.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Random.h Range.h SimplexMin.h TextFormat.h
 SpaceGroup.o : SpaceGroup.cpp Matrix_3x3.h SpaceGroup.h Vec3.h
 Spline.o : Spline.cpp CpptrajStdio.h Spline.h
 StringRoutines.o : StringRoutines.cpp CpptrajStdio.h StringRoutines.h
 StructureCheck.o : StructureCheck.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImagedAction.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StructureCheck.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Vec3.h
-StructureMapper.o : StructureMapper.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StructureMapper.h SymbolExporting.h TextFormat.h Topology.h TorsionRoutines.h TypeNameHolder.h Vec3.h
+StructureMapper.o : StructureMapper.cpp AssociatedData.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StructureMapper.h SymbolExporting.h TextFormat.h Topology.h TorsionRoutines.h TypeNameHolder.h Vec3.h
 SymmetricRmsdCalc.o : SymmetricRmsdCalc.cpp ArrayIterator.h Atom.h AtomExtra.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h Hungarian.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h SymmetricRmsdCalc.h Topology.h TypeNameHolder.h Vec3.h
 TextFormat.o : TextFormat.cpp StringRoutines.h TextFormat.h
 Timer.o : Timer.cpp CpptrajStdio.h Timer.h
 TinkerFile.o : TinkerFile.cpp ArgList.h Atom.h AtomMask.h Box.h BufferedLine.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TinkerFile.h Vec3.h
-TopInfo.o : TopInfo.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h DistRoutines.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Mol.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h TopInfo.h Topology.h TorsionRoutines.h TypeNameHolder.h Vec3.h
+TopInfo.o : TopInfo.cpp AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h DistRoutines.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Mol.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h TopInfo.h Topology.h TorsionRoutines.h TypeNameHolder.h Vec3.h
 Topology.o : Topology.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h UpdateParameters.h Vec3.h
 TorsionRoutines.o : TorsionRoutines.cpp Constants.h TorsionRoutines.h Vec3.h
 TrajFrameCounter.o : TrajFrameCounter.cpp ArgList.h CpptrajStdio.h TrajFrameCounter.h
@@ -367,15 +376,14 @@ Traj_SDF.o : Traj_SDF.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h
 Traj_SQM.o : Traj_SQM.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h Topology.h Traj_SQM.h TrajectoryIO.h TypeNameHolder.h Vec3.h
 Traj_Tinker.o : Traj_Tinker.cpp Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h TinkerFile.h Topology.h Traj_Tinker.h TrajectoryIO.h TypeNameHolder.h Vec3.h
 Traj_XYZ.o : Traj_XYZ.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Traj_XYZ.h TrajectoryIO.h TypeNameHolder.h Vec3.h
-TrajectoryFile.o : TrajectoryFile.cpp 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_GmxDump.h Traj_GmxTng.h Traj_GmxTrX.h Traj_GmxXtc.h Traj_Gro.h Traj_Mol2File.h Traj_NcEnsemble.h Traj_PDBfile.h Traj_SDF.h Traj_SQM.h Traj_Tinker.h Traj_XYZ.h TrajectoryFile.h TrajectoryIO.h Vec3.h
+TrajectoryFile.o : TrajectoryFile.cpp Atom.h AtomMask.h BaseIOtype.h Box.h BufferedFrame.h BufferedLine.h CIFfile.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Mol2File.h Molecule.h NameType.h NetcdfFile.h PDBfile.h Parallel.h ReplicaDimArray.h Residue.h SDFfile.h SymbolExporting.h TextFormat.h TinkerFile.h Traj_AmberCoord.h Traj_AmberNetcdf.h Traj_AmberRestart.h Traj_AmberRestartNC.h Traj_Binpos.h Traj_CIF.h Traj_CharmmCor.h Traj_CharmmDcd.h Traj_CharmmRestart.h Traj_Conflib.h Traj_GmxDump.h Traj_GmxTng.h Traj_GmxTrX.h Traj_GmxXtc.h Traj_Gro.h Traj_Mol2File.h Traj_NcEnsemble.h Traj_PDBfile.h Traj_SDF.h Traj_SQM.h Traj_Tinker.h Traj_XYZ.h TrajectoryFile.h TrajectoryIO.h Vec3.h
 TrajectoryIO.o : TrajectoryIO.cpp BaseIOtype.h Box.h CoordinateInfo.h FramePtrArray.h Matrix_3x3.h Parallel.h ReplicaDimArray.h TrajectoryIO.h Vec3.h
 TrajinList.o : TrajinList.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_RemLog.h Dimension.h EnsembleIn.h EnsembleIn_Multi.h EnsembleIn_Single.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h ReplicaInfo.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h Trajin_Multi.h Trajin_Single.h TypeNameHolder.h Vec3.h
 Trajin_Multi.o : Trajin_Multi.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h ReplicaInfo.h Residue.h StringRoutines.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryIO.h Trajin.h Trajin_Multi.h TypeNameHolder.h Vec3.h
 Trajin_Single.o : Trajin_Single.cpp ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Trajin.h Trajin_Single.h TypeNameHolder.h Vec3.h
 TrajoutList.o : TrajoutList.cpp ActionFrameCounter.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Vec3.h
 Trajout_Single.o : Trajout_Single.cpp ActionFrameCounter.h ArgList.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h Topology.h TrajectoryFile.h TrajectoryIO.h Trajout_Single.h TypeNameHolder.h Vec3.h
-VariableArray.o : VariableArray.cpp ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h VariableArray.h Vec3.h
 Vec3.o : Vec3.cpp Constants.h CpptrajStdio.h Vec3.h
 ViewRst.o : ViewRst.cpp ActionFrameCounter.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h ParmIO.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Vec3.h ViewRst.h
-main.o : main.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h Cpptraj.h CpptrajFile.h CpptrajState.h DataFile.h DataFileList.h 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 ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
+main.o : main.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomExtra.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h Cpptraj.h CpptrajFile.h CpptrajState.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Vec3.h
 molsurf.o : molsurf.c molsurf.h
diff --git a/src/cpptrajfiles b/src/cpptrajfiles
index 4c67cbea53..ec7fc7982f 100644
--- a/src/cpptrajfiles
+++ b/src/cpptrajfiles
@@ -162,7 +162,7 @@ COMMON_SOURCES= \
         CmdList.cpp \
         ComplexArray.cpp \
         Constraints.cpp \
-        Control.cpp \
+        ControlBlock_For.cpp \
         CoordinateInfo.cpp \
         Corr.cpp \
         Cph.cpp \
@@ -222,6 +222,7 @@ COMMON_SOURCES= \
         DataSet_integer_disk.cpp \
         DataSet_integer_mem.cpp \
         DataSet_string.cpp \
+        DataSet_StringVar.cpp \
         DataSet_Tensor.cpp \
         Deprecated.cpp \
         DihedralSearch.cpp \
@@ -270,7 +271,9 @@ COMMON_SOURCES= \
         Exec_RotateDihedral.cpp \
         Exec_RunAnalysis.cpp \
         Exec_ScaleDihedralK.cpp \
+        Exec_Set.cpp \
         Exec_SequenceAlign.cpp \
+        Exec_Show.cpp \
         Exec_SortEnsembleData.cpp \
         Exec_SplitCoords.cpp \
         Exec_System.cpp \
@@ -286,6 +289,12 @@ COMMON_SOURCES= \
         FileIO_Std.cpp \
         FileName.cpp \
         FileTypes.cpp \
+        ForLoop.cpp \
+        ForLoop_dataSetBlocks.cpp \
+        ForLoop_integer.cpp \
+        ForLoop_list.cpp \
+        ForLoop_mask.cpp \
+        ForLoop_overSets.cpp \
         Frame.cpp \
         GridAction.cpp \
         HistBin.cpp \
@@ -372,7 +381,6 @@ COMMON_SOURCES= \
         TrajIOarray.cpp \
         Trajout_Single.cpp \
         TrajoutList.cpp \
-        VariableArray.cpp \
         Vec3.cpp \
         ViewRst.cpp
 
diff --git a/test/Test_Calc/RunTest.sh b/test/Test_Calc/RunTest.sh
index b8b0437e04..0c69578c50 100755
--- a/test/Test_Calc/RunTest.sh
+++ b/test/Test_Calc/RunTest.sh
@@ -2,7 +2,7 @@
 
 . ../MasterTest.sh
 
-CleanFiles calc.in calc.dat mag.dat
+CleanFiles calc.in calc.dat mag.dat mag2.dat sumtotal.dat
 
 INPUT='-i calc.in'
 cat > calc.in <<EOF
@@ -25,9 +25,25 @@ Y2pZ2  =  (Vec:3^2) + (Vec:4 * Vec:4)
 Mag    = sqrt(X2 + Y2pZ2)
 AvgMag = avg(Mag)
 writedata mag.dat AvgMag
+Mag2   = Mag
+Mag2   = Mag2 + 1
+writedata mag2.dat Mag Mag2
+
+Mag = Mag
 EOF
 RunCpptraj "Calc test with data sets"
 DoTest mag.dat.save mag.dat
+DoTest mag2.dat.save mag2.dat
+
+UNITNAME='Test math functions'
+cat > calc.in <<EOF
+readdata ../Test_General/distance.dat.save name Dist
+sumTotal = Dist:2 + Dist:3
+result = sum( sumTotal )
+writedata sumtotal.dat result
+EOF
+RunCpptraj "$UNITNAME"
+DoTest sumtotal.dat.save sumtotal.dat
 
 EndTest
 exit 0
diff --git a/test/Test_Calc/mag2.dat.save b/test/Test_Calc/mag2.dat.save
new file mode 100644
index 0000000000..b521945130
--- /dev/null
+++ b/test/Test_Calc/mag2.dat.save
@@ -0,0 +1,11 @@
+#Frame            Mag         Mag2
+       1       1.0000       2.0000
+       2       1.0000       2.0000
+       3       1.0000       2.0000
+       4       1.0000       2.0000
+       5       1.0000       2.0000
+       6       1.0000       2.0000
+       7       1.0000       2.0000
+       8       1.0000       2.0000
+       9       1.0000       2.0000
+      10       1.0000       2.0000
diff --git a/test/Test_Calc/sumtotal.dat.save b/test/Test_Calc/sumtotal.dat.save
new file mode 100644
index 0000000000..e09f1241b1
--- /dev/null
+++ b/test/Test_Calc/sumtotal.dat.save
@@ -0,0 +1,2 @@
+#Frame         result
+       1    2663.8302
diff --git a/test/Test_Control/DataOut.dat.save b/test/Test_Control/DataOut.dat.save
new file mode 100644
index 0000000000..9852374137
--- /dev/null
+++ b/test/Test_Control/DataOut.dat.save
@@ -0,0 +1,11 @@
+#Frame        NewSet1      NewSet2      NewSet3      NewSet4
+       1      10.6343       9.5164       5.2418      12.0643
+       2      11.2847      11.0308       5.3879      13.5070
+       3      11.5477      11.1152       7.7881      13.5915
+       4      12.7339      10.7999       8.8446      12.9947
+       5       9.5089      10.9447       7.1706      13.2821
+       6       6.4920      10.5278       6.4794      11.9478
+       7       5.2119      10.2123       4.9592      10.9038
+       8       7.1330       9.0511       3.9076       9.9153
+       9       7.6805       8.7576       3.9218       9.4367
+      10       6.0858      10.6187       3.9928      11.2655
diff --git a/test/Test_Control/EndToEnd1.dat.save b/test/Test_Control/EndToEnd1.dat.save
new file mode 100644
index 0000000000..df7bff3d0d
--- /dev/null
+++ b/test/Test_Control/EndToEnd1.dat.save
@@ -0,0 +1,11 @@
+#Frame   EndToEndAll_1-10 EndToEndAll_11-20 EndToEndAll_21-30 EndToEndAll_31-40 EndToEndAll_41-50 EndToEndAll_51-60 EndToEndAll_61-70 EndToEndAll_71-80 EndToEndAll_81-90 EndToEndAll_91-100
+       1          19.5966           15.7380           24.1724           26.5708           25.4524           27.2384           24.8268           23.5536           13.9835            16.2193
+       2          17.3480           16.1633           26.6273           24.8831           24.3159           26.9608           23.8860           22.1018           16.3418            14.9303
+       3          17.8450           20.5872           28.6254           26.6288           23.6855           24.3911           24.7488           23.8363           16.3319            12.2398
+       4          15.6454           25.1923           27.0966           25.2180           27.2770           22.0174           27.7153           25.4201           19.1379            13.2966
+       5          14.3931           26.6599           26.6521           28.1164           27.6559           25.8095           26.6599           23.2907           18.0394            17.2469
+       6          18.5833           29.1215           24.6119           28.1434           25.2341           27.6918           21.8790           19.5656           14.0243            17.0445
+       7          18.6442           30.8099           25.5315           27.5044           23.4983           28.7332           21.3410           19.7663           15.5260            15.3262
+       8          10.4004           29.4083           28.3073           28.3307           24.5663           25.4913           24.2118           19.3969           13.9823            13.5809
+       9          12.8161           24.8295           28.1660           29.3041           25.6547           25.5589           21.0304           17.1379           17.9049            14.7931
+      10          13.8327           22.8733           28.4593           27.2524           26.9956           27.9087           24.6680           15.2635           18.6844            16.1738
diff --git a/test/Test_Control/EndToEnd2.agr.save b/test/Test_Control/EndToEnd2.agr.save
new file mode 100644
index 0000000000..d817f7b9bb
--- /dev/null
+++ b/test/Test_Control/EndToEnd2.agr.save
@@ -0,0 +1,473 @@
+@with g0
+@  xaxis label "Frame"
+@  yaxis label ""
+@  legend 0.2, 0.995
+@  legend char size 0.60
+@  s0 legend "EndToEndAll_1-50"
+@target G0.S0
+@type xy
+   1.000      19.5966
+   2.000      17.3480
+   3.000      17.8450
+   4.000      15.6454
+   5.000      14.3931
+   6.000      18.5833
+   7.000      18.6442
+   8.000      10.4004
+   9.000      12.8161
+  10.000      13.8327
+  11.000      15.7380
+  12.000      16.1633
+  13.000      20.5872
+  14.000      25.1923
+  15.000      26.6599
+  16.000      29.1215
+  17.000      30.8099
+  18.000      29.4083
+  19.000      24.8295
+  20.000      22.8733
+  21.000      24.1724
+  22.000      26.6273
+  23.000      28.6254
+  24.000      27.0966
+  25.000      26.6521
+  26.000      24.6119
+  27.000      25.5315
+  28.000      28.3073
+  29.000      28.1660
+  30.000      28.4593
+  31.000      26.5708
+  32.000      24.8831
+  33.000      26.6288
+  34.000      25.2180
+  35.000      28.1164
+  36.000      28.1434
+  37.000      27.5044
+  38.000      28.3307
+  39.000      29.3041
+  40.000      27.2524
+  41.000      25.4524
+  42.000      24.3159
+  43.000      23.6855
+  44.000      27.2770
+  45.000      27.6559
+  46.000      25.2341
+  47.000      23.4983
+  48.000      24.5663
+  49.000      25.6547
+  50.000      26.9956
+@  s1 legend "EndToEndAll_1-60"
+@target G0.S1
+@type xy
+   1.000      19.5966
+   2.000      17.3480
+   3.000      17.8450
+   4.000      15.6454
+   5.000      14.3931
+   6.000      18.5833
+   7.000      18.6442
+   8.000      10.4004
+   9.000      12.8161
+  10.000      13.8327
+  11.000      15.7380
+  12.000      16.1633
+  13.000      20.5872
+  14.000      25.1923
+  15.000      26.6599
+  16.000      29.1215
+  17.000      30.8099
+  18.000      29.4083
+  19.000      24.8295
+  20.000      22.8733
+  21.000      24.1724
+  22.000      26.6273
+  23.000      28.6254
+  24.000      27.0966
+  25.000      26.6521
+  26.000      24.6119
+  27.000      25.5315
+  28.000      28.3073
+  29.000      28.1660
+  30.000      28.4593
+  31.000      26.5708
+  32.000      24.8831
+  33.000      26.6288
+  34.000      25.2180
+  35.000      28.1164
+  36.000      28.1434
+  37.000      27.5044
+  38.000      28.3307
+  39.000      29.3041
+  40.000      27.2524
+  41.000      25.4524
+  42.000      24.3159
+  43.000      23.6855
+  44.000      27.2770
+  45.000      27.6559
+  46.000      25.2341
+  47.000      23.4983
+  48.000      24.5663
+  49.000      25.6547
+  50.000      26.9956
+  51.000      27.2384
+  52.000      26.9608
+  53.000      24.3911
+  54.000      22.0174
+  55.000      25.8095
+  56.000      27.6918
+  57.000      28.7332
+  58.000      25.4913
+  59.000      25.5589
+  60.000      27.9087
+@  s2 legend "EndToEndAll_1-70"
+@target G0.S2
+@type xy
+   1.000      19.5966
+   2.000      17.3480
+   3.000      17.8450
+   4.000      15.6454
+   5.000      14.3931
+   6.000      18.5833
+   7.000      18.6442
+   8.000      10.4004
+   9.000      12.8161
+  10.000      13.8327
+  11.000      15.7380
+  12.000      16.1633
+  13.000      20.5872
+  14.000      25.1923
+  15.000      26.6599
+  16.000      29.1215
+  17.000      30.8099
+  18.000      29.4083
+  19.000      24.8295
+  20.000      22.8733
+  21.000      24.1724
+  22.000      26.6273
+  23.000      28.6254
+  24.000      27.0966
+  25.000      26.6521
+  26.000      24.6119
+  27.000      25.5315
+  28.000      28.3073
+  29.000      28.1660
+  30.000      28.4593
+  31.000      26.5708
+  32.000      24.8831
+  33.000      26.6288
+  34.000      25.2180
+  35.000      28.1164
+  36.000      28.1434
+  37.000      27.5044
+  38.000      28.3307
+  39.000      29.3041
+  40.000      27.2524
+  41.000      25.4524
+  42.000      24.3159
+  43.000      23.6855
+  44.000      27.2770
+  45.000      27.6559
+  46.000      25.2341
+  47.000      23.4983
+  48.000      24.5663
+  49.000      25.6547
+  50.000      26.9956
+  51.000      27.2384
+  52.000      26.9608
+  53.000      24.3911
+  54.000      22.0174
+  55.000      25.8095
+  56.000      27.6918
+  57.000      28.7332
+  58.000      25.4913
+  59.000      25.5589
+  60.000      27.9087
+  61.000      24.8268
+  62.000      23.8860
+  63.000      24.7488
+  64.000      27.7153
+  65.000      26.6599
+  66.000      21.8790
+  67.000      21.3410
+  68.000      24.2118
+  69.000      21.0304
+  70.000      24.6680
+@  s3 legend "EndToEndAll_1-80"
+@target G0.S3
+@type xy
+   1.000      19.5966
+   2.000      17.3480
+   3.000      17.8450
+   4.000      15.6454
+   5.000      14.3931
+   6.000      18.5833
+   7.000      18.6442
+   8.000      10.4004
+   9.000      12.8161
+  10.000      13.8327
+  11.000      15.7380
+  12.000      16.1633
+  13.000      20.5872
+  14.000      25.1923
+  15.000      26.6599
+  16.000      29.1215
+  17.000      30.8099
+  18.000      29.4083
+  19.000      24.8295
+  20.000      22.8733
+  21.000      24.1724
+  22.000      26.6273
+  23.000      28.6254
+  24.000      27.0966
+  25.000      26.6521
+  26.000      24.6119
+  27.000      25.5315
+  28.000      28.3073
+  29.000      28.1660
+  30.000      28.4593
+  31.000      26.5708
+  32.000      24.8831
+  33.000      26.6288
+  34.000      25.2180
+  35.000      28.1164
+  36.000      28.1434
+  37.000      27.5044
+  38.000      28.3307
+  39.000      29.3041
+  40.000      27.2524
+  41.000      25.4524
+  42.000      24.3159
+  43.000      23.6855
+  44.000      27.2770
+  45.000      27.6559
+  46.000      25.2341
+  47.000      23.4983
+  48.000      24.5663
+  49.000      25.6547
+  50.000      26.9956
+  51.000      27.2384
+  52.000      26.9608
+  53.000      24.3911
+  54.000      22.0174
+  55.000      25.8095
+  56.000      27.6918
+  57.000      28.7332
+  58.000      25.4913
+  59.000      25.5589
+  60.000      27.9087
+  61.000      24.8268
+  62.000      23.8860
+  63.000      24.7488
+  64.000      27.7153
+  65.000      26.6599
+  66.000      21.8790
+  67.000      21.3410
+  68.000      24.2118
+  69.000      21.0304
+  70.000      24.6680
+  71.000      23.5536
+  72.000      22.1018
+  73.000      23.8363
+  74.000      25.4201
+  75.000      23.2907
+  76.000      19.5656
+  77.000      19.7663
+  78.000      19.3969
+  79.000      17.1379
+  80.000      15.2635
+@  s4 legend "EndToEndAll_1-90"
+@target G0.S4
+@type xy
+   1.000      19.5966
+   2.000      17.3480
+   3.000      17.8450
+   4.000      15.6454
+   5.000      14.3931
+   6.000      18.5833
+   7.000      18.6442
+   8.000      10.4004
+   9.000      12.8161
+  10.000      13.8327
+  11.000      15.7380
+  12.000      16.1633
+  13.000      20.5872
+  14.000      25.1923
+  15.000      26.6599
+  16.000      29.1215
+  17.000      30.8099
+  18.000      29.4083
+  19.000      24.8295
+  20.000      22.8733
+  21.000      24.1724
+  22.000      26.6273
+  23.000      28.6254
+  24.000      27.0966
+  25.000      26.6521
+  26.000      24.6119
+  27.000      25.5315
+  28.000      28.3073
+  29.000      28.1660
+  30.000      28.4593
+  31.000      26.5708
+  32.000      24.8831
+  33.000      26.6288
+  34.000      25.2180
+  35.000      28.1164
+  36.000      28.1434
+  37.000      27.5044
+  38.000      28.3307
+  39.000      29.3041
+  40.000      27.2524
+  41.000      25.4524
+  42.000      24.3159
+  43.000      23.6855
+  44.000      27.2770
+  45.000      27.6559
+  46.000      25.2341
+  47.000      23.4983
+  48.000      24.5663
+  49.000      25.6547
+  50.000      26.9956
+  51.000      27.2384
+  52.000      26.9608
+  53.000      24.3911
+  54.000      22.0174
+  55.000      25.8095
+  56.000      27.6918
+  57.000      28.7332
+  58.000      25.4913
+  59.000      25.5589
+  60.000      27.9087
+  61.000      24.8268
+  62.000      23.8860
+  63.000      24.7488
+  64.000      27.7153
+  65.000      26.6599
+  66.000      21.8790
+  67.000      21.3410
+  68.000      24.2118
+  69.000      21.0304
+  70.000      24.6680
+  71.000      23.5536
+  72.000      22.1018
+  73.000      23.8363
+  74.000      25.4201
+  75.000      23.2907
+  76.000      19.5656
+  77.000      19.7663
+  78.000      19.3969
+  79.000      17.1379
+  80.000      15.2635
+  81.000      13.9835
+  82.000      16.3418
+  83.000      16.3319
+  84.000      19.1379
+  85.000      18.0394
+  86.000      14.0243
+  87.000      15.5260
+  88.000      13.9823
+  89.000      17.9049
+  90.000      18.6844
+@  s5 legend "EndToEndAll_1-100"
+@target G0.S5
+@type xy
+   1.000      19.5966
+   2.000      17.3480
+   3.000      17.8450
+   4.000      15.6454
+   5.000      14.3931
+   6.000      18.5833
+   7.000      18.6442
+   8.000      10.4004
+   9.000      12.8161
+  10.000      13.8327
+  11.000      15.7380
+  12.000      16.1633
+  13.000      20.5872
+  14.000      25.1923
+  15.000      26.6599
+  16.000      29.1215
+  17.000      30.8099
+  18.000      29.4083
+  19.000      24.8295
+  20.000      22.8733
+  21.000      24.1724
+  22.000      26.6273
+  23.000      28.6254
+  24.000      27.0966
+  25.000      26.6521
+  26.000      24.6119
+  27.000      25.5315
+  28.000      28.3073
+  29.000      28.1660
+  30.000      28.4593
+  31.000      26.5708
+  32.000      24.8831
+  33.000      26.6288
+  34.000      25.2180
+  35.000      28.1164
+  36.000      28.1434
+  37.000      27.5044
+  38.000      28.3307
+  39.000      29.3041
+  40.000      27.2524
+  41.000      25.4524
+  42.000      24.3159
+  43.000      23.6855
+  44.000      27.2770
+  45.000      27.6559
+  46.000      25.2341
+  47.000      23.4983
+  48.000      24.5663
+  49.000      25.6547
+  50.000      26.9956
+  51.000      27.2384
+  52.000      26.9608
+  53.000      24.3911
+  54.000      22.0174
+  55.000      25.8095
+  56.000      27.6918
+  57.000      28.7332
+  58.000      25.4913
+  59.000      25.5589
+  60.000      27.9087
+  61.000      24.8268
+  62.000      23.8860
+  63.000      24.7488
+  64.000      27.7153
+  65.000      26.6599
+  66.000      21.8790
+  67.000      21.3410
+  68.000      24.2118
+  69.000      21.0304
+  70.000      24.6680
+  71.000      23.5536
+  72.000      22.1018
+  73.000      23.8363
+  74.000      25.4201
+  75.000      23.2907
+  76.000      19.5656
+  77.000      19.7663
+  78.000      19.3969
+  79.000      17.1379
+  80.000      15.2635
+  81.000      13.9835
+  82.000      16.3418
+  83.000      16.3319
+  84.000      19.1379
+  85.000      18.0394
+  86.000      14.0243
+  87.000      15.5260
+  88.000      13.9823
+  89.000      17.9049
+  90.000      18.6844
+  91.000      16.2193
+  92.000      14.9303
+  93.000      12.2398
+  94.000      13.2966
+  95.000      17.2469
+  96.000      17.0445
+  97.000      15.3262
+  98.000      13.5809
+  99.000      14.7931
+ 100.000      16.1738
diff --git a/test/Test_Control/RunTest.sh b/test/Test_Control/RunTest.sh
index 86b2a61c16..396a8cb218 100755
--- a/test/Test_Control/RunTest.sh
+++ b/test/Test_Control/RunTest.sh
@@ -3,7 +3,9 @@
 . ../MasterTest.sh
 
 CleanFiles for.in TRP.vec.dat TRP.rms.dat TRP.CA.dist.dat TRP.tocenter.dat \
-           nh.dat rms.nofit.dat last10.dat distance.dat
+           nh.dat rms.nofit.dat last10.dat distance.dat nested.agr \
+           EndToEnd0.dat EndToEnd1.dat EndToEnd2.agr temp.*.dat \
+           DataOut.dat
 
 TESTNAME='Loop tests'
 Requires netcdf maxthreads 10
@@ -13,22 +15,22 @@ cat > for.in <<EOF
 set FNAME= ../tz2.nc
 parm ../tz2.parm7
 trajin \$FNAME 1 10
-for residues T inmask :TRP
-  vector \$T center out TRP.vec.dat
-  rms first \$T out TRP.rms.dat
+for residues T inmask :TRP nvec=1;nvec++
+  vector v\$nvec \$T center out TRP.vec.dat
+  rms RMS\$T first \$T out TRP.rms.dat
   for atoms A0 inmask @CA
-    distance \$T \$A0 out TRP.CA.dist.dat
+    distance d\$T\$A0 \$T \$A0 out TRP.CA.dist.dat
   done
-  distance \$T :1-12 out TRP.tocenter.dat
+  distance dcenter\$T \$T :1-12 out TRP.tocenter.dat
 done
 
 for atoms A0 inmask :2-4@N atoms A1 inmask :2-4@H
-  distance \$A0 \$A1 out nh.dat
+  distance d\$A0\$A1 \$A0 \$A1 out nh.dat
 done
 
 rms :1-12&!@H=
-for residues R1 inmask :1-12 r=1;r++
-  rms R\$r \$R1&!@H= nofit out rms.nofit.dat
+for residues MyRes inmask :1-12 r=1;r++
+  rms R\$r \$MyRes&!@H= nofit out rms.nofit.dat
 done
 show
 
@@ -68,5 +70,84 @@ EOF
   DoTest distance.dat.save distance.dat
 fi
 
+UNITNAME='Test nested loops and variables in loops'
+cat > for.in <<EOF
+parm ../tz2.parm7
+trajin ../tz2.nc
+
+set maxval = 4
+set maxval1 = 3
+set val = 0
+for i=1;i<\$maxval;i++ myval=0;myval+=10
+  startj = \$i + 1
+  for j=\$startj;j<=\$maxval1;j++
+    distance d\$i\$j @\$i @\$j out nested.agr
+  done
+done
+run
+show
+list
+EOF
+RunCpptraj "$UNITNAME"
+DoTest nested.agr nested.agr.save
+
+UNITNAME='Test loop over data set blocks'
+CheckFor maxthreads 1
+if [ $? -eq 0 ] ; then
+  cat > for.in <<EOF
+parm ../tz2.parm7
+
+starttraj = 1
+endtraj = 10
+offset = 10
+for i=1;i<=10;i++
+  trajin ../tz2.nc \$starttraj \$endtraj
+  distance EndToEnd\$endtraj :1 :12
+  run
+  starttraj = \$starttraj + \$offset
+  endtraj = \$endtraj + \$offset
+  clear trajin
+done
+writedata EndToEnd0.dat EndToEnd*
+
+trajin ../tz2.nc 1 100
+distance EndToEndAll :1 :12
+run
+
+for DS datasetblocks EndToEndAll blocksize 10 i=1;i++
+  set WriteVars1 += " \$DS "
+  show DS WriteVars1
+done
+writedata EndToEnd1.dat \$WriteVars1 
+
+for ES datasetblocks EndToEndAll blocksize 10 firstblock 50 cumulative j=\$i;j++
+  set WriteVars2 += " \$ES "
+  show ES WriteVars2
+done
+writedata EndToEnd2.agr \$WriteVars2
+list
+EOF
+  RunCpptraj "$UNITNAME"
+  DoTest EndToEnd1.dat.save EndToEnd1.dat
+  DoTest EndToEnd2.agr.save EndToEnd2.agr
+fi
+
+UNITNAME='Test for filename wildcards and oversets'
+cat > for.in <<EOF
+for FILE in distance.dat.save,last10.dat.save,doesnot*,TRP.*.dat.save
+  readdata \$FILE
+done
+
+for SET1 oversets TRP.rms.dat.save* SET2 oversets TRP.tocenter.dat.save* i=1;i++
+  show SET1 SET2
+  NewSet\$i = \$SET1 + \$SET2
+  set DataOut += " NewSet\$i "
+done
+writedata DataOut.dat \$DataOut
+list datasets
+EOF
+RunCpptraj "$UNITNAME"
+DoTest DataOut.dat.save DataOut.dat
+
 EndTest
 exit 0
diff --git a/test/Test_Control/TRP.CA.dist.dat.save b/test/Test_Control/TRP.CA.dist.dat.save
index a01dfb9215..80e705ed07 100644
--- a/test/Test_Control/TRP.CA.dist.dat.save
+++ b/test/Test_Control/TRP.CA.dist.dat.save
@@ -1,4 +1,4 @@
-#Frame      Dis_00003    Dis_00004    Dis_00005    Dis_00006    Dis_00007    Dis_00008    Dis_00009    Dis_00010    Dis_00011    Dis_00012    Dis_00013    Dis_00014    Dis_00018    Dis_00019    Dis_00020    Dis_00021    Dis_00022    Dis_00023    Dis_00024    Dis_00025    Dis_00026    Dis_00027    Dis_00028    Dis_00029    Dis_00033    Dis_00034    Dis_00035    Dis_00036    Dis_00037    Dis_00038    Dis_00039    Dis_00040    Dis_00041    Dis_00042    Dis_00043    Dis_00044    Dis_00048    Dis_00049    Dis_00050    Dis_00051    Dis_00052    Dis_00053    Dis_00054    Dis_00055    Dis_00056    Dis_00057    Dis_00058    Dis_00059
+#Frame          d:2@5       d:2@16       d:2@40       d:2@54       d:2@78       d:2@93      d:2@107      d:2@114      d:2@136      d:2@160      d:2@174      d:2@198        d:4@5       d:4@16       d:4@40       d:4@54       d:4@78       d:4@93      d:4@107      d:4@114      d:4@136      d:4@160      d:4@174      d:4@198        d:9@5       d:9@16       d:9@40       d:9@54       d:9@78       d:9@93      d:9@107      d:9@114      d:9@136      d:9@160      d:9@174      d:9@198       d:11@5      d:11@16      d:11@40      d:11@54      d:11@78      d:11@93     d:11@107     d:11@114     d:11@136     d:11@160     d:11@174     d:11@198
        1       6.7443       2.8352       4.5946       7.4907       9.2455       9.9894      13.4395      16.4273      15.1781      17.5350      19.9707      21.3728       7.2153       6.4149       4.9995       2.6011       6.0222       9.3504      12.7357      15.9296      15.3399      17.0610      18.2553      18.5355      15.8182      14.2323      11.0719      11.8949       9.6380       6.3658       6.6084       5.7932       2.3643       4.7669       7.8160      10.5976      23.4702      22.7840      19.0791      18.1056      15.3842      13.4254      11.6459       8.6478       8.5210       6.3707       2.7811       3.9029
        2       6.4868       2.8755       4.4092       7.8393       9.9504      11.5650      12.1810      13.3248      14.5561      18.0553      20.7480      22.5921       6.9221       6.2039       4.3803       2.3162       5.9695       8.8578      11.2656      14.1667      15.3382      18.8862      20.3734      21.4913       9.9631      12.7271      12.3231      12.6981      11.1107       7.6845       7.6492       6.0090       2.6349       4.4150       6.8584       8.6031      19.1326      21.8961      20.6061      20.1528      17.3704      13.7086      12.7877      11.0618       8.9671       6.5987       2.8937       4.3860
        3       6.3323       2.6960       4.1419       6.8452       9.7148      11.2381      11.0427      13.4736      16.3162      17.3658      21.1737      23.7666       7.7327       6.2901       5.0341       2.5197       6.1027       7.7065       9.7340      13.0271      15.5857      17.8280      21.3183      24.4891      12.0185      15.7894      15.6899      15.7782      14.9369      11.4024       9.4023       6.1441       2.4551       3.9119       4.8583       8.5013      17.5845      21.3395      21.3787      21.9455      20.8560      17.5043      15.0200      11.2888       8.0499       6.5029       2.8242       4.1358
diff --git a/test/Test_Control/TRP.rms.dat.save b/test/Test_Control/TRP.rms.dat.save
index 80e3590b40..db2147d4c3 100644
--- a/test/Test_Control/TRP.rms.dat.save
+++ b/test/Test_Control/TRP.rms.dat.save
@@ -1,4 +1,4 @@
-#Frame     RMSD_00002   RMSD_00017   RMSD_00032   RMSD_00047
+#Frame          RMS:2        RMS:4        RMS:9       RMS:11
        1       0.0000       0.0000       0.0000       0.0000
        2       0.4543       0.7856       0.5907       0.8269
        3       0.4360       0.4415       0.5069       0.5077
diff --git a/test/Test_Control/TRP.tocenter.dat.save b/test/Test_Control/TRP.tocenter.dat.save
index 2068843465..5917065cf1 100644
--- a/test/Test_Control/TRP.tocenter.dat.save
+++ b/test/Test_Control/TRP.tocenter.dat.save
@@ -1,4 +1,4 @@
-#Frame      Dis_00015    Dis_00030    Dis_00045    Dis_00060
+#Frame      dcenter:2    dcenter:4    dcenter:9   dcenter:11
        1      10.6343       9.5164       5.2418      12.0643
        2      10.8304      10.2452       4.7972      12.6801
        3      11.1117      10.6737       7.2812      13.0838
diff --git a/test/Test_Control/TRP.vec.dat.save b/test/Test_Control/TRP.vec.dat.save
index 84844ec8b7..b41443ce33 100644
--- a/test/Test_Control/TRP.vec.dat.save
+++ b/test/Test_Control/TRP.vec.dat.save
@@ -1,4 +1,4 @@
-#Frame                                               Vec_00001                                             Vec_00016                                             Vec_00031                                             Vec_00046
+#Frame                                                      v1                                                    v2                                                    v3                                                    v4
        1   2.2688  10.6610   1.8271   0.0000   0.0000   0.0000  -5.0140   8.5220   0.7127   0.0000   0.0000   0.0000   4.1747  -2.6373   0.7737   0.0000   0.0000   0.0000  -1.0550 -11.5578  -0.9597   0.0000   0.0000   0.0000
        2   3.5228  10.6182   1.1629   0.0000   0.0000   0.0000  -5.1336   9.4783   0.6271   0.0000   0.0000   0.0000  -3.1029  -4.7145   6.8363   0.0000   0.0000   0.0000  -1.0554  -9.6015   4.9042   0.0000   0.0000   0.0000
        3   3.6077  10.8602   1.4127   0.0000   0.0000   0.0000  -2.8415   8.5871  -1.5978   0.0000   0.0000   0.0000   0.0604  -2.0471  13.4624   0.0000   0.0000   0.0000   4.2305  -4.8478   6.8845   0.0000   0.0000   0.0000
diff --git a/test/Test_Control/nested.agr.save b/test/Test_Control/nested.agr.save
new file mode 100644
index 0000000000..5b1b205776
--- /dev/null
+++ b/test/Test_Control/nested.agr.save
@@ -0,0 +1,317 @@
+@with g0
+@  xaxis label "Frame"
+@  yaxis label ""
+@  legend 0.2, 0.995
+@  legend char size 0.60
+@  s0 legend "d12"
+@target G0.S0
+@type xy
+   1.000       1.0097
+   2.000       1.0102
+   3.000       1.0104
+   4.000       1.0095
+   5.000       1.0103
+   6.000       1.0104
+   7.000       1.0092
+   8.000       1.0102
+   9.000       1.0102
+  10.000       1.0098
+  11.000       1.0099
+  12.000       1.0100
+  13.000       1.0095
+  14.000       1.0100
+  15.000       1.0099
+  16.000       1.0095
+  17.000       1.0096
+  18.000       1.0097
+  19.000       1.0103
+  20.000       1.0095
+  21.000       1.0099
+  22.000       1.0096
+  23.000       1.0092
+  24.000       1.0105
+  25.000       1.0104
+  26.000       1.0103
+  27.000       1.0101
+  28.000       1.0096
+  29.000       1.0102
+  30.000       1.0098
+  31.000       1.0106
+  32.000       1.0109
+  33.000       1.0101
+  34.000       1.0098
+  35.000       1.0097
+  36.000       1.0104
+  37.000       1.0102
+  38.000       1.0099
+  39.000       1.0091
+  40.000       1.0098
+  41.000       1.0096
+  42.000       1.0100
+  43.000       1.0099
+  44.000       1.0099
+  45.000       1.0096
+  46.000       1.0099
+  47.000       1.0104
+  48.000       1.0099
+  49.000       1.0104
+  50.000       1.0094
+  51.000       1.0099
+  52.000       1.0107
+  53.000       1.0097
+  54.000       1.0101
+  55.000       1.0098
+  56.000       1.0100
+  57.000       1.0100
+  58.000       1.0091
+  59.000       1.0102
+  60.000       1.0103
+  61.000       1.0096
+  62.000       1.0101
+  63.000       1.0101
+  64.000       1.0098
+  65.000       1.0101
+  66.000       1.0097
+  67.000       1.0095
+  68.000       1.0103
+  69.000       1.0099
+  70.000       1.0097
+  71.000       1.0097
+  72.000       1.0101
+  73.000       1.0099
+  74.000       1.0102
+  75.000       1.0097
+  76.000       1.0092
+  77.000       1.0101
+  78.000       1.0107
+  79.000       1.0105
+  80.000       1.0101
+  81.000       1.0099
+  82.000       1.0105
+  83.000       1.0104
+  84.000       1.0103
+  85.000       1.0098
+  86.000       1.0102
+  87.000       1.0100
+  88.000       1.0099
+  89.000       1.0100
+  90.000       1.0096
+  91.000       1.0095
+  92.000       1.0100
+  93.000       1.0098
+  94.000       1.0104
+  95.000       1.0102
+  96.000       1.0102
+  97.000       1.0102
+  98.000       1.0106
+  99.000       1.0094
+ 100.000       1.0098
+ 101.000       1.0096
+@  s1 legend "d13"
+@target G0.S1
+@type xy
+   1.000       1.0097
+   2.000       1.0101
+   3.000       1.0094
+   4.000       1.0101
+   5.000       1.0103
+   6.000       1.0094
+   7.000       1.0110
+   8.000       1.0097
+   9.000       1.0102
+  10.000       1.0104
+  11.000       1.0100
+  12.000       1.0090
+  13.000       1.0100
+  14.000       1.0100
+  15.000       1.0093
+  16.000       1.0103
+  17.000       1.0095
+  18.000       1.0106
+  19.000       1.0095
+  20.000       1.0105
+  21.000       1.0102
+  22.000       1.0093
+  23.000       1.0099
+  24.000       1.0096
+  25.000       1.0098
+  26.000       1.0104
+  27.000       1.0099
+  28.000       1.0107
+  29.000       1.0101
+  30.000       1.0104
+  31.000       1.0102
+  32.000       1.0092
+  33.000       1.0097
+  34.000       1.0100
+  35.000       1.0095
+  36.000       1.0100
+  37.000       1.0097
+  38.000       1.0097
+  39.000       1.0103
+  40.000       1.0103
+  41.000       1.0098
+  42.000       1.0094
+  43.000       1.0098
+  44.000       1.0094
+  45.000       1.0100
+  46.000       1.0099
+  47.000       1.0092
+  48.000       1.0101
+  49.000       1.0101
+  50.000       1.0109
+  51.000       1.0102
+  52.000       1.0098
+  53.000       1.0094
+  54.000       1.0095
+  55.000       1.0100
+  56.000       1.0101
+  57.000       1.0102
+  58.000       1.0100
+  59.000       1.0096
+  60.000       1.0099
+  61.000       1.0093
+  62.000       1.0093
+  63.000       1.0099
+  64.000       1.0101
+  65.000       1.0101
+  66.000       1.0100
+  67.000       1.0105
+  68.000       1.0096
+  69.000       1.0095
+  70.000       1.0103
+  71.000       1.0096
+  72.000       1.0099
+  73.000       1.0100
+  74.000       1.0100
+  75.000       1.0095
+  76.000       1.0104
+  77.000       1.0110
+  78.000       1.0098
+  79.000       1.0099
+  80.000       1.0096
+  81.000       1.0099
+  82.000       1.0096
+  83.000       1.0103
+  84.000       1.0098
+  85.000       1.0101
+  86.000       1.0099
+  87.000       1.0106
+  88.000       1.0099
+  89.000       1.0108
+  90.000       1.0104
+  91.000       1.0102
+  92.000       1.0109
+  93.000       1.0096
+  94.000       1.0099
+  95.000       1.0091
+  96.000       1.0097
+  97.000       1.0100
+  98.000       1.0101
+  99.000       1.0095
+ 100.000       1.0098
+ 101.000       1.0110
+@  s2 legend "d23"
+@target G0.S2
+@type xy
+   1.000       1.6534
+   2.000       1.6825
+   3.000       1.6456
+   4.000       1.5687
+   5.000       1.6655
+   6.000       1.7182
+   7.000       1.6537
+   8.000       1.6363
+   9.000       1.6435
+  10.000       1.6251
+  11.000       1.7268
+  12.000       1.5821
+  13.000       1.5781
+  14.000       1.6567
+  15.000       1.6710
+  16.000       1.6165
+  17.000       1.6295
+  18.000       1.5779
+  19.000       1.6149
+  20.000       1.6986
+  21.000       1.6573
+  22.000       1.6355
+  23.000       1.6081
+  24.000       1.6549
+  25.000       1.6353
+  26.000       1.6316
+  27.000       1.6456
+  28.000       1.6844
+  29.000       1.6303
+  30.000       1.6511
+  31.000       1.6626
+  32.000       1.6565
+  33.000       1.6912
+  34.000       1.5852
+  35.000       1.6964
+  36.000       1.5594
+  37.000       1.6265
+  38.000       1.6222
+  39.000       1.5309
+  40.000       1.6723
+  41.000       1.5385
+  42.000       1.6462
+  43.000       1.5763
+  44.000       1.6299
+  45.000       1.6707
+  46.000       1.6848
+  47.000       1.5644
+  48.000       1.6810
+  49.000       1.6558
+  50.000       1.6036
+  51.000       1.6469
+  52.000       1.7486
+  53.000       1.6263
+  54.000       1.5874
+  55.000       1.5326
+  56.000       1.6741
+  57.000       1.7328
+  58.000       1.6478
+  59.000       1.6418
+  60.000       1.5677
+  61.000       1.5851
+  62.000       1.5332
+  63.000       1.6295
+  64.000       1.6438
+  65.000       1.6845
+  66.000       1.5576
+  67.000       1.7146
+  68.000       1.6201
+  69.000       1.6896
+  70.000       1.6875
+  71.000       1.6502
+  72.000       1.6602
+  73.000       1.6827
+  74.000       1.7606
+  75.000       1.6828
+  76.000       1.5857
+  77.000       1.6710
+  78.000       1.5514
+  79.000       1.5544
+  80.000       1.6257
+  81.000       1.6348
+  82.000       1.6835
+  83.000       1.6502
+  84.000       1.6473
+  85.000       1.6414
+  86.000       1.6552
+  87.000       1.7204
+  88.000       1.6655
+  89.000       1.5471
+  90.000       1.5439
+  91.000       1.7248
+  92.000       1.6398
+  93.000       1.5976
+  94.000       1.6767
+  95.000       1.6522
+  96.000       1.6186
+  97.000       1.6372
+  98.000       1.6599
+  99.000       1.6041
+ 100.000       1.5521
+ 101.000       1.6979
diff --git a/test/Test_Control/nh.dat.save b/test/Test_Control/nh.dat.save
index 98d9b56ad2..f5eb79da3e 100644
--- a/test/Test_Control/nh.dat.save
+++ b/test/Test_Control/nh.dat.save
@@ -1,4 +1,4 @@
-#Frame      Dis_00061    Dis_00062    Dis_00063
+#Frame        d@14@15      d@38@39      d@52@53
        1       1.0106       1.0100       1.0095
        2       1.0102       1.0104       1.0099
        3       1.0096       1.0101       1.0105
diff --git a/test/Test_ReadData/RunTest.sh b/test/Test_ReadData/RunTest.sh
index 3cda24d154..a69409d36d 100755
--- a/test/Test_ReadData/RunTest.sh
+++ b/test/Test_ReadData/RunTest.sh
@@ -5,13 +5,13 @@
 CleanFiles vector.in v6and7.dat rex-d.dat MD.ene.dat out.dx out.dat \
            truncoct.dat out?.dx append.dx append.dat temp.dat \
            truncsparse.dat temp2.dat truncoct.dat.save sparse.dat \
-           xyz.dat
+           xyz.dat v7and6.dat
 
 TESTNAME='Read data tests'
 
 INPUT="-i vector.in"
 # Test read/append of vector dataset
-UNITNAME='Read vector data test'
+UNITNAME='Read vector data test (no origins, origins)'
 cat > vector.in <<EOF
 readdata ../Test_Vector/vtest.dat.6.save vector name v6and7
 readdata ../Test_Vector/vtest.dat.7.save vector name v6and7
@@ -20,6 +20,15 @@ EOF
 RunCpptraj "$UNITNAME"
 DoTest v6and7.dat.save v6and7.dat
 
+UNITNAME='Read vector data set (origins, no origins)'
+cat > vector.in <<EOF
+readdata ../Test_Vector/vtest.dat.7.save vector name v7and6
+readdata ../Test_Vector/vtest.dat.6.save vector name v7and6
+writedata v7and6.dat v7and6
+EOF
+RunCpptraj "$UNITNAME"
+DoTest v7and6.dat.save v7and6.dat
+
 UNITNAME='Read Amber output test'
 cat > vector.in <<EOF
 readdata md.initial.out md.restart.out name MD
diff --git a/test/Test_ReadData/v7and6.dat.save b/test/Test_ReadData/v7and6.dat.save
new file mode 100644
index 0000000000..97c18eeb02
--- /dev/null
+++ b/test/Test_ReadData/v7and6.dat.save
@@ -0,0 +1,21 @@
+#Frame                                                  v7and6
+       1  -0.1061  -0.5897  -0.8006   2.7365  -3.4377 -10.4497
+       2  -0.1981  -0.6871  -0.6991   2.7009  -3.1927 -10.6120
+       3  -0.2450  -0.7862  -0.5673   2.5670  -2.9200 -11.0045
+       4  -0.0534  -0.5643  -0.8238   2.6592  -2.8662 -11.0590
+       5  -0.2147  -0.8075  -0.5494   1.8750  -2.3342 -10.6993
+       6  -0.1470  -0.6957  -0.7032   1.2559  -2.4981 -11.3585
+       7  -0.2579  -0.6287  -0.7336   1.7818  -2.2653 -11.1011
+       8   0.0162  -0.8438  -0.5363   1.7862  -2.3400 -10.8160
+       9  -0.0333  -0.7966  -0.6036   2.0910  -2.6649 -10.0043
+      10  -0.1603  -0.8612  -0.4824   2.0788  -2.4333  -9.7001
+      11   0.6960   3.3509 -10.5253   0.0000   0.0000   0.0000
+      12   0.2322   3.3274 -10.4556   0.0000   0.0000   0.0000
+      13   0.6774   3.4414 -10.4385   0.0000   0.0000   0.0000
+      14   0.8361   3.8291 -10.8334   0.0000   0.0000   0.0000
+      15   0.6335   3.8861 -11.2222   0.0000   0.0000   0.0000
+      16   0.6094   3.9142 -10.8067   0.0000   0.0000   0.0000
+      17   0.6716   4.1697 -10.6828   0.0000   0.0000   0.0000
+      18   0.6235   4.0479 -11.5095   0.0000   0.0000   0.0000
+      19   1.0135   3.9018 -10.9440   0.0000   0.0000   0.0000
+      20   0.8498   3.8457 -11.3054   0.0000   0.0000   0.0000