Amber-MD · drroe · May 21, 2019 · May 17, 2019 · May 17, 2019 · May 17, 2019
diff --git a/doc/CpptrajManual.pdf b/doc/CpptrajManual.pdf
diff --git a/doc/cpptraj.lyx b/doc/cpptraj.lyx
@@ -13929,15 +13929,27 @@ Options for pdb format:
 \end_layout
 
 \begin_layout LyX-Code
-  [model | multi] [dumpq | parse | vdw] [chainid <ID>]
+  [dumpq | parse | vdw] [pdbres] [pdbatom]
 \end_layout
 
 \begin_layout LyX-Code
-  [pdbres] [pdbatom] [pdbv3] [teradvance] [usecol21]
-\begin_inset Separator latexpar
-\end_inset
+  [pdbv3] [teradvance] [terbyres | pdbter | noter] 
+\end_layout
+
+\begin_layout LyX-Code
+  [model | multi] [chainid <ID>] [sg <group>]
+\end_layout
 
+\begin_layout LyX-Code
+  [include_ep] [conect] [keepext] [usecol21]
+\end_layout
+
+\begin_layout LyX-Code
+  [bfacdata <set>] [occdata <set>] [bfacbyres] [occbyres]
+\end_layout
 
+\begin_layout LyX-Code
+  [bfacscale] [occscale] [bfacmax <max>] [occmax <max>]
 \end_layout
 
 \begin_deeper
@@ -14026,6 +14038,56 @@ keepext Keep filename extension; write '<name>.<num>.<ext>' instead (implies
 usecol21 Use column 21 for 4-letter residue names.
 \end_layout
 
+\begin_layout Description
+bfacdata
+\begin_inset space ~
+\end_inset
+
+<set> Use data in <set> for B-factor column.
+\end_layout
+
+\begin_layout Description
+occdata
+\begin_inset space ~
+\end_inset
+
+<set> Use data in <set> for occupancy column.
+\end_layout
+
+\begin_layout Description
+bfacbyres If specified assume X values in B-factor data set are residue
+ numbers.
+\end_layout
+
+\begin_layout Description
+occbyres If specified assume X values in occupancy data set are residue
+ numbers.
+\end_layout
+
+\begin_layout Description
+bfacscale If specified scale values in B-factor column between 0 and <bfacmax>.
+\end_layout
+
+\begin_layout Description
+occscale If specified scale values in occupancy column between 0 and <occmax>.
+\end_layout
+
+\begin_layout Description
+bfacmax
+\begin_inset space ~
+\end_inset
+
+<max> Max value for bfacscale.
+\end_layout
+
+\begin_layout Description
+occmax
+\begin_inset space ~
+\end_inset
+
+<max> Max value for occscale.
+\end_layout
+
 \end_deeper
 \begin_layout Subsubsection
 

diff --git a/src/Action_Average.cpp b/src/Action_Average.cpp
@@ -59,6 +59,7 @@ Action::RetType Action_Average::Init(ArgList& actionArgs, ActionInit& init, int
   if (crdset_ == 0) {
     outtraj_.SetDebug( debug_ );
     if (outtraj_.InitEnsembleTrajWrite(avgfilename, actionArgs.RemainingArgs(),
+                                       init.DSL(),
                                        TrajectoryFile::UNKNOWN_TRAJ, init.DSL().EnsembleNum()))
       return Action::ERR;
   }

diff --git a/src/Action_LESsplit.cpp b/src/Action_LESsplit.cpp
@@ -41,12 +41,13 @@ Action::RetType Action_LESsplit::Init(ArgList& actionArgs, ActionInit& init, int
   // NOTE: Cannot yet init split traj since we dont know how many.
   if (lesAverage_) {
     avgTraj_.SetDebug( debugIn );
-    if (avgTraj_.InitTrajWrite( avgfilename, trajArgs_, TrajectoryFile::UNKNOWN_TRAJ ))
+    if (avgTraj_.InitTrajWrite( avgfilename, trajArgs_, init.DSL(), TrajectoryFile::UNKNOWN_TRAJ ))
       return Action::ERR;
 #   ifdef MPI
     avgTraj_.SetTrajComm( trajComm_ );
 #   endif
   }
+  masterDSL_ = init.DslPtr();
 
   mprintf("    LESSPLIT:\n");
   if (lesSplit_) mprintf("\tSplit output to '%s.X'\n", splitfilename_.c_str());
@@ -93,7 +94,7 @@ Action::RetType Action_LESsplit::Setup(ActionSetup& setup) {
       for (unsigned int idx = 0; idx != lesMasks_.size(); idx++) {
         // FIXME this will have to be changed if lessplit every enabled for ensemble
         lesTraj_.push_back( new Trajout_Single() );
-        if (lesTraj_.back()->InitEnsembleTrajWrite( splitfilename_, trajArgs_,
+        if (lesTraj_.back()->InitEnsembleTrajWrite( splitfilename_, trajArgs_, *masterDSL_,
                                                     TrajectoryFile::UNKNOWN_TRAJ, idx ))
           return Action::ERR;
 #       ifdef MPI

diff --git a/src/Action_LESsplit.h b/src/Action_LESsplit.h
@@ -27,6 +27,7 @@ class Action_LESsplit : public Action {
     Frame lesFrame_;            ///< Frame for LES split
     Frame avgFrame_;            ///< Frame for LES average
     Topology* lesParm_;         ///< Topology for LES split/average
+    DataSetList* masterDSL_;
 #   ifdef MPI
     Parallel::Comm trajComm_;
 #   endif

diff --git a/src/Action_Mask.cpp b/src/Action_Mask.cpp
@@ -62,7 +62,7 @@ Action::RetType Action_Mask::Init(ArgList& actionArgs, ActionInit& init, int deb
       trajFmt = TrajectoryFile::MOL2FILE;
       trajArgs = ArgList("multi nobox");
     }
-    if (outtraj_.InitEnsembleTrajWrite(maskpdb, trajArgs, trajFmt, init.DSL().EnsembleNum()))
+    if (outtraj_.InitEnsembleTrajWrite(maskpdb, trajArgs, init.DSL(), trajFmt, init.DSL().EnsembleNum()))
       return Action::ERR;
     writeTraj_ = true;
   } else

diff --git a/src/Action_Outtraj.cpp b/src/Action_Outtraj.cpp
@@ -78,7 +78,7 @@ Action::RetType Action_Outtraj::Init(ArgList& actionArgs, ActionInit& init, int
   // Initialize output trajectory with remaining arguments
   if (isActive_) {
     outtraj_.SetDebug(debugIn);
-    if ( outtraj_.InitEnsembleTrajWrite(trajfilename, actionArgs.RemainingArgs(),
+    if ( outtraj_.InitEnsembleTrajWrite(trajfilename, actionArgs.RemainingArgs(), init.DSL(), 
                                         TrajectoryFile::UNKNOWN_TRAJ, init.DSL().EnsembleNum()) )
       return Action::ERR;
   }

diff --git a/src/Action_Pairwise.cpp b/src/Action_Pairwise.cpp
@@ -428,7 +428,8 @@ int Action_Pairwise::WriteCutFrame(int frameNum, Topology const& Parm, AtomMask
     CutParm->SetAtom(i).SetCharge( CutCharges[i] );
   int err = 0;
   Trajout_Single tout;
-  if (tout.PrepareTrajWrite(outfilename, "multi", CutParm, CoordinateInfo(), 1,
+  // NOTE: Since no user-specified arguments, pass in blank data set list.
+  if (tout.PrepareTrajWrite(outfilename, "multi", DataSetList(), CutParm, CoordinateInfo(), 1,
                             TrajectoryFile::MOL2FILE))
   {
     mprinterr("Error: Could not set up cut mol2 file %s\n", outfilename.c_str());

diff --git a/src/Action_ReplicateCell.cpp b/src/Action_ReplicateCell.cpp
@@ -98,7 +98,7 @@ Action::RetType Action_ReplicateCell::Init(ArgList& actionArgs, ActionInit& init
   // Initialize output trajectory with remaining arguments
   if (!trajfilename.empty()) {
     outtraj_.SetDebug( debugIn );
-    if ( outtraj_.InitEnsembleTrajWrite(trajfilename, actionArgs.RemainingArgs(),
+    if ( outtraj_.InitEnsembleTrajWrite(trajfilename, actionArgs.RemainingArgs(), init.DSL(),
                                         TrajectoryFile::UNKNOWN_TRAJ, init.DSL().EnsembleNum()) )
       return Action::ERR;
     writeTraj_ = true;

diff --git a/src/Analysis_Clustering.cpp b/src/Analysis_Clustering.cpp
@@ -1005,7 +1005,7 @@ void Analysis_Clustering::WriteClusterTraj( ClusterList const& CList ) {
     std::string cfilename =  clusterfile_ + ".c" + integerToString( cnum );
     // Set up trajectory file 
     Trajout_Single clusterout;
-    if (clusterout.PrepareTrajWrite(cfilename, ArgList(), clusterparm,
+    if (clusterout.PrepareTrajWrite(cfilename, ArgList(), DataSetList(), clusterparm,
                                     coords_->CoordsInfo(), C->Nframes(),
                                     clusterfmt_)) 
     {
@@ -1041,7 +1041,7 @@ void Analysis_Clustering::WriteAvgStruct( ClusterList const& CList ) {
     std::string cfilename = avgfile_ + ".c" + integerToString( cnum ) + tmpExt;
     // Set up trajectory file
     Trajout_Single clusterout; // FIXME CoordinateInfo OK for just coords?
-    if (clusterout.PrepareTrajWrite(cfilename, ArgList(), &avgparm,
+    if (clusterout.PrepareTrajWrite(cfilename, ArgList(), DataSetList(), &avgparm,
                                     CoordinateInfo(), 1, avgfmt_))
     {
       mprinterr("Error: Could not set up cluster average file %s for write.\n",
@@ -1075,7 +1075,7 @@ void Analysis_Clustering::WriteSingleRepTraj( ClusterList const& CList ) {
   Trajout_Single clusterout;
   // Set up trajectory file. Use parm from COORDS DataSet. 
   Topology *clusterparm = coords_->TopPtr();
-  if (clusterout.PrepareTrajWrite(singlerepfile_, ArgList(), clusterparm,
+  if (clusterout.PrepareTrajWrite(singlerepfile_, ArgList(), DataSetList(), clusterparm,
                                   coords_->CoordsInfo(), CList.Nclusters() * nRepsToSave_,
                                   singlerepfmt_)) 
   {
@@ -1127,7 +1127,7 @@ void Analysis_Clustering::WriteRepTraj( ClusterList const& CList ) {
         std::string cfilename = reptrajfile_ + ".c" + integerToString(C->Num()) +
                                 ("." + integerToString(framenum+1)) + tmpExt;
         // Set up trajectory file.
-        if (clusterout.PrepareTrajWrite(cfilename, ArgList(), clusterparm,
+        if (clusterout.PrepareTrajWrite(cfilename, ArgList(), DataSetList(), clusterparm,
                                         coords_->CoordsInfo(), 1, reptrajfmt_))
         {
           mprinterr("Error: Could not set up representative trajectory file %s for write.\n",
@@ -1146,7 +1146,7 @@ void Analysis_Clustering::WriteRepTraj( ClusterList const& CList ) {
       // Create filename based on cluster number
       std::string cfilename = reptrajfile_ + ".c" + integerToString(C->Num()) + tmpExt;
       // Set up trajectory file.
-      if (clusterout.PrepareTrajWrite(cfilename, ArgList(), clusterparm,
+      if (clusterout.PrepareTrajWrite(cfilename, ArgList(), DataSetList(), clusterparm,
                                       coords_->CoordsInfo(), nRepsToSave_, reptrajfmt_))
       {
         mprinterr("Error: Could not set up representative trajectory file %s for write.\n",

diff --git a/src/Analysis_Hist.cpp b/src/Analysis_Hist.cpp
@@ -483,7 +483,7 @@ Analysis::RetType Analysis_Hist::Analyze() {
             mprinterr("Error: Could not write pseudo topology to '%s'\n", parmoutName_.c_str());
         }
         Trajout_Single out;
-        if (out.PrepareTrajWrite(traj3dName_, ArgList(), &pseudo, CoordinateInfo(),
+        if (out.PrepareTrajWrite(traj3dName_, ArgList(), DataSetList(), &pseudo, CoordinateInfo(),
                                  Ndata, traj3dFmt_) == 0)
         {
           Frame outFrame(1);

diff --git a/src/Analysis_Modes.cpp b/src/Analysis_Modes.cpp
@@ -155,7 +155,7 @@ Analysis::RetType Analysis_Modes::Setup(ArgList& analyzeArgs, AnalysisSetup& set
       return Analysis::ERR;
     }
     // Setup output traj
-    if (trajout_.InitTrajWrite( tOutName, ArgList(), tOutFmt ) != 0) {
+    if (trajout_.InitTrajWrite( tOutName, ArgList(), DataSetList(), tOutFmt ) != 0) {
       mprinterr("Error: Could not init output trajectory.\n");
       return Analysis::ERR;
     }

diff --git a/src/Analysis_Wavelet.cpp b/src/Analysis_Wavelet.cpp
@@ -520,7 +520,7 @@ int Analysis_Wavelet::WAFEX(DataSet_MatrixFlt const& matrix) {
       // Set up trajectory file
       int nframes = CL->MaxCol() - CL->MinCol() + 1;
       Trajout_Single clusterout;
-      if (clusterout.PrepareTrajWrite(cfilename, ArgList(), regionTop,
+      if (clusterout.PrepareTrajWrite(cfilename, ArgList(), DataSetList(), regionTop,
                                       CoordinateInfo(), nframes, TrajectoryFile::PDBFILE))
         return Analysis::ERR;
       // Setup frame for region
@@ -564,6 +564,7 @@ int Analysis_Wavelet::WAFEX(DataSet_MatrixFlt const& matrix) {
     int nframes = (int)coords_->Size();
     Trajout_Single overlay;
     if (overlay.PrepareTrajWrite(overlayName_, "title 'Wavelet trajectory'",
+                                 DataSetList(),
                                  maskTop, CoordinateInfo(), nframes,
                                  TrajectoryFile::UNKNOWN_TRAJ))
       return Analysis::ERR; 

diff --git a/src/Box.h b/src/Box.h
@@ -1,6 +1,7 @@
 #ifndef INC_BOX_H
 #define INC_BOX_H
 #include "Matrix_3x3.h"
+#include "Vec3.h"
 #ifdef MPI
 # include "Parallel.h"
 #endif

diff --git a/src/CoordinateInfo.h b/src/CoordinateInfo.h
@@ -3,9 +3,6 @@
 #include <string>
 #include "ReplicaDimArray.h"
 #include "Box.h"
-#ifdef MPI
-# include "Parallel.h"
-#endif
 /// All metadata associated with a Frame.
 class CoordinateInfo {
   public:

diff --git a/src/Cpptraj.cpp b/src/Cpptraj.cpp
@@ -14,6 +14,7 @@
 #include "TopInfo.h" // ProcessMask
 #include "Timer.h"
 #include "StringRoutines.h" // TimeString
+#include "TrajectoryFile.h" // for autodetect
 #ifdef CUDA
 # include <cuda_runtime_api.h>
 #endif

diff --git a/src/CpptrajState.cpp b/src/CpptrajState.cpp
@@ -3,6 +3,7 @@
 #include "Action_CreateCrd.h" // in case default COORDS need to be created
 #include "DataSet_Coords_REF.h" // AddReference
 #include "DataSet_Topology.h" // AddTopology
+#include "FrameArray.h" // RunEnsemble
 #include "ProgressBar.h"
 #ifdef MPI
 # include "Parallel.h"
@@ -127,9 +128,9 @@ int CpptrajState::AddOutputTrajectory( ArgList& argIn ) {
   Topology* top = DSL_.GetTopology( argIn );
   int err = 1;
   if (mode_ == NORMAL)
-    err = trajoutList_.AddTrajout( fname, argIn, top );
+    err = trajoutList_.AddTrajout( fname, argIn, DSL_, top );
   else if (mode_ == ENSEMBLE)
-    err = ensembleOut_.AddEnsembleOut( fname, argIn, top, trajinList_.EnsembleSize() );
+    err = ensembleOut_.AddEnsembleOut( fname, argIn, DSL_, top, trajinList_.EnsembleSize() );
   return err;
 }
 

diff --git a/src/DataIO_VecTraj.cpp b/src/DataIO_VecTraj.cpp
@@ -84,7 +84,7 @@ int DataIO_VecTraj::WriteData(FileName const& fname, DataSetList const& SetList)
   }
   // Write out vectors
   Trajout_Single out;
-  if (out.PrepareTrajWrite(fname, ArgList(), &pseudo, CoordinateInfo(),
+  if (out.PrepareTrajWrite(fname, ArgList(), DataSetList(), &pseudo, CoordinateInfo(),
                            vec_size, trajoutFmt_) == 0)
   {
     Frame outFrame(pseudo.Natom());

diff --git a/src/DataSetList.h b/src/DataSetList.h
@@ -1,12 +1,13 @@
 #ifndef INC_DATASETLIST_H
 #define INC_DATASETLIST_H
 #include <vector>
-#include "DataSet.h"
-#include "ArgList.h" // GetReferenceFrame, GetTopology
 #include "ReferenceFrame.h" // GetReferenceFrame
 #ifdef TIMER
 # include "Timer.h"
 #endif
+// Forward declarations
+class DataSet;
+class ArgList;
 /// Hold list of DataSets.
 /** Main class for handling DataSets. All DataSet types can be allocated 
   * by DataSetList. There is a master DataSetList in CpptrajState that will

diff --git a/src/DataSet_Coords_REF.h b/src/DataSet_Coords_REF.h
@@ -1,7 +1,8 @@
 #ifndef INC_DATASET_COORDS_REF_H
 #define INC_DATASET_COORDS_REF_H
 #include "DataSet_Coords.h"
-#include "ArgList.h"
+// Forward declarations
+class ArgList;
 /// Store a single reference frame in double precision.
 class DataSet_Coords_REF : public DataSet_Coords {
   public:

diff --git a/src/EnsembleIn.h b/src/EnsembleIn.h
@@ -1,15 +1,19 @@
 #ifndef INC_ENSEMBLEIN_H
 #define INC_ENSEMBLEIN_H
 #include "InputTrajCommon.h"
-#include "FrameArray.h"
+// Not forward-declared because is just a typedef
 #include "FramePtrArray.h"
 #include "ReplicaInfo.h"
+#include "Frame.h" // For RemdIdxType TODO put RemdIdxType in ReplicaInfo
 #ifdef MPI
 # include "Parallel.h"
 # ifdef TIMER
 #   include "Timer.h"
 # endif
 #endif
+// Forward declarations
+class FrameArray;
+class CoordinateInfo;
 /// Read in an array of frames at a time.
 class EnsembleIn {
   public:

diff --git a/src/EnsembleIn_Multi.cpp b/src/EnsembleIn_Multi.cpp
@@ -1,4 +1,5 @@
 #include "EnsembleIn_Multi.h"
+#include "FrameArray.h"
 #include "CpptrajStdio.h"
 #include "DataFile.h" // TODO remove
 #include "StringRoutines.h" // integerToString TODO remove

diff --git a/src/EnsembleIn_Single.cpp b/src/EnsembleIn_Single.cpp
@@ -1,5 +1,8 @@
 #ifdef ENABLE_SINGLE_ENSEMBLE
 #include "EnsembleIn_Single.h"
+#include "TrajectoryIO.h"
+#include "Topology.h"
+#include "FrameArray.h"
 #include "TrajectoryFile.h"
 #include "CpptrajStdio.h"
 

diff --git a/src/EnsembleIn_Single.h b/src/EnsembleIn_Single.h
@@ -2,7 +2,8 @@
 #define INC_ENSEMBLEIN_SINGLE_H
 #ifdef ENABLE_SINGLE_ENSEMBLE
 #include "EnsembleIn.h"
-#include "TrajectoryIO.h"
+// Forward declarations
+class TrajectoryIO;
 /// Read in an array of frames at a time from a single file.
 class EnsembleIn_Single : public EnsembleIn {
   public:

diff --git a/src/EnsembleOut.h b/src/EnsembleOut.h
@@ -1,6 +1,9 @@
 #ifndef INC_ENSEMBLEOUT_H
 #define INC_ENSEMBLEOUT_H
 #include "OutputTrajCommon.h"
+#include "FramePtrArray.h"
+// Forward Declarations
+class DataSetList;
 /// Write out an array of frames at a time.
 class EnsembleOut {
   public:
@@ -9,7 +12,7 @@ class EnsembleOut {
     void SetDebug(int d) { debug_ = d; }
     // ----- Inherited Functions -----------------
     /// Prepare ensemble for writing given format, no Topology setup.
-    virtual int InitEnsembleWrite(std::string const&, ArgList const&,
+    virtual int InitEnsembleWrite(std::string const&, ArgList const&, DataSetList const&,
                                   int, TrajectoryFile::TrajFormatType) = 0;
     /// Perform Topology-related setup for ensemble and open. TODO const&
     virtual int SetupEnsembleWrite(Topology*, CoordinateInfo const&, int) = 0;