Fix detection of NAMD-style unit cell parameters for NAMD DCD (#1081)

* Ensure box coords are properly reordered to what Cpptraj Box expects during NAMD dcd unit cell setup

* Start making X-align/symmetric warnings less verbose unless the debug
level demands it

* Print warnings for ensemble output

* Use new warnings

* Add check for if 'namdcell' keyword should be used. Only reorder box
elements if NAMD cell was actually detected.

* Hide debug info, improve warning messages. If unit cell has not been
user specified and strange box orthogonal skeww is detected, assume this
might be a DCD from NAMD with a non-orthogonal cell

* 6.26.0. Fix handling of NAMD DCD trajectories with non-orthogonal unit
cell information.

* Add some debug

src/EnsembleOut_Multi.cpp

@@ -121,12 +121,15 @@ int EnsembleOut_Multi::InitEnsembleWrite(std::string const& tnameIn,
 void EnsembleOut_Multi::EndEnsemble() {
   //if (TrajIsOpen()) {
     for (IOarrayType::const_iterator tio = ioarray_.begin(); tio != ioarray_.end(); ++tio)
+    {
 #     ifdef MPI
       if (trajComm_.Size() > 1)
         (*tio)->parallelCloseTraj();
       else
 #     endif
         (*tio)->closeTraj();
+      (*tio)->PrintWarnings( fileNames_[tio-ioarray_.begin()] );
+    }
   //  SetTrajIsOpen( false );
   //}
 }

src/EnsembleOut_Single.cpp

@@ -25,6 +25,7 @@ int EnsembleOut_Single::InitEnsembleWrite(std::string const& tnameIn,
     mprinterr("Internal Error: InitTrajWrite: No filename given.\n");
     return 1;
   }
+  fname_ = tnameIn;
   // Require that ensemble size is set.
   ensembleSize_ = ensembleSizeIn; 
   if (ensembleSize_ < 1) {
@@ -74,7 +75,10 @@ int EnsembleOut_Single::InitEnsembleWrite(std::string const& tnameIn,
 // EnsembleOut_Single::EndEnsemble()
 void EnsembleOut_Single::EndEnsemble() {
   //if (TrajIsOpen()) {
-  if (eio_ != 0) eio_->closeTraj(); // Handle no init case
+  if (eio_ != 0) {
+    eio_->closeTraj(); // Handle no init case
+    eio_->PrintWarnings(fname_);
+  }
   //  SetTrajIsOpen(false);
   //}
 }

src/EnsembleOut_Single.h

@@ -19,6 +19,7 @@ class EnsembleOut_Single : public EnsembleOut {
   private:
     TrajectoryIO* eio_; // TODO Make EnsembleIO
     int ensembleSize_;
+    std::string fname_;
 };
 #endif
 #endif

src/Traj_AmberCoord.cpp

@@ -168,7 +168,7 @@ int Traj_AmberCoord::writeFrame(int set, Frame const& frameOut) {
 
   if (numBoxCoords_ != 0) {
     if (!frameOut.BoxCrd().Is_X_Aligned())
-      mprintf("Warning: Set %i; unit cell is not X-aligned. Box cannot be properly stored as Amber ASCII trajectory.\n", set+1);
+      incrementXalignWarnCount(set, "Amber ASCII trajectory");
     file_.DoubleToBuffer(frameOut.BoxCrd().XyzPtr(), numBoxCoords_, outfmt_);
   }
 

src/Traj_AmberNetcdf.cpp

@@ -447,7 +447,7 @@ int Traj_AmberNetcdf::writeFrame(int set, Frame const& frameOut) {
   // Write box
   if (cellLengthVID_ != -1) {
     if (!frameOut.BoxCrd().Is_X_Aligned())
-      mprintf("Warning: Set %i; unit cell is not X-aligned. Box cannot be properly stored as Amber NetCDF trajectory.\n", set+1);
+      incrementXalignWarnCount(set, "Amber NetCDF trajectory");
     count_[1] = 3;
     count_[2] = 0;
     if (NC::CheckErr(nc_put_vara_double(ncid_, cellLengthVID_, start_, count_,

src/Traj_AmberRestart.cpp

@@ -344,7 +344,7 @@ int Traj_AmberRestart::writeFrame(int set, Frame const& frameOut) {
   // Write box to buffer
   if (numBoxCoords_!=0) {
     if (!frameOut.BoxCrd().Is_X_Aligned())
-      mprintf("Warning: Set %i; unit cell is not X-aligned. Box cannot be properly stored as Amber ASCII restart.\n", set+1);
+      incrementXalignWarnCount(set, "Amber ASCII restart");
     file_.DoubleToBuffer(frameOut.BoxCrd().XyzPtr(), numBoxCoords_, "%12.7f");
   }
 

src/Traj_AmberRestartNC.cpp

@@ -294,7 +294,7 @@ int Traj_AmberRestartNC::writeFrame(int set, Frame const& frameOut) {
   // write box
   if (cellLengthVID_ != -1) {
     if (!frameOut.BoxCrd().Is_X_Aligned())
-      mprintf("Warning: Set %i; unit cell is not X-aligned. Box cannot be properly stored as Amber NetCDF restart.\n", set+1);
+      incrementXalignWarnCount(set, "Amber NetCDF restart");
     count_[0] = 3;
     count_[1] = 0;
     if (NC::CheckErr(nc_put_vara_double(ncid_,cellLengthVID_,start_,count_,frameOut.BoxCrd().XyzPtr())))

src/Traj_CharmmDcd.cpp

@@ -375,8 +375,7 @@ int Traj_CharmmDcd::readDcdHeader() {
     if (charmmCellType_ != UNKNOWN) {
       // Box info type was specified by option.
       if (buffer.i[19] >= 22 && charmmCellType_ != SHAPE)
-        mprintf("Warning: CHARMM version is >= 22 but 'shape' not specified.\n"
-                "Warning: Assuming box info is stored as unit cell and not shape matrix.\n");
+        mprintf("Warning: CHARMM version is >= 22 but an option other than 'shape' was specified.\n");
     }
   } else
     boxBytes_ = 0;
@@ -470,6 +469,7 @@ int Traj_CharmmDcd::setupBox(double* boxtmp) {
   file_.Read(boxtmp, sizeof(double)*6);
   if (isBigEndian_) endian_swap8(boxtmp,6);
   if ( ReadBlock(-1) < 0) return 1;
+  if (debug_ > 0) mprintf("DEBUG: Raw box values: %g %g %g %g %g %g\n", boxtmp[0], boxtmp[1], boxtmp[2], boxtmp[3], boxtmp[4], boxtmp[5]);
   // Test shape matrix
   if (charmmCellType_ == UNKNOWN || charmmCellType_ == SHAPE) {
     int nIssues = 0;
@@ -478,6 +478,31 @@ int Traj_CharmmDcd::setupBox(double* boxtmp) {
     for (int i = 0; i < 6; i++) shape[i] = 0;
     Box::CheckType check;
     testBox.SetupFromShapeMatrix( boxtmp, check );
+    // NAMD stores a pseudo-shape matrix that fails for non-orthogonal cells.
+    // Check if a non-orthogonal cell has angles close to but not quite 90 deg.
+    Box::CellShapeType boxShape = testBox.CellShape();
+    if (boxShape != Box::CUBIC && boxShape != Box::TETRAGONAL && boxShape != Box::ORTHORHOMBIC) {
+      if (debug_ > 0) testBox.PrintDebug("DCD Shape Matrix Check"); // DEBUG
+      double deltaA = fabs( 90.0 - testBox.Param(Box::ALPHA) );
+      double deltaB = fabs( 90.0 - testBox.Param(Box::BETA) );
+      double deltaG = fabs( 90.0 - testBox.Param(Box::GAMMA) );
+      if ( deltaA > Constants::SMALL && deltaA < 1.0 &&
+           deltaB > Constants::SMALL && deltaB < 1.0 &&
+           deltaG > Constants::SMALL && deltaG < 1.0 )
+      {
+        if (charmmCellType_ != UNKNOWN) {
+          mprintf("Warning: Cell is non-orthogonal but all angles from the symmetric shape\n"
+                  "Warning: matrix are close to 90 deg (%g %g %g).\n",
+                  testBox.Param(Box::ALPHA), testBox.Param(Box::BETA), testBox.Param(Box::GAMMA));
+          mprintf("Warning: If this trajectory is from NAMD with a non-orthogonal cell\n"
+                  "Warning: the 'namdcell' option must be used since NAMD does not store\n"
+                  "Warning: the actual symmetric shape matrix.\n");
+        } else {
+          // User has not specified box; this is likely a NAMD DCD with non-orthogonal cell
+          check = Box::BOX_IS_SKEWED;
+        }
+      }
+    }
     if (check != Box::BOX_OK) {
       nIssues = 1;
     } else {
@@ -513,6 +538,14 @@ int Traj_CharmmDcd::setupBox(double* boxtmp) {
   }
   // Test NAMD unit cell
   if (charmmCellType_ == UNKNOWN || charmmCellType_ == NAMD) {
+    //mprintf("DEBUG: NAMD unit cell test, celltype %i\n", (int)charmmCellType_);
+    // Expect that values are stored as X, gamma, Y, beta, alpha, Z
+    //                                  0  1      2  3     4      5
+    // Will need to resort them as expected by Box (X Y Z alpha beta gamma)
+    double newbox[6];
+    newbox[0] = boxtmp[0];
+    newbox[1] = boxtmp[2];
+    newbox[2] = boxtmp[5];
     // Since NAMD stores the box angles as cos(angle), determine if the angle values are bounded between -1 and 1.
     if ( boxtmp[4] >= -1 && boxtmp[4] <= 1 &&
          boxtmp[3] >= -1 && boxtmp[3] <= 1 &&
@@ -521,9 +554,23 @@ int Traj_CharmmDcd::setupBox(double* boxtmp) {
       if (charmmCellType_ == UNKNOWN)
         mprintf("\tNAMD unit cell detected.\n");
       charmmCellType_ = NAMD;
+      // Convert the angles back to degrees
+      newbox[3] = CosRadToDeg( boxtmp[4] );
+      newbox[4] = CosRadToDeg( boxtmp[3] );
+      newbox[5] = CosRadToDeg( boxtmp[1] );
+      if (debug_ > 0) mprintf("DEBUG: angles in degrees: %g %g %g\n", newbox[3], newbox[4], newbox[5]);
     } else if (charmmCellType_ == NAMD) {
       mprintf("Warning: NAMD unit cell specified but cos(angle) values not bounded by -1, 1\n",
               "Warning: Values: %g %g %g\n", boxtmp[4], boxtmp[3], boxtmp[1]);
+      // Assume the angles are already in degrees
+      newbox[3] = boxtmp[4];
+      newbox[4] = boxtmp[3];
+      newbox[5] = boxtmp[1];
+    }
+    if (charmmCellType_ == NAMD) {
+      // Set with re-ordered (and possibly converted) values
+      for (int i = 0; i < 6; i++)
+        boxtmp[i] = newbox[i];
     }
   }
   // Test CHARMM unit cell
@@ -539,7 +586,7 @@ int Traj_CharmmDcd::setupBox(double* boxtmp) {
       charmmCellType_ = CHARMM;
     } else if (charmmCellType_ == CHARMM) {
       mprintf("Warning: CHARMM unit cell specified but bad box values detected.\n"
-              "Warning: Box values : %g %g %g %g %g %g\n",
+              "Warning: Box values (XYZ, ABG) : %g %g %g Ang., %g %g %g deg.\n",
               boxtmp[0], boxtmp[1], boxtmp[2], boxtmp[3], boxtmp[4], boxtmp[5]);
     }
   }
@@ -565,6 +612,7 @@ int Traj_CharmmDcd::ReadBox(double* boxtmp) {
   if (isBigEndian_) endian_swap8(boxtmp,6);
   if ( ReadBlock(-1) < 0) return 1;
   if (charmmCellType_ == NAMD) {
+    // Expect that values are stored as X, gamma, Y, beta, alpha, Z
     // Box lengths
     double box[6];
     box[0] = boxtmp[0];
@@ -870,7 +918,7 @@ int Traj_CharmmDcd::writeFrame(int set, Frame const& frameOut) {
     double boxtmp[6];
     if (charmmCellType_ == SHAPE) {
       if (!frameOut.BoxCrd().Is_Symmetric())
-        mprintf("Warning: Set %i; unit cell is not symmetric. Box cannot be properly stored as Charmm DCD.\n", set+1);
+        incrementSymmetricWarnCount(set, "Charmm DCD");
       //frameOut.BoxCrd().GetSymmetricShapeMatrix( boxtmp );
       Matrix_3x3 const& ucell = frameOut.BoxCrd().UnitCell();
       boxtmp[0] = ucell[0]; // XX
@@ -881,7 +929,7 @@ int Traj_CharmmDcd::writeFrame(int set, Frame const& frameOut) {
       boxtmp[5] = ucell[8]; // ZZ
     } else {
       if (!frameOut.BoxCrd().Is_X_Aligned())
-        mprintf("Warning: Set %i; unit cell is not X-aligned. Box cannot be properly stored as Charmm DCD.\n", set+1);
+        incrementXalignWarnCount(set, "Charmm DCD");
       if (charmmCellType_ == NAMD) {
         /* The format for the 'box' array used in cpptraj is not the same as the
          * one used for NAMD dcd files.  Refer to the reading routine above

src/Traj_NcEnsemble.cpp

@@ -388,7 +388,7 @@ int Traj_NcEnsemble::writeArray(int set, FramePtrArray const& Farray) {
     // Write box
     if (cellLengthVID_ != -1) {
       if (!frm->BoxCrd().Is_X_Aligned())
-      mprintf("Warning: Set %i; unit cell is not X-aligned. Box cannot be properly stored as Amber NetCDF ensemble.\n", set+1);
+        incrementXalignWarnCount(set,"Amber NetCDF ensemble");
       count_[2] = 3;
 #     ifdef HAS_PNETCDF
       if (ncmpi_put_vara_double_all(ncid_,cellLengthVID_,start_,count_,frm->BoxCrd().XyzPtr()))

src/Traj_PDBfile.cpp

@@ -837,7 +837,7 @@ void Traj_PDBfile::WriteBonds() {
 void Traj_PDBfile::writeBox(int set, Box const& box) {
   if (write_cryst1_) {
     if (!box.Is_X_Aligned())
-      mprintf("Warning: Set %i; unit cell is not X-aligned. Box cannot be properly stored in PDB CRYST1.\n", set+1);
+      incrementXalignWarnCount(set, "PDB CRYST1");
     file_.WriteCRYST1( box.XyzPtr(), space_group_.c_str() );
   }
 }

src/TrajectoryIO.cpp

@@ -1,4 +1,49 @@
 #include "TrajectoryIO.h"
+#include "CpptrajStdio.h"
+
+/** CONSTRUCTOR */
+TrajectoryIO::TrajectoryIO() :
+  debug_(0),
+  nwarn_cell_not_xaligned_(0),
+  nwarn_cell_not_symmetric_(0)
+{}
+
+/** Increment count of frames where it is an issue that the
+  * unit cell is not X-aligned. Print a warning only the 
+  * first time.
+  */
+void TrajectoryIO::incrementXalignWarnCount(int set, const char* desc) {
+  if (nwarn_cell_not_xaligned_ == 0 || debug_ > 0)
+    mprintf("Warning: Set %i; unit cell is not X-aligned. Box cannot be properly stored as %s.\n", set+1, desc);
+  nwarn_cell_not_xaligned_++;
+}
+
+/** Increment count of frames where it is an issue that the
+  * unit cell is not symmetric. Print a warning only the 
+  * first time.
+  */
+void TrajectoryIO::incrementSymmetricWarnCount(int set, const char* desc) {
+  if (nwarn_cell_not_symmetric_ == 0 || debug_ > 0)
+    mprintf("Warning: Set %i; unit cell is not symmetric. Box cannot be properly stored as %s.\n", set+1, desc);
+  nwarn_cell_not_symmetric_++;
+}
+
+/** Print any warnings. Ideally called just before or just after closeTraj() */
+void TrajectoryIO::PrintWarnings(std::string const& fname) {
+  if (nwarn_cell_not_xaligned_ > 0) {
+    mprintf("Warning: %s: unit cell was not X-aligned for %u frames.\n", fname.c_str(), nwarn_cell_not_xaligned_);
+    mprintf("Warning: This trajectory format expects unit cells to be X-aligned,\n"
+            "Warning: so the unit cell orientation may not be correct.\n");
+  }
+  if (nwarn_cell_not_symmetric_ > 0) {
+    mprintf("Warning: %s: unit cell axes were not symmetric for %u frames.\n", fname.c_str(), nwarn_cell_not_symmetric_);
+    mprintf("Warning: This trajectory format expects unit cell info to be symmetric,\n"
+            "Warning: so the unit cell orientation may not be correct.\n");
+  }
+  nwarn_cell_not_xaligned_ = 0;
+  nwarn_cell_not_symmetric_ = 0;
+}
+
 #ifdef MPI
 /** Broadcast trajectory IO info from master. */
 int TrajectoryIO::BroadcastTrajIO(Parallel::Comm const& commIn) {

src/TrajectoryIO.h

@@ -26,8 +26,10 @@ class FrameArray;
   */
 class TrajectoryIO : public BaseIOtype {
   public:
-    TrajectoryIO() : debug_(0) {}
-    virtual ~TrajectoryIO() {} // virtual since this class is inherited.
+    /// CONSTRUCTOR
+    TrajectoryIO();
+    /// DESTRUCTOR - virtual since this class is inherited.
+    virtual ~TrajectoryIO() {}
     // -----------===== Inherited functions =====-----------
     /// \return true if file format matches trajectory type.
     virtual bool ID_TrajFormat(CpptrajFile&) = 0;
@@ -105,13 +107,21 @@ class TrajectoryIO : public BaseIOtype {
     virtual void parallelCloseTraj() { return ; }
 #   endif
     // -----------------------------------------------------
+    /// Print any warnings. Resets warning counts.
+    void PrintWarnings(std::string const&);
+
     CoordinateInfo const& CoordInfo() const { return coordInfo_; }
     std::string const& Title()        const { return title_;     }
 
     void SetDebug(int dIn)                       { debug_ = dIn;     }
     void SetTitle(std::string const& tIn)        { title_ = tIn;     }
   protected:
     void SetCoordInfo(CoordinateInfo const& cIn) { coordInfo_ = cIn; }
+    /// Increment X-align warn count
+    void incrementXalignWarnCount(int, const char*);
+    /// Increment symmetric warn count
+    void incrementSymmetricWarnCount(int, const char*);
+
     int debug_;               ///< Trajectory debug level.
 #   ifdef MPI
     /// Broadcast coordinate info etc. to non-master processes
@@ -120,5 +130,7 @@ class TrajectoryIO : public BaseIOtype {
   private:
     CoordinateInfo coordInfo_; ///< Metadata associated with coordinate Frame
     std::string title_;        ///< Set to trajectory title.
+    unsigned int nwarn_cell_not_xaligned_; ///< Count of frames where unit cell is not X-aligned
+    unsigned int nwarn_cell_not_symmetric_; ///< Count of frames where unit cell is not symmetric
 }; 
 #endif

src/Trajout_Single.cpp

@@ -103,6 +103,7 @@ void Trajout_Single::EndTraj() {
     else
 #   endif
       trajio_->closeTraj();
+    trajio_->PrintWarnings(traj_.Filename().Base());
   }
   //  SetTrajIsOpen(false);
   //}

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 "V6.25.3"
+#define CPPTRAJ_INTERNAL_VERSION "V6.26.0"
 /// PYTRAJ relies on this
 #define CPPTRAJ_VERSION_STRING CPPTRAJ_INTERNAL_VERSION
 #endif

src/cpptrajdepend

@@ -495,7 +495,7 @@ Traj_SQM.o : Traj_SQM.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Bo
 Traj_Tinker.o : Traj_Tinker.cpp Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TinkerFile.h Topology.h Traj_Tinker.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
 Traj_XYZ.o : Traj_XYZ.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Frame.h FramePtrArray.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Topology.h Traj_XYZ.h TrajectoryIO.h TypeNameHolder.h Unit.h Vec3.h
 TrajectoryFile.o : TrajectoryFile.cpp Atom.h BaseIOtype.h Box.h BufferedFrame.h BufferedLine.h CIFfile.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h FileTypes.h FramePtrArray.h Matrix_3x3.h Mol2File.h NC_Routines.h NameType.h NetcdfFile.h PDBfile.h Parallel.h ReplicaDimArray.h Residue.h SDFfile.h SymbolExporting.h TextFormat.h TinkerFile.h Traj_AmberCoord.h Traj_AmberNetcdf.h Traj_AmberRestart.h Traj_AmberRestartNC.h Traj_Binpos.h Traj_CIF.h Traj_CharmmCor.h Traj_CharmmDcd.h Traj_CharmmRestart.h Traj_Conflib.h Traj_DTR.h Traj_GmxDump.h Traj_GmxTng.h Traj_GmxTrX.h Traj_GmxXtc.h Traj_Gro.h Traj_H5.h Traj_H5MD.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
+TrajectoryIO.o : TrajectoryIO.cpp BaseIOtype.h Box.h CoordinateInfo.h CpptrajStdio.h FramePtrArray.h Matrix_3x3.h Parallel.h ReplicaDimArray.h TrajectoryIO.h Vec3.h
 TrajinList.o : TrajinList.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_RemLog.h Dimension.h EnsembleIn.h EnsembleIn_Multi.h EnsembleIn_Single.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryFile.h TrajectoryIO.h Trajin.h TrajinList.h Trajin_Multi.h Trajin_Single.h TypeNameHolder.h Unit.h Vec3.h
 Trajin_Multi.o : Trajin_Multi.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajIOarray.h TrajectoryIO.h Trajin.h Trajin_Multi.h TypeNameHolder.h Unit.h Vec3.h
 Trajin_Single.o : Trajin_Single.cpp ArgList.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TrajFrameCounter.h TrajectoryFile.h TrajectoryIO.h Trajin.h Trajin_Single.h TypeNameHolder.h Unit.h Vec3.h