Fix to align and displace values output by pathtools

Previously, pathtools ignored the align and displace values that the user provided in input pdb files when outputting the finalized path.
These values are now output in this updated version of the tool

src/generic/DumpPDB.cpp

@@ -48,6 +48,7 @@ class DumpPDB :
   std::string fmt;
   std::string file;
   std::string description;
+  std::vector<double> beta, occupancy;
   std::vector<std::string> argnames;
   std::vector<AtomNumber> pdb_atom_indices;
   void buildArgnames();
@@ -70,6 +71,8 @@ void DumpPDB::registerKeywords( Keywords& keys ) {
   keys.add("compulsory","STRIDE","0","the frequency with which the atoms should be output");
   keys.add("compulsory","FILE","the name of the file on which to output these quantities");
   keys.add("compulsory","FMT","%f","the format that should be used to output real numbers");
+  keys.add("compulsory","OCCUPANCY","1.0","vector of values to output in the occupancy column of the pdb file");
+  keys.add("compulsory","BETA","1.0","vector of values to output in the beta column of the pdb file");
   keys.add("optional","DESCRIPTION","the title to use for your PDB output");
   keys.add("optional","ATOM_INDICES","the indices of the atoms in your PDB output");
   keys.add("optional","ARG_NAMES","the names of the arguments that are being output");
@@ -94,6 +97,8 @@ DumpPDB::DumpPDB(const ActionOptions&ao):
     for(unsigned i=0; i<indices.size(); ++i) log.printf("%d ", pdb_atom_indices[i].serial() );
     log.printf("\n");
     if( pdb_atom_indices.size()!=atom_args[0]->getShape()[1]/3 ) error("mismatch between size of matrix containing positions and vector of atom indices");
+    beta.resize( atom_args[0]->getShape()[1]/3 ); occupancy.resize( atom_args[0]->getShape()[1]/3 );
+    parseVector("OCCUPANCY", occupancy ); parseVector("BETA", beta );
   }
   log.printf("  printing configurations to PDB file to file named %s \n", file.c_str() );
   parseVector("ARG_NAMES",argnames); if( argnames.size()==0 ) buildArgnames();
@@ -172,7 +177,7 @@ void DumpPDB::update() {
         pos[0]=getPntrToArgument(atomarg)->get(npos*(3*i+0) + k);
         pos[1]=getPntrToArgument(atomarg)->get(npos*(3*i+1) + k);
         pos[2]=getPntrToArgument(atomarg)->get(npos*(3*i+2) + k);
-        printAtom( opdbf, pdb_atom_indices[k].serial(), pos, 1.0, 1.0 );
+        printAtom( opdbf, pdb_atom_indices[k].serial(), pos, occupancy[k], beta[k] );
       }
     }
     opdbf.printf("END\n");

src/mapping/PathTools.cpp

@@ -212,7 +212,12 @@ int PathTools::main(FILE* in, FILE*out,Communicator& pc) {
     std::string pinput="DUMPPDB STRIDE=1 DESCRIPTION=PATH FILE=" + ofilename + " FMT=" + ofmt;
     if( argstr.size()>0 ) {
       pinput += " ARG=" + argstr[0]; for(unsigned i=1; i<argstr.size(); ++i ) pinput += "," + argstr[i];
-    } else { std::string num; Tools::convert( indices[0].serial(), num ); pinput += " ATOMS=data ATOM_INDICES=" + num; for(unsigned i=1; i<indices.size(); ++i ) { Tools::convert( indices[i].serial(), num ); pinput += "," + num; } }
+    } else {
+      std::string num; Tools::convert( indices[0].serial(), num ); pinput += " ATOMS=data ATOM_INDICES=" + num; for(unsigned i=1; i<indices.size(); ++i ) { Tools::convert( indices[i].serial(), num ); pinput += "," + num; }
+      std::string anum, dnum; Tools::convert( alig[0], anum ); Tools::convert( disp[0], dnum );
+      pinput += " OCCUPANCY=" + anum; for(unsigned i=1; i<alig.size(); ++i) { Tools::convert( alig[i], anum ); pinput += "," + anum; }
+      pinput += " BETA=" + dnum; for(unsigned i=1; i<disp.size(); ++i) { Tools::convert( disp[i], dnum ); pinput += "," + dnum; }
+    }
     const char* pcinp=pinput.c_str(); plmd.cmd("readInputLine",pcinp);
     Action* paction = plmd.getActionSet()[plmd.getActionSet().size()-1].get();
     paction->update();
@@ -271,11 +276,13 @@ int PathTools::main(FILE* in, FILE*out,Communicator& pc) {
   }
 
 // Now create the metric object
+  std::vector<double> alig, disp;
   if( mtype=="OPTIMAL-FAST" || mtype=="OPTIMAL" || mtype=="SIMPLE" ) {
     std::string trinput = "endT: TRANSPOSE ARG=end";
     const char* tinp=trinput.c_str(); plmd.cmd("readInputLine",tinp);
     PDB pdb; pdb.read(istart,false,0.1);
-    std::vector<double> alig( pdb.getOccupancy() ), disp( pdb.getBeta() );
+    alig.resize( pdb.getOccupancy().size() ); disp.resize( pdb.getBeta().size() );
+    for(unsigned i=0; i<alig.size(); ++i) { alig[i] = pdb.getOccupancy()[i]; disp[i]= pdb.getBeta()[i]; }
     std::string minput = "d: RMSD_VECTOR DISPLACEMENT SQUARED UNORMALIZED TYPE=" + mtype + " ARG=endT,start";
     // Get the align values
     std::string anum; Tools::convert( alig[0], anum ); minput += " ALIGN=" + anum;
@@ -354,6 +361,9 @@ int PathTools::main(FILE* in, FILE*out,Communicator& pc) {
     }
     const char* icinp=inpt.c_str(); plmd.cmd("readInputLine",icinp); std::string num; Tools::convert( indices[0].serial(), num );
     pinput += " ATOMS=atom_data ATOM_INDICES=" + num; for(unsigned i=1; i<indices.size(); ++i ) { Tools::convert( indices[i].serial(), num ); pinput += "," + num; }
+    std::string anum, dnum; Tools::convert( alig[0], anum ); Tools::convert( disp[0], dnum );
+    pinput += " OCCUPANCY=" + anum; for(unsigned i=1; i<alig.size(); ++i) { Tools::convert( alig[i], anum ); pinput += "," + anum; }
+    pinput += " BETA=" + dnum; for(unsigned i=1; i<disp.size(); ++i) { Tools::convert( disp[i], dnum ); pinput += "," + dnum; }
   }
   const char* pcinp=pinput.c_str(); plmd.cmd("readInputLine",pcinp);
   Action* paction = plmd.getActionSet()[plmd.getActionSet().size()-1].get();