Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2012-2023 The plumed team
       3             :    (see the PEOPLE file at the root of the distribution for a list of names)
       4             : 
       5             :    See http://www.plumed.org for more information.
       6             : 
       7             :    This file is part of plumed, version 2.
       8             : 
       9             :    plumed is free software: you can redistribute it and/or modify
      10             :    it under the terms of the GNU Lesser General Public License as published by
      11             :    the Free Software Foundation, either version 3 of the License, or
      12             :    (at your option) any later version.
      13             : 
      14             :    plumed is distributed in the hope that it will be useful,
      15             :    but WITHOUT ANY WARRANTY; without even the implied warranty of
      16             :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
      17             :    GNU Lesser General Public License for more details.
      18             : 
      19             :    You should have received a copy of the GNU Lesser General Public License
      20             :    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
      21             : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
      22             : #include "core/ActionShortcut.h"
      23             : #include "core/ActionRegister.h"
      24             : #include "core/ActionWithArguments.h"
      25             : #include "core/PlumedMain.h"
      26             : #include "tools/PDB.h"
      27             : 
      28             : namespace PLMD {
      29             : namespace generic {
      30             : 
      31             : //+PLUMEDOC COLVAR PDB2CONSTANT
      32             : /*
      33             : Create a constant value from a PDB input file
      34             : 
      35             : \par Examples
      36             : 
      37             : */
      38             : //+ENDPLUMEDOC
      39             : 
      40             : class PDB2Constant : public ActionShortcut {
      41             : public:
      42             :   static void registerKeywords(Keywords& keys);
      43             :   explicit PDB2Constant(const ActionOptions&);
      44             : };
      45             : 
      46             : PLUMED_REGISTER_ACTION(PDB2Constant,"PDB2CONSTANT")
      47             : 
      48         168 : void PDB2Constant::registerKeywords(Keywords& keys) {
      49         168 :   ActionShortcut::registerKeywords( keys );
      50         336 :   keys.add("compulsory","REFERENCE","a file in pdb format containing the reference structure");
      51         336 :   keys.add("compulsory","NUMBER","0","if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here. If NUMBER=0 then the RMSD from all structures are computed");
      52         336 :   keys.addFlag("NOARGS",false,"the arguments that are being read from the PDB file are not in the plumed input");
      53         336 :   keys.addInputKeyword("optional","ARG","scalar/vector","read this single argument from the input rather than the atomic structure");
      54         336 :   keys.setValueDescription("scalar/vector/matrix","a value that is constructed from the information in the PDB file");
      55         168 :   keys.needsAction("CONSTANT");
      56         168 : }
      57             : 
      58         115 : PDB2Constant::PDB2Constant(const ActionOptions& ao):
      59             :   Action(ao),
      60         115 :   ActionShortcut(ao)
      61             : {
      62         115 :   std::string input; parse("REFERENCE",input);
      63         230 :   unsigned frame; parse("NUMBER",frame); bool noargs=false;
      64         230 :   std::vector<std::string> argn; parseVector("ARG",argn); std::vector<Value*> theargs;
      65         115 :   if( argn.size()>0 ) {
      66          75 :     parseFlag("NOARGS",noargs);
      67          75 :     if( !noargs ) ActionWithArguments::interpretArgumentList( argn, plumed.getActionSet(), this, theargs );
      68           2 :     else if( argn.size()>1 ) error("can only read one argument at a time from input pdb file");
      69           2 :     else log.printf("  reading argument %s from file \n", argn[0].c_str() );
      70             :   }
      71         115 :   if( theargs.size()>1 ) error("can only read one argument at a time from input pdb file");
      72             : 
      73         115 :   FILE* fp=std::fopen(input.c_str(),"r"); bool do_read=true; std::vector<double> vals;
      74         115 :   if(!fp) plumed_merror("could not open reference file " + input); unsigned natoms=0, nframes=0;
      75             : 
      76        2235 :   while ( do_read ) {
      77        2235 :     PDB mypdb; do_read=mypdb.readFromFilepointer(fp,plumed.usingNaturalUnits(),0.1/plumed.getUnits().getLength());
      78        2235 :     if( !do_read && nframes>0 ) break ;
      79             : 
      80        2120 :     if( natoms==0 ) natoms = mypdb.getPositions().size();
      81         742 :     else if( mypdb.getPositions().size()!=natoms ) plumed_merror("mismatch between sizes of reference configurations");
      82             : 
      83        2120 :     if( nframes+1==frame || frame==0 ) {
      84        1642 :       std::vector<double> align( mypdb.getOccupancy() );
      85       10326 :       double asum=0; for(unsigned i=0; i<align.size(); ++i) asum += align[i];
      86        1642 :       if( asum>epsilon ) {
      87        9358 :         double iasum = 1 / asum; for(unsigned i=0; i<align.size(); ++i) align[i] *= iasum;
      88         968 :       } else if( mypdb.size()>0 ) {
      89           0 :         double iasum = 1 / mypdb.size(); for(unsigned i=0; i<align.size(); ++i) align[i] = iasum;
      90             :       }
      91       10326 :       Vector center; center.zero(); for(unsigned i=0; i<mypdb.getPositions().size(); ++i) center += align[i]*mypdb.getPositions()[i];
      92             : 
      93        1642 :       if( theargs.size()==0 && argn.size()==0 ) {
      94        1688 :         for(unsigned j=0; j<3; ++j) {
      95       17490 :           for(unsigned i=0; i<mypdb.getPositions().size(); ++i) vals.push_back( mypdb.getPositions()[i][j] - center[j] );
      96             :         }
      97        1220 :       } else if( noargs ) {
      98          20 :         std::vector<double> argvals( 1 );
      99          20 :         if( !mypdb.getArgumentValue(argn[0], argvals ) ) error("argument " + argn[0] + " was not set in pdb input");
     100          20 :         vals.push_back( argvals[0] );
     101             :       } else {
     102        1200 :         std::vector<double> argvals( theargs[0]->getNumberOfValues() );
     103        1200 :         if( !mypdb.getArgumentValue(theargs[0]->getName(), argvals ) ) error("argument " + theargs[0]->getName() + " was not set in pdb input");
     104        2402 :         for(unsigned i=0; i<argvals.size(); ++i) vals.push_back( argvals[i] );
     105             :       }
     106             :     }
     107        2120 :     nframes++;
     108        2235 :   }
     109         115 :   if( frame>0 ) nframes=1;
     110         115 :   std::fclose(fp); std::string rnum; plumed_assert( vals.size()>0 );
     111         115 :   Tools::convert( vals[0], rnum ); std::string valstr = " VALUES=" + rnum;
     112       17446 :   for(unsigned i=1; i<vals.size(); ++i) { Tools::convert( vals[i], rnum ); valstr += "," + rnum; }
     113         115 :   if( vals.size()>nframes ) {
     114          41 :     std::string nc, nr; Tools::convert( nframes, nr ); Tools::convert( vals.size()/nframes, nc );
     115          82 :     readInputLine( getShortcutLabel() + ": CONSTANT NROWS=" + nr + " NCOLS=" + nc + valstr );
     116         148 :   } else readInputLine( getShortcutLabel() + ": CONSTANT" + valstr );
     117         230 : }
     118             : 
     119             : }
     120             : }