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         170 : void PDB2Constant::registerKeywords(Keywords& keys) {
      49         170 :   ActionShortcut::registerKeywords( keys );
      50         340 :   keys.add("compulsory","REFERENCE","a file in pdb format containing the reference structure");
      51         340 :   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         340 :   keys.addFlag("NOARGS",false,"the arguments that are being read from the PDB file are not in the plumed input");
      53         340 :   keys.add("optional","ARG","read this single argument from the input rather than the atomic structure");
      54         170 :   keys.setValueDescription("a value that is constructed from the information in the PDB file");
      55         170 :   keys.needsAction("CONSTANT");
      56         170 : }
      57             : 
      58         115 : PDB2Constant::PDB2Constant(const ActionOptions& ao):
      59             :   Action(ao),
      60         115 :   ActionShortcut(ao) {
      61             :   std::string input;
      62         115 :   parse("REFERENCE",input);
      63             :   unsigned frame;
      64         115 :   parse("NUMBER",frame);
      65         115 :   bool noargs=false;
      66             :   std::vector<std::string> argn;
      67         230 :   parseVector("ARG",argn);
      68             :   std::vector<Value*> theargs;
      69         115 :   if( argn.size()>0 ) {
      70          75 :     parseFlag("NOARGS",noargs);
      71          75 :     if( !noargs ) {
      72          73 :       ActionWithArguments::interpretArgumentList( argn, plumed.getActionSet(), this, theargs );
      73           2 :     } else if( argn.size()>1 ) {
      74           0 :       error("can only read one argument at a time from input pdb file");
      75             :     } else {
      76           2 :       log.printf("  reading argument %s from file \n", argn[0].c_str() );
      77             :     }
      78             :   }
      79         115 :   if( theargs.size()>1 ) {
      80           0 :     error("can only read one argument at a time from input pdb file");
      81             :   }
      82             : 
      83         115 :   FILE* fp=std::fopen(input.c_str(),"r");
      84             :   bool do_read=true;
      85             :   std::vector<double> vals;
      86         115 :   if(!fp) {
      87           0 :     plumed_merror("could not open reference file " + input);
      88             :   }
      89         115 :   unsigned natoms=0, nframes=0;
      90             : 
      91        2235 :   while ( do_read ) {
      92        2235 :     PDB mypdb;
      93        2235 :     do_read=mypdb.readFromFilepointer(fp,plumed.usingNaturalUnits(),0.1/plumed.getUnits().getLength());
      94        2235 :     if( !do_read && nframes>0 ) {
      95             :       break ;
      96             :     }
      97             : 
      98        2120 :     if( natoms==0 ) {
      99        1378 :       natoms = mypdb.getPositions().size();
     100         742 :     } else if( mypdb.getPositions().size()!=natoms ) {
     101           0 :       plumed_merror("mismatch between sizes of reference configurations");
     102             :     }
     103             : 
     104        2120 :     if( nframes+1==frame || frame==0 ) {
     105        1642 :       std::vector<double> align( mypdb.getOccupancy() );
     106             :       double asum=0;
     107       10326 :       for(unsigned i=0; i<align.size(); ++i) {
     108        8684 :         asum += align[i];
     109             :       }
     110        1642 :       if( asum>epsilon ) {
     111         674 :         double iasum = 1 / asum;
     112        9358 :         for(unsigned i=0; i<align.size(); ++i) {
     113        8684 :           align[i] *= iasum;
     114             :         }
     115         968 :       } else if( mypdb.size()>0 ) {
     116           0 :         double iasum = 1 / mypdb.size();
     117           0 :         for(unsigned i=0; i<align.size(); ++i) {
     118           0 :           align[i] = iasum;
     119             :         }
     120             :       }
     121        1642 :       Vector center;
     122        1642 :       center.zero();
     123       10326 :       for(unsigned i=0; i<mypdb.getPositions().size(); ++i) {
     124        8684 :         center += align[i]*mypdb.getPositions()[i];
     125             :       }
     126             : 
     127        1642 :       if( theargs.size()==0 && argn.size()==0 ) {
     128        1688 :         for(unsigned j=0; j<3; ++j) {
     129       17490 :           for(unsigned i=0; i<mypdb.getPositions().size(); ++i) {
     130       16224 :             vals.push_back( mypdb.getPositions()[i][j] - center[j] );
     131             :           }
     132             :         }
     133        1220 :       } else if( noargs ) {
     134          20 :         std::vector<double> argvals( 1 );
     135          20 :         if( !mypdb.getArgumentValue(argn[0], argvals ) ) {
     136           0 :           error("argument " + argn[0] + " was not set in pdb input");
     137             :         }
     138          20 :         vals.push_back( argvals[0] );
     139             :       } else {
     140        1200 :         std::vector<double> argvals( theargs[0]->getNumberOfValues() );
     141        1200 :         if( !mypdb.getArgumentValue(theargs[0]->getName(), argvals ) ) {
     142           0 :           error("argument " + theargs[0]->getName() + " was not set in pdb input");
     143             :         }
     144        2402 :         for(unsigned i=0; i<argvals.size(); ++i) {
     145        1202 :           vals.push_back( argvals[i] );
     146             :         }
     147             :       }
     148             :     }
     149        2120 :     nframes++;
     150        2235 :   }
     151         115 :   if( frame>0 ) {
     152          68 :     nframes=1;
     153             :   }
     154         115 :   std::fclose(fp);
     155             :   std::string rnum;
     156         115 :   plumed_assert( vals.size()>0 );
     157         115 :   Tools::convert( vals[0], rnum );
     158         115 :   std::string valstr = " VALUES=" + rnum;
     159       17446 :   for(unsigned i=1; i<vals.size(); ++i) {
     160       17331 :     Tools::convert( vals[i], rnum );
     161       34662 :     valstr += "," + rnum;
     162             :   }
     163         115 :   if( vals.size()>nframes ) {
     164             :     std::string nc, nr;
     165          41 :     Tools::convert( nframes, nr );
     166          41 :     Tools::convert( vals.size()/nframes, nc );
     167          82 :     readInputLine( getShortcutLabel() + ": CONSTANT NROWS=" + nr + " NCOLS=" + nc + valstr );
     168             :   } else {
     169         148 :     readInputLine( getShortcutLabel() + ": CONSTANT" + valstr );
     170             :   }
     171         230 : }
     172             : 
     173             : }
     174             : }