Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2011-2023 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 "tools/PDB.h"
      26             : #include "core/PlumedMain.h"
      27             : 
      28             : namespace PLMD {
      29             : namespace colvar {
      30             : 
      31             : class RMSDShortcut : public ActionShortcut {
      32             : public:
      33             :   static void registerKeywords(Keywords& keys);
      34             :   explicit RMSDShortcut(const ActionOptions&);
      35             : };
      36             : 
      37             : PLUMED_REGISTER_ACTION(RMSDShortcut,"RMSD")
      38             : 
      39         119 : void RMSDShortcut::registerKeywords(Keywords& keys) {
      40         119 :   ActionShortcut::registerKeywords( keys );
      41         119 :   keys.add("compulsory","REFERENCE","a file in pdb format containing the reference structure and the atoms involved in the CV");
      42         119 :   keys.add("compulsory","TYPE","SIMPLE","the manner in which RMSD alignment is performed.  Should be OPTIMAL or SIMPLE.");
      43         119 :   keys.addFlag("SQUARED",false," This should be setted if you want MSD instead of RMSD ");
      44         119 :   keys.addFlag("NOPBC",false,"ignore the periodic boundary conditions when calculating distances");
      45         119 :   keys.addFlag("NUMERICAL_DERIVATIVES", false, "calculate the derivatives for these quantities numerically");
      46         119 :   keys.addFlag("DISPLACEMENT",false,"Calculate the vector of displacements instead of the length of this vector");
      47         119 :   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");
      48         238 :   keys.addOutputComponent("disp","DISPLACEMENT","vector/matrix","the vector of displacements for the atoms");
      49         238 :   keys.addOutputComponent("dist","DISPLACEMENT","scalar/vector","the RMSD distance the atoms have moved");
      50         238 :   keys.setValueDescription("scalar/vector","the RMSD distance between the instaneous structure and the reference structure/s that were input");
      51         119 :   keys.addActionNameSuffix("_SCALAR");
      52         119 :   keys.addActionNameSuffix("_VECTOR");
      53         119 :   keys.needsAction("PDB2CONSTANT");
      54         119 :   keys.needsAction("WHOLEMOLECULES");
      55         119 :   keys.needsAction("POSITION");
      56         119 :   keys.needsAction("CONCATENATE");
      57         119 :   keys.addDOI("10.1107/S0108767388010128");
      58         119 : }
      59             : 
      60         105 : RMSDShortcut::RMSDShortcut(const ActionOptions& ao):
      61             :   Action(ao),
      62         105 :   ActionShortcut(ao) {
      63             :   bool disp;
      64         210 :   parseFlag("DISPLACEMENT",disp);
      65             :   std::string reference;
      66         107 :   parse("REFERENCE",reference);
      67             :   // Read the reference pdb file
      68         105 :   PDB pdb;
      69         105 :   if( !pdb.read(reference,plumed.usingNaturalUnits(),0.1/plumed.getUnits().getLength()) ) {
      70           3 :     plumed_merror("missing file " + reference );
      71             :   }
      72             :   unsigned frame;
      73         104 :   parse("NUMBER",frame);
      74             :   unsigned nf=1;
      75         104 :   if( frame==0 ) {
      76          95 :     FILE* fp=std::fopen(reference.c_str(),"r");
      77             :     bool do_read=true;
      78             :     nf=0;
      79         563 :     while ( do_read ) {
      80         496 :       PDB mypdb;
      81         496 :       do_read=mypdb.readFromFilepointer(fp,plumed.usingNaturalUnits(),0.1/plumed.getUnits().getLength());
      82         496 :       if( !do_read && nf>0 ) {
      83             :         break ;
      84             :       }
      85         468 :       nf++;
      86         496 :     }
      87             :   }
      88             :   bool nopbc;
      89         104 :   parseFlag("NOPBC",nopbc);
      90             :   // Now create the RMSD object
      91         104 :   std::string rmsd_line = getShortcutLabel() + ": ";
      92         104 :   if( nf==1 && !disp ) {
      93          82 :     rmsd_line += "RMSD_SCALAR REFERENCE=" + reference;
      94          82 :     if(nopbc) {
      95             :       rmsd_line += " NOPBC";
      96             :     }
      97             :   } else {
      98             :     std::string ffnum;
      99          22 :     Tools::convert( frame, ffnum );
     100          44 :     readInputLine( getShortcutLabel() + "_ref: PDB2CONSTANT REFERENCE=" + reference + " NUMBER=" + ffnum );
     101          22 :     std::vector<AtomNumber> anum( pdb.getAtomNumbers() );
     102          22 :     if( !nopbc ) {
     103             :       std::string num;
     104          20 :       Tools::convert( anum[0].serial(), num );
     105          20 :       std::string wm_line = "WHOLEMOLECULES ENTITY0=" + num;
     106         196 :       for(unsigned i=1; i<anum.size(); ++i) {
     107         176 :         Tools::convert( anum[i].serial(), num );
     108         352 :         wm_line += "," + num;
     109             :       }
     110          20 :       readInputLine( wm_line );
     111             :     }
     112             :     std::string num;
     113          22 :     Tools::convert( anum[0].serial(), num );
     114          22 :     std::string pos_line = getShortcutLabel() + "_cpos: POSITION NOPBC ATOMS=" + num;
     115         210 :     for(unsigned i=1; i<anum.size(); ++i) {
     116         188 :       Tools::convert( anum[i].serial(), num );
     117         376 :       pos_line += "," + num;
     118             :     }
     119          22 :     readInputLine( pos_line );
     120             :     // Concatenate the three positions together
     121          44 :     readInputLine( getShortcutLabel() + "_pos: CONCATENATE ARG=" + getShortcutLabel() + "_cpos.x," + getShortcutLabel() + "_cpos.y," + getShortcutLabel() + "_cpos.z");
     122          44 :     rmsd_line += "RMSD_VECTOR ARG=" + getShortcutLabel() + "_pos," + getShortcutLabel() + "_ref";
     123          22 :     if( disp ) {
     124             :       rmsd_line += " DISPLACEMENT";
     125             :     }
     126             :     // Now align
     127          22 :     std::vector<double> align( pdb.getOccupancy() );
     128          22 :     Tools::convert( align[0], num );
     129          22 :     rmsd_line += " ALIGN=" + num;
     130         210 :     for(unsigned i=1; i<align.size(); ++i) {
     131         188 :       Tools::convert( align[i], num );
     132         376 :       rmsd_line += "," + num;
     133             :     }
     134             :     // And displace
     135          22 :     std::vector<double> displace( pdb.getBeta() );
     136          22 :     Tools::convert( displace[0], num );
     137          22 :     rmsd_line += " DISPLACE=" + num;
     138         210 :     for(unsigned i=1; i<displace.size(); ++i) {
     139         188 :       Tools::convert( displace[i], num );
     140         376 :       rmsd_line += "," + num;
     141             :     }
     142             :   }
     143             :   // And create the RMSD object
     144             :   bool numder;
     145         104 :   parseFlag("NUMERICAL_DERIVATIVES",numder);
     146         104 :   if(numder && nf==1 && !disp ) {
     147             :     rmsd_line += " NUMERICAL_DERIVATIVES";
     148          99 :   } else if( numder ) {
     149           0 :     error("can only use NUMERICAL_DERIVATIVES flag when RMSD is calculating a single scalar value");
     150             :   }
     151             :   bool squared;
     152         105 :   parseFlag("SQUARED",squared);
     153         104 :   if(squared) {
     154             :     rmsd_line += " SQUARED";
     155             :   }
     156             :   std::string tt;
     157         104 :   parse("TYPE",tt);
     158         209 :   readInputLine( rmsd_line + " TYPE=" + tt );
     159         212 : }
     160             : 
     161             : }
     162             : }