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         118 : void RMSDShortcut::registerKeywords(Keywords& keys) {
      40         118 :   ActionShortcut::registerKeywords( keys );
      41         236 :   keys.add("compulsory","REFERENCE","a file in pdb format containing the reference structure and the atoms involved in the CV");
      42         236 :   keys.add("compulsory","TYPE","SIMPLE","the manner in which RMSD alignment is performed.  Should be OPTIMAL or SIMPLE.");
      43         236 :   keys.addFlag("SQUARED",false," This should be setted if you want MSD instead of RMSD ");
      44         236 :   keys.addFlag("NOPBC",false,"ignore the periodic boundary conditions when calculating distances");
      45         236 :   keys.addFlag("NUMERICAL_DERIVATIVES", false, "calculate the derivatives for these quantities numerically");
      46         236 :   keys.addFlag("DISPLACEMENT",false,"Calculate the vector of displacements instead of the length of this vector");
      47         236 :   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         118 :   keys.setValueDescription("the RMSD distance between the instaneous structure and the reference structure/s that were input");
      49         118 :   keys.addActionNameSuffix("_SCALAR");
      50         118 :   keys.addActionNameSuffix("_VECTOR");
      51         118 :   keys.needsAction("PDB2CONSTANT");
      52         118 :   keys.needsAction("WHOLEMOLECULES");
      53         118 :   keys.needsAction("POSITION");
      54         118 :   keys.needsAction("CONCATENATE");
      55         118 : }
      56             : 
      57         104 : RMSDShortcut::RMSDShortcut(const ActionOptions& ao):
      58             :   Action(ao),
      59         104 :   ActionShortcut(ao) {
      60             :   bool disp;
      61         208 :   parseFlag("DISPLACEMENT",disp);
      62             :   std::string reference;
      63         106 :   parse("REFERENCE",reference);
      64             :   // Read the reference pdb file
      65         104 :   PDB pdb;
      66         104 :   if( !pdb.read(reference,plumed.usingNaturalUnits(),0.1/plumed.getUnits().getLength()) ) {
      67           3 :     plumed_merror("missing file " + reference );
      68             :   }
      69             :   unsigned frame;
      70         103 :   parse("NUMBER",frame);
      71             :   unsigned nf=1;
      72         103 :   if( frame==0 ) {
      73          94 :     FILE* fp=std::fopen(reference.c_str(),"r");
      74             :     bool do_read=true;
      75             :     nf=0;
      76         561 :     while ( do_read ) {
      77         495 :       PDB mypdb;
      78         495 :       do_read=mypdb.readFromFilepointer(fp,plumed.usingNaturalUnits(),0.1/plumed.getUnits().getLength());
      79         495 :       if( !do_read && nf>0 ) {
      80             :         break ;
      81             :       }
      82         467 :       nf++;
      83         495 :     }
      84             :   }
      85             :   bool nopbc;
      86         103 :   parseFlag("NOPBC",nopbc);
      87             :   // Now create the RMSD object
      88         103 :   std::string rmsd_line = getShortcutLabel() + ": ";
      89         103 :   if( nf==1 && !disp ) {
      90          81 :     rmsd_line += "RMSD_SCALAR REFERENCE=" + reference;
      91          81 :     if(nopbc) {
      92             :       rmsd_line += " NOPBC";
      93             :     }
      94             :   } else {
      95             :     std::string ffnum;
      96          22 :     Tools::convert( frame, ffnum );
      97          44 :     readInputLine( getShortcutLabel() + "_ref: PDB2CONSTANT REFERENCE=" + reference + " NUMBER=" + ffnum );
      98          22 :     std::vector<AtomNumber> anum( pdb.getAtomNumbers() );
      99          22 :     if( !nopbc ) {
     100             :       std::string num;
     101          20 :       Tools::convert( anum[0].serial(), num );
     102          20 :       std::string wm_line = "WHOLEMOLECULES ENTITY0=" + num;
     103         196 :       for(unsigned i=1; i<anum.size(); ++i) {
     104         176 :         Tools::convert( anum[i].serial(), num );
     105         352 :         wm_line += "," + num;
     106             :       }
     107          20 :       readInputLine( wm_line );
     108             :     }
     109             :     std::string num;
     110          22 :     Tools::convert( anum[0].serial(), num );
     111          22 :     std::string pos_line = getShortcutLabel() + "_cpos: POSITION NOPBC ATOMS=" + num;
     112         210 :     for(unsigned i=1; i<anum.size(); ++i) {
     113         188 :       Tools::convert( anum[i].serial(), num );
     114         376 :       pos_line += "," + num;
     115             :     }
     116          22 :     readInputLine( pos_line );
     117             :     // Concatenate the three positions together
     118          44 :     readInputLine( getShortcutLabel() + "_pos: CONCATENATE ARG=" + getShortcutLabel() + "_cpos.x," + getShortcutLabel() + "_cpos.y," + getShortcutLabel() + "_cpos.z");
     119          44 :     rmsd_line += "RMSD_VECTOR ARG=" + getShortcutLabel() + "_pos," + getShortcutLabel() + "_ref";
     120          22 :     if( disp ) {
     121             :       rmsd_line += " DISPLACEMENT";
     122             :     }
     123             :     // Now align
     124          22 :     std::vector<double> align( pdb.getOccupancy() );
     125          22 :     Tools::convert( align[0], num );
     126          22 :     rmsd_line += " ALIGN=" + num;
     127         210 :     for(unsigned i=1; i<align.size(); ++i) {
     128         188 :       Tools::convert( align[i], num );
     129         376 :       rmsd_line += "," + num;
     130             :     }
     131             :     // And displace
     132          22 :     std::vector<double> displace( pdb.getBeta() );
     133          22 :     Tools::convert( displace[0], num );
     134          22 :     rmsd_line += " DISPLACE=" + num;
     135         210 :     for(unsigned i=1; i<displace.size(); ++i) {
     136         188 :       Tools::convert( displace[i], num );
     137         376 :       rmsd_line += "," + num;
     138             :     }
     139             :   }
     140             :   // And create the RMSD object
     141             :   bool numder;
     142         103 :   parseFlag("NUMERICAL_DERIVATIVES",numder);
     143         103 :   if(numder && nf==1 && !disp ) {
     144             :     rmsd_line += " NUMERICAL_DERIVATIVES";
     145          98 :   } else if( numder ) {
     146           0 :     error("can only use NUMERICAL_DERIVATIVES flag when RMSD is calculating a single scalar value");
     147             :   }
     148             :   bool squared;
     149         104 :   parseFlag("SQUARED",squared);
     150         103 :   if(squared) {
     151             :     rmsd_line += " SQUARED";
     152             :   }
     153             :   std::string tt;
     154         103 :   parse("TYPE",tt);
     155         207 :   readInputLine( rmsd_line + " TYPE=" + tt );
     156         210 : }
     157             : 
     158             : }
     159             : }