Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2013-2023 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 "SingleDomainRMSD.h"
      23             : #include "tools/PDB.h"
      24             : #include "DRMSD.h"
      25             : 
      26             : namespace PLMD {
      27             : 
      28         494 : SingleDomainRMSD::SingleDomainRMSD( const ReferenceConfigurationOptions& ro ):
      29             :   ReferenceConfiguration(ro),
      30         494 :   ReferenceAtoms(ro)
      31             : {
      32         494 : }
      33             : 
      34         452 : void SingleDomainRMSD::readReference( const PDB& pdb ) {
      35         452 :   readAtomsFromPDB( pdb );
      36             :   double wa=0, wd=0;
      37        8327 :   for(unsigned i=0; i<pdb.size(); ++i) { wa+=align[i]; wd+=displace[i]; }
      38             : 
      39         452 :   if(wa>epsilon) {
      40         450 :     double w=1.0/wa;
      41        8295 :     for(unsigned i=0; i<pdb.size(); ++i) align[i] *= w;
      42             :   } else {
      43           2 :     double w=1.0/pdb.size();
      44          32 :     for(unsigned i=0; i<pdb.size(); ++i) align[i] = w;
      45             :   }
      46             : 
      47         452 :   if(wd>epsilon) {
      48         450 :     double w=1.0/wd;
      49        8295 :     for(unsigned i=0; i<pdb.size(); ++i) displace[i] *= w;
      50             :   } else {
      51           2 :     double w=1.0/pdb.size();
      52          32 :     for(unsigned i=0; i<pdb.size(); ++i) displace[i] = w;
      53             :   }
      54             : 
      55         452 :   Vector center;
      56        8327 :   for(unsigned i=0; i<pdb.size(); ++i) {
      57        7875 :     center+=reference_atoms[i]*align[i];
      58             :   }
      59        8327 :   for(unsigned i=0; i<pdb.size(); ++i) reference_atoms[i]-=center;
      60         452 : }
      61             : 
      62          45 : void SingleDomainRMSD::setReferenceAtoms( const std::vector<Vector>& conf, const std::vector<double>& align_in, const std::vector<double>& displace_in ) {
      63          45 :   reference_atoms.resize( conf.size() ); align.resize( conf.size() );
      64          45 :   displace.resize( conf.size() ); atom_der_index.resize( conf.size() );
      65             :   double wa=0, wd=0;
      66        1154 :   for(unsigned i=0; i<conf.size(); ++i) { wa+=align_in[i]; wd+=displace_in[i]; }
      67             : 
      68          45 :   if(wa>epsilon) {
      69          44 :     double w=1.0/wa;
      70        1145 :     for(unsigned i=0; i<conf.size(); ++i) align[i] = align_in[i] * w;
      71             :   } else {
      72           1 :     double w=1.0/conf.size();
      73           9 :     for(unsigned i=0; i<conf.size(); ++i) align[i] = w;
      74             :   }
      75             : 
      76          45 :   if(wd>epsilon) {
      77          44 :     double w=1.0/wd;
      78        1146 :     for(unsigned i=0; i<conf.size(); ++i) displace[i] = displace_in[i] * w;
      79             :   } else {
      80           1 :     double w=1.0/conf.size();
      81           8 :     for(unsigned i=0; i<conf.size(); ++i) displace[i] = w;
      82             :   }
      83             : 
      84          45 :   Vector center;
      85        1154 :   for(unsigned i=0; i<conf.size(); ++i) {
      86        1109 :     center+=conf[i]*align[i]; atom_der_index[i]=i;
      87             :   }
      88        1154 :   for(unsigned i=0; i<conf.size(); ++i) reference_atoms[i]=conf[i]-center;
      89          45 :   setupRMSDObject();
      90          45 : }
      91             : 
      92       58046 : double SingleDomainRMSD::calculate( const std::vector<Vector>& pos, const Pbc& pbc, ReferenceValuePack& myder, const bool& squared ) const {
      93       58046 :   return calc( pos, pbc, myder, squared );
      94             : }
      95             : 
      96      140941 : double SingleDomainRMSD::calc( const std::vector<Vector>& pos, const Pbc& pbc, const std::vector<Value*>& vals, const std::vector<double>& arg,
      97             :                                ReferenceValuePack& myder, const bool& squared ) const {
      98             :   plumed_dbg_assert( vals.size()==0 && pos.size()==getNumberOfAtoms() && arg.size()==0 );
      99      140941 :   return calc( pos, pbc, myder, squared );
     100             : }
     101             : 
     102             : }