Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2013-2019 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 "ReferenceAtoms.h"
23 : #include "tools/OFile.h"
24 : #include "tools/PDB.h"
25 :
26 : namespace PLMD {
27 :
28 1256 : ReferenceAtoms::ReferenceAtoms( const ReferenceConfigurationOptions& ro ):
29 : ReferenceConfiguration(ro),
30 1256 : checks_were_disabled(false)
31 : {
32 1256 : }
33 :
34 446 : void ReferenceAtoms::readAtomsFromPDB( const PDB& pdb, const bool allowblocks ) {
35 446 : if( !allowblocks && pdb.getNumberOfAtomBlocks()!=1 ) error("found multi-atom-block pdb format but expecting only one block of atoms");
36 :
37 16006 : for(unsigned i=0; i<pdb.size(); ++i) {
38 23340 : indices.push_back( pdb.getAtomNumbers()[i] ); reference_atoms.push_back( pdb.getPositions()[i] );
39 23340 : align.push_back( pdb.getOccupancy()[i] ); displace.push_back( pdb.getBeta()[i] );
40 : }
41 892 : atom_der_index.resize( reference_atoms.size() );
42 446 : }
43 :
44 764 : void ReferenceAtoms::setAtomNumbers( const std::vector<AtomNumber>& numbers ) {
45 2292 : reference_atoms.resize( numbers.size() ); align.resize( numbers.size() );
46 2292 : displace.resize( numbers.size() ); atom_der_index.resize( numbers.size() );
47 1528 : indices.resize( numbers.size() );
48 39610 : for(unsigned i=0; i<numbers.size(); ++i) {
49 25388 : indices[i]=numbers[i]; atom_der_index[i]=i;
50 : }
51 764 : }
52 :
53 18 : void ReferenceAtoms::printAtoms( OFile& ofile, const double& lunits ) const {
54 54 : plumed_assert( indices.size()==reference_atoms.size() && align.size()==reference_atoms.size() && displace.size()==reference_atoms.size() );
55 741 : for(unsigned i=0; i<reference_atoms.size(); ++i) {
56 1410 : ofile.printf("ATOM %5d X RES %4u %8.3f%8.3f%8.3f%6.2f%6.2f\n",
57 : indices[i].serial(), i,
58 940 : lunits*reference_atoms[i][0], lunits*reference_atoms[i][1], lunits*reference_atoms[i][2],
59 : align[i], displace[i] );
60 : }
61 18 : }
62 :
63 0 : bool ReferenceAtoms::parseAtomList( const std::string& key, std::vector<unsigned>& numbers ) {
64 0 : plumed_assert( numbers.size()==0 );
65 :
66 0 : std::vector<std::string> strings;
67 0 : if( !parseVector(key,strings,true) ) return false;
68 0 : Tools::interpretRanges(strings);
69 :
70 0 : numbers.resize( strings.size() );
71 0 : for(unsigned i=0; i<strings.size(); ++i) {
72 : AtomNumber atom;
73 0 : if( !Tools::convert(strings[i],atom ) ) error("could not convert " + strings[i] + " into atom number");
74 :
75 : bool found=false;
76 0 : for(unsigned j=0; j<indices.size(); ++j) {
77 0 : if( atom==indices[j] ) { found=true; numbers[i]=j; break; }
78 : }
79 0 : if(!found) error("atom labelled " + strings[i] + " is not present in pdb input file");
80 : }
81 : return true;
82 : }
83 :
84 445 : void ReferenceAtoms::getAtomRequests( std::vector<AtomNumber>& numbers, bool disable_checks ) {
85 445 : singleDomainRequests(numbers,disable_checks);
86 445 : }
87 :
88 445 : void ReferenceAtoms::singleDomainRequests( std::vector<AtomNumber>& numbers, bool disable_checks ) {
89 445 : checks_were_disabled=disable_checks;
90 890 : atom_der_index.resize( indices.size() );
91 :
92 445 : if( numbers.size()==0 ) {
93 10263 : for(unsigned i=0; i<indices.size(); ++i) {
94 3355 : numbers.push_back( indices[i] );
95 3355 : atom_der_index[i]=i;
96 : }
97 : } else {
98 346 : if(!disable_checks) {
99 346 : if( numbers.size()!=indices.size() ) error("mismatched numbers of atoms in pdb frames");
100 : }
101 :
102 14042 : for(unsigned i=0; i<indices.size(); ++i) {
103 : bool found=false;
104 4450 : if(!disable_checks) {
105 4450 : if( indices[i]!=numbers[i] ) error("found mismatched reference atoms in pdb frames");
106 4450 : atom_der_index[i]=i;
107 : } else {
108 0 : for(unsigned j=0; j<numbers.size(); ++j) {
109 0 : if( indices[i]==numbers[j] ) { found=true; atom_der_index[i]=j; break; }
110 : }
111 : if( !found ) {
112 0 : atom_der_index[i]=numbers.size(); numbers.push_back( indices[i] );
113 : }
114 : }
115 : }
116 : }
117 445 : }
118 :
119 494 : void ReferenceAtoms::displaceReferenceAtoms( const double& weight, const std::vector<Vector>& dir ) {
120 : plumed_dbg_assert( dir.size()==reference_atoms.size() );
121 1872 : for(unsigned i=0; i<dir.size(); ++i) reference_atoms[i] += weight*dir.size()*dir[i];
122 494 : }
123 :
124 4839 : }
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