Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2013-2018 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 :
28 992 : ReferenceAtoms::ReferenceAtoms( const ReferenceConfigurationOptions& ro ):
29 : ReferenceConfiguration(ro),
30 992 : checks_were_disabled(false)
31 : {
32 992 : }
33 :
34 386 : void ReferenceAtoms::readAtomsFromPDB( const PDB& pdb, const bool allowblocks ) {
35 386 : if( !allowblocks && pdb.getNumberOfAtomBlocks()!=1 ) error("found multi-atom-block pdb format but expecting only one block of atoms");
36 :
37 7426 : for(unsigned i=0; i<pdb.size(); ++i) {
38 7040 : indices.push_back( pdb.getAtomNumbers()[i] ); reference_atoms.push_back( pdb.getPositions()[i] );
39 7040 : align.push_back( pdb.getOccupancy()[i] ); displace.push_back( pdb.getBeta()[i] );
40 : }
41 386 : atom_der_index.resize( reference_atoms.size() );
42 386 : }
43 :
44 560 : void ReferenceAtoms::setAtomNumbers( const std::vector<AtomNumber>& numbers ) {
45 560 : reference_atoms.resize( numbers.size() ); align.resize( numbers.size() );
46 560 : displace.resize( numbers.size() ); atom_der_index.resize( numbers.size() );
47 560 : indices.resize( numbers.size() );
48 12717 : for(unsigned i=0; i<numbers.size(); ++i) {
49 12157 : indices[i]=numbers[i]; atom_der_index[i]=i;
50 : }
51 560 : }
52 :
53 5 : void ReferenceAtoms::printAtoms( OFile& ofile, const double& lunits ) const {
54 5 : plumed_assert( indices.size()==reference_atoms.size() && align.size()==reference_atoms.size() && displace.size()==reference_atoms.size() );
55 71 : for(unsigned i=0; i<reference_atoms.size(); ++i) {
56 : ofile.printf("ATOM %5d X RES %4u %8.3f%8.3f%8.3f%6.2f%6.2f\n",
57 66 : indices[i].serial(), i,
58 198 : lunits*reference_atoms[i][0], lunits*reference_atoms[i][1], lunits*reference_atoms[i][2],
59 330 : align[i], displace[i] );
60 : }
61 5 : }
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 0 : AtomNumber atom;
73 0 : if( !Tools::convert(strings[i],atom ) ) error("could not convert " + strings[i] + " into atom number");
74 :
75 0 : 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 0 : return true;
82 : }
83 :
84 389 : void ReferenceAtoms::getAtomRequests( std::vector<AtomNumber>& numbers, bool disable_checks ) {
85 389 : singleDomainRequests(numbers,disable_checks);
86 389 : }
87 :
88 389 : void ReferenceAtoms::singleDomainRequests( std::vector<AtomNumber>& numbers, bool disable_checks ) {
89 389 : checks_were_disabled=disable_checks;
90 389 : atom_der_index.resize( indices.size() );
91 :
92 389 : if( numbers.size()==0 ) {
93 3392 : for(unsigned i=0; i<indices.size(); ++i) {
94 3298 : numbers.push_back( indices[i] );
95 3298 : atom_der_index[i]=i;
96 : }
97 : } else {
98 295 : if(!disable_checks) {
99 295 : if( numbers.size()!=indices.size() ) error("mismatched numbers of atoms in pdb frames");
100 : }
101 :
102 : bool found;
103 4082 : for(unsigned i=0; i<indices.size(); ++i) {
104 3787 : found=false;
105 3787 : if(!disable_checks) {
106 3787 : if( indices[i]!=numbers[i] ) error("found mismatched reference atoms in pdb frames");
107 3787 : atom_der_index[i]=i;
108 : } else {
109 0 : for(unsigned j=0; j<numbers.size(); ++j) {
110 0 : if( indices[i]==numbers[j] ) { found=true; atom_der_index[i]=j; break; }
111 : }
112 0 : if( !found ) {
113 0 : atom_der_index[i]=numbers.size(); numbers.push_back( indices[i] );
114 : }
115 : }
116 : }
117 : }
118 389 : }
119 :
120 2523 : }
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