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 "PDB.h"
23 : #include "Tools.h"
24 : #include "Log.h"
25 : #include "h36.h"
26 : #include <cstdio>
27 : #include <iostream>
28 : #include "core/GenericMolInfo.h"
29 : #include "Tensor.h"
30 :
31 : //+PLUMEDOC INTERNAL pdbreader
32 : /*
33 : PLUMED can use the PDB format in several places
34 :
35 : - To read molecular structure (\ref MOLINFO).
36 : - To read reference conformations (\ref RMSD, but also many other methods in \ref dists, \ref FIT_TO_TEMPLATE, etc).
37 :
38 : The implemented PDB reader expects a file formatted correctly according to the
39 : [PDB standard](http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html).
40 : In particular, the following columns are read from ATOM records
41 : \verbatim
42 : columns | content
43 : 1-6 | record name (ATOM or HETATM)
44 : 7-11 | serial number of the atom (starting from 1)
45 : 13-16 | atom name
46 : 18-20 | residue name
47 : 22 | chain id
48 : 23-26 | residue number
49 : 31-38 | x coordinate
50 : 39-46 | y coordinate
51 : 47-54 | z coordinate
52 : 55-60 | occupancy
53 : 61-66 | beta factor
54 : \endverbatim
55 : PLUMED parser is slightly more permissive than the official PDB format
56 : in the fact that the format of real numbers is not fixed. In other words,
57 : any real number that can be parsed is OK and the dot can be placed anywhere. However,
58 : __columns are interpret strictly__. A sample PDB should look like the following
59 : \verbatim
60 : ATOM 2 CH3 ACE 1 12.932 -14.718 -6.016 1.00 1.00
61 : ATOM 5 C ACE 1 21.312 -9.928 -5.946 1.00 1.00
62 : ATOM 9 CA ALA 2 19.462 -11.088 -8.986 1.00 1.00
63 : \endverbatim
64 :
65 : Notice that serial numbers need not to be consecutive. In the three-line example above,
66 : only the coordinates of three atoms are provided. This is perfectly legal and indicates PLUMED
67 : that information about these atoms only is available. This could be both for structural
68 : information in \ref MOLINFO, where the other atoms would have no name assigned, and for
69 : reference structures used in \ref RMSD, where only the provided atoms would be used to compute RMSD.
70 :
71 : \par Occupancy and beta factors
72 :
73 : PLUMED reads also occupancy and beta factors that however are given a very special meaning.
74 : In cases where the PDB structure is used as a reference for an alignment (that's the case
75 : for instance in \ref RMSD and in \ref FIT_TO_TEMPLATE), the occupancy column is used
76 : to provide the weight of each atom in the alignment. In cases where, perhaps after alignment,
77 : the displacement between running coordinates and the provided PDB is computed, the beta factors
78 : are used as weight for the displacement.
79 : Since setting the weights to zero is the same as __not__ including an atom in the alignment or
80 : displacement calculation, the two following reference files would be equivalent when used in an \ref RMSD
81 : calculation. First file:
82 : \verbatim
83 : ATOM 2 CH3 ACE 1 12.932 -14.718 -6.016 1.00 1.00
84 : ATOM 5 C ACE 1 21.312 -9.928 -5.946 1.00 1.00
85 : ATOM 9 CA ALA 2 19.462 -11.088 -8.986 0.00 0.00
86 : \endverbatim
87 : Second file:
88 : \verbatim
89 : ATOM 2 CH3 ACE 1 12.932 -14.718 -6.016 1.00 1.00
90 : ATOM 5 C ACE 1 21.312 -9.928 -5.946 1.00 1.00
91 : \endverbatim
92 : However notice that many extra atoms with zero weight might slow down the calculation, so
93 : removing lines is better than setting their weights to zero.
94 : In addition, weights for alignment need not to be equivalent to weights for displacement.
95 : Starting with PLUMED 2.7, if all the weights are set to zero they will be normalized to be equal to the
96 : inverse of the number of involved atoms. This means that it will be possible to use files with
97 : the weight columns set to zero obtaining a meaningful result. In previous PLUMED versions,
98 : setting all weights to zero was resulting in an error instead.
99 :
100 :
101 : \par Systems with more than 100k atoms
102 :
103 : Notice that it very likely does not make any sense to compute the \ref RMSD or any other structural
104 : deviation __using__ so many atoms. However, if the protein for which you want to compute \ref RMSD
105 : has atoms with large serial numbers (e.g. because it is located __after__ solvent in the sorted list of atoms)
106 : you might end up with troubles with the limitations of the PDB format. Indeed, since there are 5
107 : columns available for atom serial number, this number cannot be larger than 99999.
108 : In addition, providing \ref MOLINFO with names associated to atoms with a serial larger than 99999 would be impossible.
109 :
110 : Since PLUMED 2.4 we allow [hybrid 36](http://cci.lbl.gov/hybrid_36/) format to be used to specify atom numbers.
111 : This format is not particularly widespread, but has the nice feature that it provides a one-to-one mapping
112 : between numbers up to approximately 80 millions and strings with 5 characters, plus it is backward compatible
113 : for numbers smaller than 100000. This is not true for notations like the hex notation exported by VMD.
114 : Using the hybrid 36 format, the ATOM records for atom ranging from 99997 to 100002 would read like these:
115 : \verbatim
116 : ATOM 99997 Ar X 1 45.349 38.631 15.116 1.00 1.00
117 : ATOM 99998 Ar X 1 46.189 38.631 15.956 1.00 1.00
118 : ATOM 99999 Ar X 1 46.189 39.471 15.116 1.00 1.00
119 : ATOM A0000 Ar X 1 45.349 39.471 15.956 1.00 1.00
120 : ATOM A0000 Ar X 1 45.349 38.631 16.796 1.00 1.00
121 : ATOM A0001 Ar X 1 46.189 38.631 17.636 1.00 1.00
122 : \endverbatim
123 : There are tools that can be found to translate from integers to strings and back using hybrid 36 format
124 : (a simple python script can be found [here](https://sourceforge.net/p/cctbx/code/HEAD/tree/trunk/iotbx/pdb/hybrid_36.py)).
125 : In addition, as of PLUMED 2.5, we provide a \ref pdbrenumber "command line tool" that can be used to renumber atoms in a PDB file.
126 :
127 : */
128 : //+ENDPLUMEDOC
129 :
130 :
131 : namespace PLMD {
132 :
133 27 : void PDB::setAtomNumbers( const std::vector<AtomNumber>& atoms ) {
134 27 : positions.resize( atoms.size() ); occupancy.resize( atoms.size() );
135 27 : beta.resize( atoms.size() ); numbers.resize( atoms.size() );
136 210 : for(unsigned i=0; i<atoms.size(); ++i) { numbers[i]=atoms[i]; beta[i]=1.0; occupancy[i]=1.0; }
137 27 : }
138 :
139 34 : void PDB::setArgumentNames( const std::vector<std::string>& argument_names ) {
140 34 : argnames.resize( argument_names.size() );
141 98 : for(unsigned i=0; i<argument_names.size(); ++i) {
142 : argnames[i]=argument_names[i];
143 64 : arg_data.insert( std::pair<std::string,double>( argnames[i], 0.0 ) );
144 : }
145 34 : }
146 :
147 1504260 : bool PDB::getArgumentValue( const std::string& name, double& value ) const {
148 : std::map<std::string,double>::const_iterator it = arg_data.find(name);
149 1504260 : if( it!=arg_data.end() ) { value = it->second; return true; }
150 : return false;
151 : }
152 :
153 493287 : void PDB::setAtomPositions( const std::vector<Vector>& pos ) {
154 493287 : plumed_assert( pos.size()==positions.size() );
155 519464 : for(unsigned i=0; i<positions.size(); ++i) positions[i]=pos[i];
156 493287 : }
157 :
158 1502798 : void PDB::setArgumentValue( const std::string& argname, const double& val ) {
159 : // First set the value of the value of the argument in the map
160 1502798 : arg_data.find(argname)->second = val;
161 1502798 : }
162 :
163 : // bool PDB::hasRequiredProperties( const std::vector<std::string>& inproperties ){
164 : // bool hasprop=false;
165 : // for(unsigned i=0;i<remark.size();++i){
166 : // if( remark[i].find("PROPERTIES=")!=std::string::npos){ hasprop=true; break; }
167 : // }
168 : // if( !hasprop ){
169 : // std::string mypropstr="PROPERTIES=" + inproperties[0];
170 : // for(unsigned i=1;i<inproperties.size();++i) mypropstr += "," + inproperties[i];
171 : // remark.push_back( mypropstr );
172 : // }
173 : // // Now check that all required properties are there
174 : // for(unsigned i=0;i<inproperties.size();++i){
175 : // hasprop=false;
176 : // for(unsigned j=0;j<remark.size();++j){
177 : // if( remark[j].find(inproperties[i]+"=")!=std::string::npos){ hasprop=true; break; }
178 : // }
179 : // if( !hasprop ) return false;
180 : // }
181 : // return true;
182 : // }
183 :
184 17 : void PDB::addBlockEnd( const unsigned& end ) {
185 17 : block_ends.push_back( end );
186 17 : }
187 :
188 468 : unsigned PDB::getNumberOfAtomBlocks()const {
189 468 : return block_ends.size();
190 : }
191 :
192 14 : const std::vector<unsigned> & PDB::getAtomBlockEnds()const {
193 14 : return block_ends;
194 : }
195 :
196 23533788 : const std::vector<Vector> & PDB::getPositions()const {
197 23533788 : return positions;
198 : }
199 :
200 0 : void PDB::setPositions(const std::vector<Vector> &v ) {
201 0 : plumed_assert( v.size()==positions.size() );
202 0 : positions=v;
203 0 : }
204 :
205 37820 : const std::vector<double> & PDB::getOccupancy()const {
206 37820 : return occupancy;
207 : }
208 :
209 37820 : const std::vector<double> & PDB::getBeta()const {
210 37820 : return beta;
211 : }
212 :
213 1339 : void PDB::addRemark( std::vector<std::string>& v1 ) {
214 1339 : Tools::parse(v1,"TYPE",mtype);
215 1339 : Tools::parseVector(v1,"ARG",argnames);
216 3759 : for(unsigned i=0; i<v1.size(); ++i) {
217 2420 : if( v1[i].find("=")!=std::string::npos ) {
218 : std::size_t eq=v1[i].find_first_of('=');
219 1864 : std::string name=v1[i].substr(0,eq);
220 1864 : std::string sval=v1[i].substr(eq+1);
221 1864 : double val; Tools::convert( sval, val );
222 1864 : arg_data.insert( std::pair<std::string,double>( name, val ) );
223 : } else {
224 556 : flags.push_back(v1[i]);
225 : }
226 : }
227 1339 : }
228 :
229 8 : bool PDB::hasFlag( const std::string& fname ) const {
230 8 : for(unsigned i=0; i<flags.size(); ++i) {
231 0 : if( flags[i]==fname ) return true;
232 : }
233 : return false;
234 : }
235 :
236 :
237 721528 : const std::vector<AtomNumber> & PDB::getAtomNumbers()const {
238 721528 : return numbers;
239 : }
240 :
241 0 : const Vector & PDB::getBoxAxs()const {
242 0 : return BoxXYZ;
243 : }
244 :
245 0 : const Vector & PDB::getBoxAng()const {
246 0 : return BoxABG;
247 : }
248 :
249 12 : const Tensor & PDB::getBoxVec()const {
250 12 : return Box;
251 : }
252 :
253 6770000 : std::string PDB::getAtomName(AtomNumber a)const {
254 : const auto p=number2index.find(a);
255 6770000 : if(p==number2index.end()) {
256 0 : std::string num; Tools::convert( a.serial(), num );
257 0 : plumed_merror("Name of atom " + num + " not found" );
258 6770000 : } else return atomsymb[p->second];
259 : }
260 :
261 166013 : unsigned PDB::getResidueNumber(AtomNumber a)const {
262 : const auto p=number2index.find(a);
263 166013 : if(p==number2index.end()) {
264 0 : std::string num; Tools::convert( a.serial(), num );
265 0 : plumed_merror("Residue for atom " + num + " not found" );
266 166013 : } else return residue[p->second];
267 : }
268 :
269 101936 : std::string PDB::getResidueName(AtomNumber a) const {
270 : const auto p=number2index.find(a);
271 101936 : if(p==number2index.end()) {
272 0 : std::string num; Tools::convert( a.serial(), num );
273 0 : plumed_merror("Residue for atom " + num + " not found" );
274 101936 : } else return residuenames[p->second];
275 : }
276 :
277 205300635 : unsigned PDB::size()const {
278 205300635 : return positions.size();
279 : }
280 :
281 2045 : bool PDB::readFromFilepointer(FILE *fp,bool naturalUnits,double scale) {
282 : //cerr<<file<<endl;
283 : bool file_is_alive=false;
284 2045 : if(naturalUnits) scale=1.0;
285 : std::string line;
286 : fpos_t pos; bool between_ters=true;
287 237748 : while(Tools::getline(fp,line)) {
288 : //cerr<<line<<"\n";
289 237543 : fgetpos (fp,&pos);
290 1342583 : while(line.length()<80) line.push_back(' ');
291 237543 : std::string record=line.substr(0,6);
292 237543 : std::string serial=line.substr(6,5);
293 237543 : std::string atomname=line.substr(12,4);
294 237543 : std::string residuename=line.substr(17,3);
295 237543 : std::string chainID=line.substr(21,1);
296 237543 : std::string resnum=line.substr(22,4);
297 237543 : std::string x=line.substr(30,8);
298 237543 : std::string y=line.substr(38,8);
299 237543 : std::string z=line.substr(46,8);
300 237543 : std::string occ=line.substr(54,6);
301 237543 : std::string bet=line.substr(60,6);
302 237543 : std::string BoxX=line.substr(6,9);
303 237543 : std::string BoxY=line.substr(15,9);
304 237543 : std::string BoxZ=line.substr(24,9);
305 237543 : std::string BoxA=line.substr(33,7);
306 237543 : std::string BoxB=line.substr(40,7);
307 237543 : std::string BoxG=line.substr(47,7);
308 237543 : Tools::trim(record);
309 237543 : if(record=="TER") { between_ters=false; block_ends.push_back( positions.size() ); }
310 237543 : if(record=="END") { file_is_alive=true; break;}
311 235840 : if(record=="ENDMDL") { file_is_alive=true; break;}
312 235703 : if(record=="REMARK") {
313 2678 : std::vector<std::string> v1; v1=Tools::getWords(line.substr(6));
314 1339 : addRemark( v1 );
315 1339 : }
316 235703 : if(record=="CRYST1") {
317 69 : Tools::convert(BoxX,BoxXYZ[0]);
318 69 : Tools::convert(BoxY,BoxXYZ[1]);
319 69 : Tools::convert(BoxZ,BoxXYZ[2]);
320 69 : Tools::convert(BoxA,BoxABG[0]);
321 69 : Tools::convert(BoxB,BoxABG[1]);
322 69 : Tools::convert(BoxG,BoxABG[2]);
323 69 : BoxXYZ*=scale;
324 69 : double cosA=std::cos(BoxABG[0]*pi/180.);
325 69 : double cosB=std::cos(BoxABG[1]*pi/180.);
326 69 : double cosG=std::cos(BoxABG[2]*pi/180.);
327 69 : double sinG=std::sin(BoxABG[2]*pi/180.);
328 276 : for (unsigned i=0; i<3; i++) {Box[i][0]=0.; Box[i][1]=0.; Box[i][2]=0.;}
329 69 : Box[0][0]=BoxXYZ[0];
330 69 : Box[1][0]=BoxXYZ[1]*cosG;
331 69 : Box[1][1]=BoxXYZ[1]*sinG;
332 69 : Box[2][0]=BoxXYZ[2]*cosB;
333 69 : Box[2][1]=(BoxXYZ[2]*BoxXYZ[1]*cosA-Box[2][0]*Box[1][0])/Box[1][1];
334 69 : Box[2][2]=std::sqrt(BoxXYZ[2]*BoxXYZ[2]-Box[2][0]*Box[2][0]-Box[2][1]*Box[2][1]);
335 : }
336 237742 : if(record=="ATOM" || record=="HETATM") {
337 : between_ters=true;
338 : AtomNumber a;
339 233664 : unsigned resno=0; // GB: when resnum string is not present, we set res number to zero
340 : double o,b;
341 233664 : Vector p;
342 : {
343 : int result;
344 233664 : auto trimmed=serial;
345 233664 : Tools::trim(trimmed);
346 233726 : while(trimmed.length()<5) trimmed = std::string(" ") + trimmed;
347 233664 : const char* errmsg = h36::hy36decode(5, trimmed.c_str(),trimmed.length(), &result);
348 233664 : if(errmsg) {
349 0 : std::string msg(errmsg);
350 0 : plumed_merror(msg);
351 : }
352 233664 : a.setSerial(result);
353 : }
354 :
355 : // allow skipping residue number
356 : {
357 233664 : auto trimmed=resnum;
358 233664 : Tools::trim(trimmed);
359 233664 : if(trimmed.length()>0) {
360 : int result;
361 227024 : while(trimmed.length()<4) trimmed = std::string(" ") + trimmed;
362 227024 : const char* errmsg = h36::hy36decode(4, trimmed.c_str(),trimmed.length(), &result);
363 227024 : if(errmsg) {
364 0 : std::string msg(errmsg);
365 0 : plumed_merror(msg);
366 : }
367 227024 : resno=result;
368 : }
369 : }
370 :
371 233664 : Tools::convert(occ,o);
372 233664 : Tools::convert(bet,b);
373 233664 : Tools::convert(x,p[0]);
374 233664 : Tools::convert(y,p[1]);
375 233664 : Tools::convert(z,p[2]);
376 : // scale into nm
377 233664 : p*=scale;
378 233664 : numbers.push_back(a);
379 233664 : number2index[a]=positions.size();
380 233664 : std::size_t startpos=atomname.find_first_not_of(" \t");
381 233664 : std::size_t endpos=atomname.find_last_not_of(" \t");
382 233664 : atomsymb.push_back( atomname.substr(startpos, endpos-startpos+1) );
383 233664 : residue.push_back(resno);
384 233664 : chain.push_back(chainID);
385 233664 : occupancy.push_back(o);
386 233664 : beta.push_back(b);
387 233664 : positions.push_back(p);
388 233664 : residuenames.push_back(residuename);
389 : }
390 : }
391 2045 : if( between_ters ) block_ends.push_back( positions.size() );
392 2045 : return file_is_alive;
393 : }
394 :
395 299 : bool PDB::read(const std::string&file,bool naturalUnits,double scale) {
396 299 : FILE* fp=fopen(file.c_str(),"r");
397 299 : if(!fp) return false;
398 297 : readFromFilepointer(fp,naturalUnits,scale);
399 297 : fclose(fp);
400 297 : return true;
401 : }
402 :
403 231 : void PDB::getChainNames( std::vector<std::string>& chains ) const {
404 231 : chains.resize(0);
405 231 : chains.push_back( chain[0] );
406 464610 : for(unsigned i=1; i<size(); ++i) {
407 464379 : if( chains[chains.size()-1]!=chain[i] ) chains.push_back( chain[i] );
408 : }
409 231 : }
410 :
411 11591 : void PDB::getResidueRange( const std::string& chainname, unsigned& res_start, unsigned& res_end, std::string& errmsg ) const {
412 : bool inres=false, foundchain=false;
413 30269701 : for(unsigned i=0; i<size(); ++i) {
414 30258110 : if( chain[i]==chainname ) {
415 26604174 : if(!inres) {
416 11591 : if(foundchain) errmsg="found second start of chain named " + chainname;
417 11591 : res_start=residue[i];
418 : }
419 : inres=true; foundchain=true;
420 3653936 : } else if( inres && chain[i]!=chainname ) {
421 : inres=false;
422 11090 : res_end=residue[i-1];
423 : }
424 : }
425 11591 : if(inres) res_end=residue[size()-1];
426 11591 : }
427 :
428 158 : void PDB::getAtomRange( const std::string& chainname, AtomNumber& a_start, AtomNumber& a_end, std::string& errmsg ) const {
429 : bool inres=false, foundchain=false;
430 432520 : for(unsigned i=0; i<size(); ++i) {
431 432362 : if( chain[i]==chainname ) {
432 89742 : if(!inres) {
433 158 : if(foundchain) errmsg="found second start of chain named " + chainname;
434 158 : a_start=numbers[i];
435 : }
436 : inres=true; foundchain=true;
437 342620 : } else if( inres && chain[i]!=chainname ) {
438 : inres=false;
439 74 : a_end=numbers[i-1];
440 : }
441 : }
442 158 : if(inres) a_end=numbers[size()-1];
443 158 : }
444 :
445 5958 : std::string PDB::getResidueName( const unsigned& resnum ) const {
446 7317600 : for(unsigned i=0; i<size(); ++i) {
447 7317600 : if( residue[i]==resnum ) return residuenames[i];
448 : }
449 0 : std::string num; Tools::convert( resnum, num );
450 0 : plumed_merror("residue " + num + " not found" );
451 : }
452 :
453 46594 : std::string PDB::getResidueName(const unsigned& resnum,const std::string& chainid ) const {
454 59112773 : for(unsigned i=0; i<size(); ++i) {
455 59159547 : if( residue[i]==resnum && ( chainid=="*" || chain[i]==chainid) ) return residuenames[i];
456 : }
457 0 : std::string num; Tools::convert( resnum, num );
458 0 : plumed_merror("residue " + num + " not found in chain " + chainid );
459 : }
460 :
461 :
462 13260 : AtomNumber PDB::getNamedAtomFromResidue( const std::string& aname, const unsigned& resnum ) const {
463 16347180 : for(unsigned i=0; i<size(); ++i) {
464 16347180 : if( residue[i]==resnum && atomsymb[i]==aname ) return numbers[i];
465 : }
466 0 : std::string num; Tools::convert( resnum, num );
467 0 : plumed_merror("residue " + num + " does not contain an atom named " + aname );
468 : }
469 :
470 2216 : AtomNumber PDB::getNamedAtomFromResidueAndChain( const std::string& aname, const unsigned& resnum, const std::string& chainid ) const {
471 1070584 : for(unsigned i=0; i<size(); ++i) {
472 1072800 : if( residue[i]==resnum && atomsymb[i]==aname && ( chainid=="*" || chain[i]==chainid) ) return numbers[i];
473 : }
474 0 : std::string num; Tools::convert( resnum, num );
475 0 : plumed_merror("residue " + num + " from chain " + chainid + " does not contain an atom named " + aname );
476 : }
477 :
478 32150 : std::vector<AtomNumber> PDB::getAtomsInResidue(const unsigned& resnum,const std::string& chainid)const {
479 : std::vector<AtomNumber> tmp;
480 84003186 : for(unsigned i=0; i<size(); ++i) {
481 84456920 : if( residue[i]==resnum && ( chainid=="*" || chain[i]==chainid) ) tmp.push_back(numbers[i]);
482 : }
483 32150 : if(tmp.size()==0) {
484 0 : std::string num; Tools::convert( resnum, num );
485 0 : plumed_merror("Cannot find residue " + num + " from chain " + chainid );
486 : }
487 32150 : return tmp;
488 : }
489 :
490 0 : std::vector<AtomNumber> PDB::getAtomsInChain(const std::string& chainid)const {
491 : std::vector<AtomNumber> tmp;
492 0 : for(unsigned i=0; i<size(); ++i) {
493 0 : if( chainid=="*" || chain[i]==chainid ) tmp.push_back(numbers[i]);
494 : }
495 0 : if(tmp.size()==0) {
496 0 : plumed_merror("Cannot find atoms from chain " + chainid );
497 : }
498 0 : return tmp;
499 : }
500 :
501 4638 : std::string PDB::getChainID(const unsigned& resnumber) const {
502 5689172 : for(unsigned i=0; i<size(); ++i) {
503 5689172 : if(resnumber==residue[i]) return chain[i];
504 : }
505 0 : plumed_merror("Not enough residues in pdb input file");
506 : }
507 :
508 0 : std::string PDB::getChainID(AtomNumber a) const {
509 : const auto p=number2index.find(a);
510 0 : if(p==number2index.end()) {
511 0 : std::string num; Tools::convert( a.serial(), num );
512 0 : plumed_merror("Chain for atom " + num + " not found" );
513 : }
514 0 : return chain[p->second];
515 : }
516 :
517 0 : bool PDB::checkForResidue( const std::string& name ) const {
518 0 : for(unsigned i=0; i<size(); ++i) {
519 0 : if( residuenames[i]==name ) return true;
520 : }
521 : return false;
522 : }
523 :
524 0 : bool PDB::checkForAtom( const std::string& name ) const {
525 0 : for(unsigned i=0; i<size(); ++i) {
526 0 : if( atomsymb[i]==name ) return true;
527 : }
528 : return false;
529 : }
530 :
531 4 : bool PDB::checkForAtom( AtomNumber a ) const {
532 : const auto p=number2index.find(a);
533 4 : return (p!=number2index.end());
534 : }
535 :
536 0 : Log& operator<<(Log& ostr, const PDB& pdb) {
537 : char buffer[1000];
538 0 : for(unsigned i=0; i<pdb.positions.size(); i++) {
539 0 : std::sprintf(buffer,"ATOM %3u %8.3f %8.3f %8.3f\n",pdb.numbers[i].serial(),pdb.positions[i][0],pdb.positions[i][1],pdb.positions[i][2]);
540 0 : ostr<<buffer;
541 : }
542 0 : return ostr;
543 : }
544 :
545 854 : Vector PDB::getPosition(AtomNumber a)const {
546 : const auto p=number2index.find(a);
547 854 : if(p==number2index.end()) plumed_merror("atom not available");
548 854 : else return positions[p->second];
549 : }
550 :
551 2539432 : std::vector<std::string> PDB::getArgumentNames()const {
552 2539432 : return argnames;
553 : }
554 :
555 10 : std::string PDB::getMtype() const {
556 10 : return mtype;
557 : }
558 :
559 497 : void PDB::print( const double& lunits, GenericMolInfo* mymoldat, OFile& ofile, const std::string& fmt ) {
560 497 : if( argnames.size()>0 ) {
561 476 : ofile.printf("REMARK ARG=%s", argnames[0].c_str() );
562 1744 : for(unsigned i=1; i<argnames.size(); ++i) ofile.printf(",%s",argnames[i].c_str() );
563 476 : ofile.printf("\n"); ofile.printf("REMARK ");
564 : }
565 : std::string descr2;
566 497 : if(fmt.find("-")!=std::string::npos) {
567 0 : descr2="%s=" + fmt + " ";
568 : } else {
569 : // This ensures numbers are left justified (i.e. next to the equals sign
570 497 : std::size_t psign=fmt.find("%");
571 497 : plumed_assert( psign!=std::string::npos );
572 994 : descr2="%s=%-" + fmt.substr(psign+1) + " ";
573 : }
574 2241 : for(std::map<std::string,double>::iterator it=arg_data.begin(); it!=arg_data.end(); ++it) ofile.printf( descr2.c_str(),it->first.c_str(), it->second );
575 497 : if( argnames.size()>0 ) ofile.printf("\n");
576 497 : if( !mymoldat ) {
577 2263 : for(unsigned i=0; i<positions.size(); ++i) {
578 : std::array<char,6> at;
579 : {
580 1769 : const char* msg = h36::hy36encode(5,numbers[i].serial(),&at[0]);
581 1769 : plumed_assert(msg==nullptr) << msg;
582 1769 : at[5]=0;
583 : }
584 : std::array<char,5> res;
585 : {
586 1769 : const char* msg = h36::hy36encode(4,i,&res[0]);
587 1769 : plumed_assert(msg==nullptr) << msg;
588 1769 : res[4]=0;
589 : }
590 1769 : ofile.printf("ATOM %s X RES %s %8.3f%8.3f%8.3f%6.2f%6.2f\n",
591 : &at[0], &res[0],
592 1769 : lunits*positions[i][0], lunits*positions[i][1], lunits*positions[i][2],
593 : occupancy[i], beta[i] );
594 : }
595 : } else {
596 69 : for(unsigned i=0; i<positions.size(); ++i) {
597 : std::array<char,6> at;
598 : {
599 66 : const char* msg = h36::hy36encode(5,numbers[i].serial(),&at[0]);
600 66 : plumed_assert(msg==nullptr) << msg;
601 66 : at[5]=0;
602 : }
603 : std::array<char,5> res;
604 : {
605 66 : const char* msg = h36::hy36encode(4,mymoldat->getResidueNumber(numbers[i]),&res[0]);
606 66 : plumed_assert(msg==nullptr) << msg;
607 66 : res[4]=0;
608 : }
609 66 : ofile.printf("ATOM %s %-4s %3s %s %8.3f%8.3f%8.3f%6.2f%6.2f\n",
610 132 : &at[0], mymoldat->getAtomName(numbers[i]).c_str(),
611 66 : mymoldat->getResidueName(numbers[i]).c_str(), &res[0],
612 66 : lunits*positions[i][0], lunits*positions[i][1], lunits*positions[i][2],
613 : occupancy[i], beta[i] );
614 : }
615 : }
616 497 : ofile.printf("END\n");
617 497 : }
618 :
619 :
620 : }
621 :
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