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 0 : void PDB::setAtomNumbers( const std::vector<AtomNumber>& atoms ) {
134 0 : positions.resize( atoms.size() );
135 0 : occupancy.resize( atoms.size() );
136 0 : beta.resize( atoms.size() );
137 0 : numbers.resize( atoms.size() );
138 0 : for(unsigned i=0; i<atoms.size(); ++i) {
139 0 : numbers[i]=atoms[i];
140 0 : beta[i]=1.0;
141 0 : occupancy[i]=1.0;
142 : }
143 0 : }
144 :
145 0 : void PDB::setArgumentNames( const std::vector<std::string>& argument_names ) {
146 0 : argnames.resize( argument_names.size() );
147 0 : std::vector<double> tmp(1,0);
148 0 : for(unsigned i=0; i<argument_names.size(); ++i) {
149 : argnames[i]=argument_names[i];
150 0 : arg_data.insert( std::pair<std::string,std::vector<double> >( argnames[i], tmp ) );
151 : }
152 0 : }
153 :
154 2148 : bool PDB::getArgumentValue( const std::string& name, std::vector<double>& value ) const {
155 : std::map<std::string,std::vector<double> >::const_iterator it = arg_data.find(name);
156 2148 : if( it!=arg_data.end() ) {
157 2148 : if( value.size()!=it->second.size() ) {
158 : return false;
159 : }
160 4300 : for(unsigned i=0; i<value.size(); ++i) {
161 2152 : value[i] = it->second[i];
162 : }
163 : return true;
164 : }
165 : return false;
166 : }
167 :
168 0 : void PDB::setAtomPositions( const std::vector<Vector>& pos ) {
169 0 : plumed_assert( pos.size()==positions.size() );
170 0 : for(unsigned i=0; i<positions.size(); ++i) {
171 0 : positions[i]=pos[i];
172 : }
173 0 : }
174 :
175 0 : void PDB::setArgumentValue( const std::string& argname, const double& val ) {
176 : // First set the value of the value of the argument in the map
177 0 : arg_data.find(argname)->second.resize(1);
178 0 : arg_data.find(argname)->second[0] = val;
179 0 : }
180 :
181 : // bool PDB::hasRequiredProperties( const std::vector<std::string>& inproperties ){
182 : // bool hasprop=false;
183 : // for(unsigned i=0;i<remark.size();++i){
184 : // if( remark[i].find("PROPERTIES=")!=std::string::npos){ hasprop=true; break; }
185 : // }
186 : // if( !hasprop ){
187 : // std::string mypropstr="PROPERTIES=" + inproperties[0];
188 : // for(unsigned i=1;i<inproperties.size();++i) mypropstr += "," + inproperties[i];
189 : // remark.push_back( mypropstr );
190 : // }
191 : // // Now check that all required properties are there
192 : // for(unsigned i=0;i<inproperties.size();++i){
193 : // hasprop=false;
194 : // for(unsigned j=0;j<remark.size();++j){
195 : // if( remark[j].find(inproperties[i]+"=")!=std::string::npos){ hasprop=true; break; }
196 : // }
197 : // if( !hasprop ) return false;
198 : // }
199 : // return true;
200 : // }
201 :
202 0 : void PDB::addBlockEnd( const unsigned& end ) {
203 0 : block_ends.push_back( end );
204 0 : }
205 :
206 3 : unsigned PDB::getNumberOfAtomBlocks()const {
207 3 : return block_ends.size();
208 : }
209 :
210 6 : const std::vector<unsigned> & PDB::getAtomBlockEnds()const {
211 6 : return block_ends;
212 : }
213 :
214 23575320 : const std::vector<Vector> & PDB::getPositions()const {
215 23575320 : return positions;
216 : }
217 :
218 0 : void PDB::setPositions(const std::vector<Vector> &v ) {
219 0 : plumed_assert( v.size()==positions.size() );
220 0 : positions=v;
221 0 : }
222 :
223 153916 : const std::vector<double> & PDB::getOccupancy()const {
224 153916 : return occupancy;
225 : }
226 :
227 152249 : const std::vector<double> & PDB::getBeta()const {
228 152249 : return beta;
229 : }
230 :
231 4607 : void PDB::addRemark( std::vector<std::string>& v1 ) {
232 4607 : Tools::parse(v1,"TYPE",mtype);
233 4607 : Tools::parseVector(v1,"ARG",argnames);
234 12385 : for(unsigned i=0; i<v1.size(); ++i) {
235 7778 : if( v1[i].find("=")!=std::string::npos ) {
236 : std::size_t eq=v1[i].find_first_of('=');
237 7164 : std::string name=v1[i].substr(0,eq);
238 7164 : std::string sval=v1[i].substr(eq+1);
239 : // double val; Tools::convert( sval, val );
240 7164 : std::vector<std::string> words=Tools::getWords(sval,"\t\n ,");
241 7164 : std::vector<double> val( words.size() );
242 14336 : for(unsigned i=0; i<val.size(); ++i) {
243 7172 : Tools::convert( words[i], val[i] );
244 : }
245 14328 : arg_data.insert( std::pair<std::string,std::vector<double> >( name, val ) );
246 7164 : } else {
247 614 : flags.push_back(v1[i]);
248 : }
249 : }
250 4607 : }
251 :
252 0 : bool PDB::hasFlag( const std::string& fname ) const {
253 0 : for(unsigned i=0; i<flags.size(); ++i) {
254 0 : if( flags[i]==fname ) {
255 : return true;
256 : }
257 : }
258 : return false;
259 : }
260 :
261 :
262 314640 : const std::vector<AtomNumber> & PDB::getAtomNumbers()const {
263 314640 : return numbers;
264 : }
265 :
266 0 : const Vector & PDB::getBoxAxs()const {
267 0 : return BoxXYZ;
268 : }
269 :
270 0 : const Vector & PDB::getBoxAng()const {
271 0 : return BoxABG;
272 : }
273 :
274 12 : const Tensor & PDB::getBoxVec()const {
275 12 : return Box;
276 : }
277 :
278 6947345 : std::string PDB::getAtomName(AtomNumber a)const {
279 : const auto p=number2index.find(a);
280 6947345 : if(p==number2index.end()) {
281 : std::string num;
282 0 : Tools::convert( a.serial(), num );
283 0 : plumed_merror("Name of atom " + num + " not found" );
284 : } else {
285 6947345 : return atomsymb[p->second];
286 : }
287 : }
288 :
289 166232 : unsigned PDB::getResidueNumber(AtomNumber a)const {
290 : const auto p=number2index.find(a);
291 166232 : if(p==number2index.end()) {
292 : std::string num;
293 0 : Tools::convert( a.serial(), num );
294 0 : plumed_merror("Residue for atom " + num + " not found" );
295 : } else {
296 166232 : return residue[p->second];
297 : }
298 : }
299 :
300 180036 : std::string PDB::getResidueName(AtomNumber a) const {
301 : const auto p=number2index.find(a);
302 180036 : if(p==number2index.end()) {
303 : std::string num;
304 0 : Tools::convert( a.serial(), num );
305 0 : plumed_merror("Residue for atom " + num + " not found" );
306 : } else {
307 180036 : return residuenames[p->second];
308 : }
309 : }
310 :
311 243528438 : unsigned PDB::size()const {
312 243528438 : return positions.size();
313 : }
314 :
315 4584 : bool PDB::readFromFilepointer(FILE *fp,bool naturalUnits,double scale) {
316 : //cerr<<file<<endl;
317 : bool file_is_alive=false;
318 4584 : if(naturalUnits) {
319 : scale=1.0;
320 : }
321 : std::string line;
322 : fpos_t pos;
323 : bool between_ters=true;
324 468132 : while(Tools::getline(fp,line)) {
325 : //cerr<<line<<"\n";
326 467624 : fgetpos (fp,&pos);
327 3354208 : while(line.length()<80) {
328 2886584 : line.push_back(' ');
329 : }
330 467624 : std::string record=line.substr(0,6);
331 467624 : std::string serial=line.substr(6,5);
332 467624 : std::string atomname=line.substr(12,4);
333 467624 : std::string residuename=line.substr(17,3);
334 467624 : std::string chainID=line.substr(21,1);
335 467624 : std::string resnum=line.substr(22,4);
336 467624 : std::string x=line.substr(30,8);
337 467624 : std::string y=line.substr(38,8);
338 467624 : std::string z=line.substr(46,8);
339 467624 : std::string occ=line.substr(54,6);
340 467624 : std::string bet=line.substr(60,6);
341 467624 : std::string BoxX=line.substr(6,9);
342 467624 : std::string BoxY=line.substr(15,9);
343 467624 : std::string BoxZ=line.substr(24,9);
344 467624 : std::string BoxA=line.substr(33,7);
345 467624 : std::string BoxB=line.substr(40,7);
346 467624 : std::string BoxG=line.substr(47,7);
347 467624 : Tools::trim(record);
348 467624 : if(record=="TER") {
349 : between_ters=false;
350 245 : block_ends.push_back( positions.size() );
351 : }
352 467624 : if(record=="END") {
353 : file_is_alive=true;
354 : break;
355 : }
356 463700 : if(record=="ENDMDL") {
357 : file_is_alive=true;
358 : break;
359 : }
360 463548 : if(record=="REMARK") {
361 : std::vector<std::string> v1;
362 9214 : v1=Tools::getWords(line.substr(6));
363 4607 : addRemark( v1 );
364 4607 : }
365 463548 : if(record=="CRYST1") {
366 80 : Tools::convert(BoxX,BoxXYZ[0]);
367 80 : Tools::convert(BoxY,BoxXYZ[1]);
368 80 : Tools::convert(BoxZ,BoxXYZ[2]);
369 80 : Tools::convert(BoxA,BoxABG[0]);
370 80 : Tools::convert(BoxB,BoxABG[1]);
371 80 : Tools::convert(BoxG,BoxABG[2]);
372 80 : BoxXYZ*=scale;
373 80 : double cosA=std::cos(BoxABG[0]*pi/180.);
374 80 : double cosB=std::cos(BoxABG[1]*pi/180.);
375 80 : double cosG=std::cos(BoxABG[2]*pi/180.);
376 80 : double sinG=std::sin(BoxABG[2]*pi/180.);
377 320 : for (unsigned i=0; i<3; i++) {
378 240 : Box[i][0]=0.;
379 240 : Box[i][1]=0.;
380 240 : Box[i][2]=0.;
381 : }
382 80 : Box[0][0]=BoxXYZ[0];
383 80 : Box[1][0]=BoxXYZ[1]*cosG;
384 80 : Box[1][1]=BoxXYZ[1]*sinG;
385 80 : Box[2][0]=BoxXYZ[2]*cosB;
386 80 : Box[2][1]=(BoxXYZ[2]*BoxXYZ[1]*cosA-Box[2][0]*Box[1][0])/Box[1][1];
387 80 : Box[2][2]=std::sqrt(BoxXYZ[2]*BoxXYZ[2]-Box[2][0]*Box[2][0]-Box[2][1]*Box[2][1]);
388 : }
389 469447 : if(record=="ATOM" || record=="HETATM") {
390 : between_ters=true;
391 : AtomNumber a;
392 457649 : unsigned resno=0; // GB: when resnum string is not present, we set res number to zero
393 : double o,b;
394 457649 : Vector p;
395 : {
396 : int result;
397 457649 : auto trimmed=serial;
398 457649 : Tools::trim(trimmed);
399 457711 : while(trimmed.length()<5) {
400 124 : trimmed = std::string(" ") + trimmed;
401 : }
402 457649 : const char* errmsg = h36::hy36decode(5, trimmed.c_str(),trimmed.length(), &result);
403 457649 : if(errmsg) {
404 0 : std::string msg(errmsg);
405 0 : plumed_merror(msg);
406 : }
407 457649 : a.setSerial(result);
408 : }
409 :
410 : // allow skipping residue number
411 : {
412 457649 : auto trimmed=resnum;
413 457649 : Tools::trim(trimmed);
414 457649 : if(trimmed.length()>0) {
415 : int result;
416 457649 : while(trimmed.length()<4) {
417 0 : trimmed = std::string(" ") + trimmed;
418 : }
419 457649 : const char* errmsg = h36::hy36decode(4, trimmed.c_str(),trimmed.length(), &result);
420 457649 : if(errmsg) {
421 0 : std::string msg(errmsg);
422 0 : plumed_merror(msg);
423 : }
424 457649 : resno=result;
425 : }
426 : }
427 :
428 457649 : Tools::convert(occ,o);
429 457649 : Tools::convert(bet,b);
430 457649 : Tools::convert(x,p[0]);
431 457649 : Tools::convert(y,p[1]);
432 457649 : Tools::convert(z,p[2]);
433 : // scale into nm
434 457649 : p*=scale;
435 457649 : numbers.push_back(a);
436 457649 : number2index[a]=positions.size();
437 457649 : std::size_t startpos=atomname.find_first_not_of(" \t");
438 457649 : std::size_t endpos=atomname.find_last_not_of(" \t");
439 457649 : atomsymb.push_back( atomname.substr(startpos, endpos-startpos+1) );
440 457649 : residue.push_back(resno);
441 457649 : chain.push_back(chainID);
442 457649 : occupancy.push_back(o);
443 457649 : beta.push_back(b);
444 457649 : positions.push_back(p);
445 457649 : residuenames.push_back(residuename);
446 : }
447 : }
448 4584 : if( between_ters ) {
449 4392 : block_ends.push_back( positions.size() );
450 : }
451 4584 : return file_is_alive;
452 : }
453 :
454 458 : bool PDB::read(const std::string&file,bool naturalUnits,double scale) {
455 458 : FILE* fp=std::fopen(file.c_str(),"r");
456 458 : if(!fp) {
457 : return false;
458 : }
459 : // call fclose when exiting this function
460 : auto deleter=[](auto f) {
461 457 : std::fclose(f);
462 : };
463 : std::unique_ptr<FILE,decltype(deleter)> fp_deleter(fp,deleter);
464 457 : readFromFilepointer(fp,naturalUnits,scale);
465 : return true;
466 : }
467 :
468 296 : void PDB::getChainNames( std::vector<std::string>& chains ) const {
469 296 : chains.resize(0);
470 296 : chains.push_back( chain[0] );
471 574777 : for(unsigned i=1; i<size(); ++i) {
472 574481 : if( chains[chains.size()-1]!=chain[i] ) {
473 756 : chains.push_back( chain[i] );
474 : }
475 : }
476 296 : }
477 :
478 11906 : void PDB::getResidueRange( const std::string& chainname, unsigned& res_start, unsigned& res_end, std::string& errmsg ) const {
479 : bool inres=false, foundchain=false;
480 31023905 : for(unsigned i=0; i<size(); ++i) {
481 31011999 : if( chain[i]==chainname ) {
482 26714341 : if(!inres) {
483 11906 : if(foundchain) {
484 0 : errmsg="found second start of chain named " + chainname;
485 : }
486 11906 : res_start=residue[i];
487 : }
488 : inres=true;
489 : foundchain=true;
490 4297658 : } else if( inres && chain[i]!=chainname ) {
491 : inres=false;
492 11340 : res_end=residue[i-1];
493 : }
494 : }
495 11906 : if(inres) {
496 566 : res_end=residue[size()-1];
497 : }
498 11906 : }
499 :
500 228 : void PDB::getAtomRange( const std::string& chainname, AtomNumber& a_start, AtomNumber& a_end, std::string& errmsg ) const {
501 : bool inres=false, foundchain=false;
502 549225 : for(unsigned i=0; i<size(); ++i) {
503 548997 : if( chain[i]==chainname ) {
504 112687 : if(!inres) {
505 228 : if(foundchain) {
506 0 : errmsg="found second start of chain named " + chainname;
507 : }
508 228 : a_start=numbers[i];
509 : }
510 : inres=true;
511 : foundchain=true;
512 436310 : } else if( inres && chain[i]!=chainname ) {
513 : inres=false;
514 110 : a_end=numbers[i-1];
515 : }
516 : }
517 228 : if(inres) {
518 118 : a_end=numbers[size()-1];
519 : }
520 228 : }
521 :
522 9900 : std::string PDB::getResidueName( const unsigned& resnum ) const {
523 12195264 : for(unsigned i=0; i<size(); ++i) {
524 12195264 : if( residue[i]==resnum ) {
525 9900 : return residuenames[i];
526 : }
527 : }
528 : std::string num;
529 0 : Tools::convert( resnum, num );
530 0 : plumed_merror("residue " + num + " not found" );
531 : }
532 :
533 50084 : std::string PDB::getResidueName(const unsigned& resnum,const std::string& chainid ) const {
534 64922933 : for(unsigned i=0; i<size(); ++i) {
535 64973197 : if( residue[i]==resnum && ( chainid=="*" || chain[i]==chainid) ) {
536 50084 : return residuenames[i];
537 : }
538 : }
539 : std::string num;
540 0 : Tools::convert( resnum, num );
541 0 : plumed_merror("residue " + num + " not found in chain " + chainid );
542 : }
543 :
544 :
545 22020 : AtomNumber PDB::getNamedAtomFromResidue( const std::string& aname, const unsigned& resnum ) const {
546 27242772 : for(unsigned i=0; i<size(); ++i) {
547 27242772 : if( residue[i]==resnum && atomsymb[i]==aname ) {
548 22020 : return numbers[i];
549 : }
550 : }
551 : std::string num;
552 0 : Tools::convert( resnum, num );
553 0 : plumed_merror("residue " + num + " does not contain an atom named " + aname );
554 : }
555 :
556 2898 : AtomNumber PDB::getNamedAtomFromResidueAndChain( const std::string& aname, const unsigned& resnum, const std::string& chainid ) const {
557 1116492 : for(unsigned i=0; i<size(); ++i) {
558 1119390 : if( residue[i]==resnum && atomsymb[i]==aname && ( chainid=="*" || chain[i]==chainid) ) {
559 2898 : return numbers[i];
560 : }
561 : }
562 : std::string num;
563 0 : Tools::convert( resnum, num );
564 0 : plumed_merror("residue " + num + " from chain " + chainid + " does not contain an atom named " + aname );
565 : }
566 :
567 35470 : std::vector<AtomNumber> PDB::getAtomsInResidue(const unsigned& resnum,const std::string& chainid)const {
568 : std::vector<AtomNumber> tmp;
569 95754470 : for(unsigned i=0; i<size(); ++i) {
570 96261470 : if( residue[i]==resnum && ( chainid=="*" || chain[i]==chainid) ) {
571 542470 : tmp.push_back(numbers[i]);
572 : }
573 : }
574 35470 : if(tmp.size()==0) {
575 : std::string num;
576 0 : Tools::convert( resnum, num );
577 0 : plumed_merror("Cannot find residue " + num + " from chain " + chainid );
578 : }
579 35470 : return tmp;
580 : }
581 :
582 0 : std::vector<AtomNumber> PDB::getAtomsInChain(const std::string& chainid)const {
583 : std::vector<AtomNumber> tmp;
584 0 : for(unsigned i=0; i<size(); ++i) {
585 0 : if( chainid=="*" || chain[i]==chainid ) {
586 0 : tmp.push_back(numbers[i]);
587 : }
588 : }
589 0 : if(tmp.size()==0) {
590 0 : plumed_merror("Cannot find atoms from chain " + chainid );
591 : }
592 0 : return tmp;
593 : }
594 :
595 7710 : std::string PDB::getChainID(const unsigned& resnumber) const {
596 9481600 : for(unsigned i=0; i<size(); ++i) {
597 9481600 : if(resnumber==residue[i]) {
598 7710 : return chain[i];
599 : }
600 : }
601 0 : plumed_merror("Not enough residues in pdb input file");
602 : }
603 :
604 0 : std::string PDB::getChainID(AtomNumber a) const {
605 : const auto p=number2index.find(a);
606 0 : if(p==number2index.end()) {
607 : std::string num;
608 0 : Tools::convert( a.serial(), num );
609 0 : plumed_merror("Chain for atom " + num + " not found" );
610 : }
611 0 : return chain[p->second];
612 : }
613 :
614 0 : bool PDB::checkForResidue( const std::string& name ) const {
615 0 : for(unsigned i=0; i<size(); ++i) {
616 0 : if( residuenames[i]==name ) {
617 : return true;
618 : }
619 : }
620 : return false;
621 : }
622 :
623 0 : bool PDB::checkForAtom( const std::string& name ) const {
624 0 : for(unsigned i=0; i<size(); ++i) {
625 0 : if( atomsymb[i]==name ) {
626 : return true;
627 : }
628 : }
629 : return false;
630 : }
631 :
632 249 : bool PDB::checkForAtom( AtomNumber a ) const {
633 : const auto p=number2index.find(a);
634 249 : return (p!=number2index.end());
635 : }
636 :
637 0 : Log& operator<<(Log& ostr, const PDB& pdb) {
638 : const std::size_t bufferlen=1000;
639 : char buffer[bufferlen];
640 0 : for(unsigned i=0; i<pdb.positions.size(); i++) {
641 0 : std::snprintf(buffer,bufferlen,"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]);
642 0 : ostr<<buffer;
643 : }
644 0 : return ostr;
645 : }
646 :
647 1038 : Vector PDB::getPosition(AtomNumber a)const {
648 : const auto p=number2index.find(a);
649 1038 : if(p==number2index.end()) {
650 0 : plumed_merror("atom not available");
651 : } else {
652 1038 : return positions[p->second];
653 : }
654 : }
655 :
656 0 : std::vector<std::string> PDB::getArgumentNames()const {
657 0 : return argnames;
658 : }
659 :
660 0 : std::string PDB::getMtype() const {
661 0 : return mtype;
662 : }
663 :
664 0 : void PDB::print( const double& lunits, GenericMolInfo* mymoldat, OFile& ofile, const std::string& fmt ) {
665 0 : if( argnames.size()>0 ) {
666 0 : ofile.printf("REMARK ARG=%s", argnames[0].c_str() );
667 0 : for(unsigned i=1; i<argnames.size(); ++i) {
668 0 : ofile.printf(",%s",argnames[i].c_str() );
669 : }
670 0 : ofile.printf("\n");
671 0 : ofile.printf("REMARK ");
672 : }
673 : std::string descr2;
674 0 : if(fmt.find("-")!=std::string::npos) {
675 0 : descr2="%s=" + fmt + " ";
676 : } else {
677 : // This ensures numbers are left justified (i.e. next to the equals sign
678 0 : std::size_t psign=fmt.find("%");
679 0 : plumed_assert( psign!=std::string::npos );
680 0 : descr2="%s=%-" + fmt.substr(psign+1) + " ";
681 : }
682 0 : for(std::map<std::string,std::vector<double> >::iterator it=arg_data.begin(); it!=arg_data.end(); ++it) {
683 0 : ofile.printf( descr2.c_str(),it->first.c_str(), it->second[0] );
684 : }
685 0 : if( argnames.size()>0 ) {
686 0 : ofile.printf("\n");
687 : }
688 0 : if( !mymoldat ) {
689 0 : for(unsigned i=0; i<positions.size(); ++i) {
690 : std::array<char,6> at;
691 : {
692 0 : const char* msg = h36::hy36encode(5,numbers[i].serial(),&at[0]);
693 0 : plumed_assert(msg==nullptr) << msg;
694 0 : at[5]=0;
695 : }
696 : std::array<char,5> res;
697 : {
698 0 : const char* msg = h36::hy36encode(4,i,&res[0]);
699 0 : plumed_assert(msg==nullptr) << msg;
700 0 : res[4]=0;
701 : }
702 0 : ofile.printf("ATOM %s X RES %s %8.3f%8.3f%8.3f%6.2f%6.2f\n",
703 : &at[0], &res[0],
704 0 : lunits*positions[i][0], lunits*positions[i][1], lunits*positions[i][2],
705 : occupancy[i], beta[i] );
706 : }
707 : } else {
708 0 : for(unsigned i=0; i<positions.size(); ++i) {
709 : std::array<char,6> at;
710 : {
711 0 : const char* msg = h36::hy36encode(5,numbers[i].serial(),&at[0]);
712 0 : plumed_assert(msg==nullptr) << msg;
713 0 : at[5]=0;
714 : }
715 : std::array<char,5> res;
716 : {
717 0 : const char* msg = h36::hy36encode(4,mymoldat->getResidueNumber(numbers[i]),&res[0]);
718 0 : plumed_assert(msg==nullptr) << msg;
719 0 : res[4]=0;
720 : }
721 0 : ofile.printf("ATOM %s %-4s %3s %s %8.3f%8.3f%8.3f%6.2f%6.2f\n",
722 0 : &at[0], mymoldat->getAtomName(numbers[i]).c_str(),
723 0 : mymoldat->getResidueName(numbers[i]).c_str(), &res[0],
724 0 : lunits*positions[i][0], lunits*positions[i][1], lunits*positions[i][2],
725 : occupancy[i], beta[i] );
726 : }
727 : }
728 0 : ofile.printf("END\n");
729 0 : }
730 :
731 59906 : bool PDB::allowedResidue( const std::string& type, const std::string& residuename ) const {
732 59906 : if( type=="protein" ) {
733 59906 : if(residuename=="ALA") {
734 : return true;
735 56756 : } else if(residuename=="ARG") {
736 : return true;
737 53172 : } else if(residuename=="ASN") {
738 : return true;
739 50100 : } else if(residuename=="ASP") {
740 : return true;
741 47412 : } else if(residuename=="CYS") {
742 : return true;
743 47204 : } else if(residuename=="GLN") {
744 : return true;
745 42844 : } else if(residuename=="GLU") {
746 : return true;
747 40828 : } else if(residuename=="GLY") {
748 : return true;
749 38036 : } else if(residuename=="HIS") {
750 : return true;
751 38036 : } else if(residuename=="ILE") {
752 : return true;
753 34436 : } else if(residuename=="LEU") {
754 : return true;
755 28052 : } else if(residuename=="LYS") {
756 : return true;
757 23732 : } else if(residuename=="MET") {
758 : return true;
759 21412 : } else if(residuename=="PHE") {
760 : return true;
761 17188 : } else if(residuename=="PRO") {
762 : return true;
763 14020 : } else if(residuename=="SER") {
764 : return true;
765 11810 : } else if(residuename=="THR") {
766 : return true;
767 9740 : } else if(residuename=="TRP") {
768 : return true;
769 9740 : } else if(residuename=="TYR") {
770 : return true;
771 7532 : } else if(residuename=="VAL") {
772 : return true;
773 : }
774 : // Terminal groups
775 3010 : else if(residuename=="ACE") {
776 : return true;
777 3010 : } else if(residuename=="NME") {
778 : return true;
779 3010 : } else if(residuename=="NH2") {
780 : return true;
781 : }
782 : // Alternative residue names in common force fields
783 3010 : else if(residuename=="GLH") {
784 : return true; // neutral GLU
785 3010 : } else if(residuename=="ASH") {
786 : return true; // neutral ASP
787 3010 : } else if(residuename=="HID") {
788 : return true; // HIS-D amber
789 3010 : } else if(residuename=="HSD") {
790 : return true; // HIS-D charmm
791 3010 : } else if(residuename=="HIE") {
792 : return true; // HIS-E amber
793 2402 : } else if(residuename=="HSE") {
794 : return true; // HIS-E charmm
795 2402 : } else if(residuename=="HIP") {
796 : return true; // HIS-P amber
797 2402 : } else if(residuename=="HSP") {
798 : return true; // HIS-P charmm
799 2402 : } else if(residuename=="CYX") {
800 : return true; // disulfide bridge CYS
801 : }
802 : // Weird amino acids
803 2402 : else if(residuename=="NLE") {
804 : return true;
805 2402 : } else if(residuename=="SFO") {
806 : return true;
807 : } else {
808 2402 : return false;
809 : }
810 0 : } else if( type=="dna" ) {
811 0 : if(residuename=="A") {
812 : return true;
813 0 : } else if(residuename=="A5") {
814 : return true;
815 0 : } else if(residuename=="A3") {
816 : return true;
817 0 : } else if(residuename=="AN") {
818 : return true;
819 0 : } else if(residuename=="G") {
820 : return true;
821 0 : } else if(residuename=="G5") {
822 : return true;
823 0 : } else if(residuename=="G3") {
824 : return true;
825 0 : } else if(residuename=="GN") {
826 : return true;
827 0 : } else if(residuename=="T") {
828 : return true;
829 0 : } else if(residuename=="T5") {
830 : return true;
831 0 : } else if(residuename=="T3") {
832 : return true;
833 0 : } else if(residuename=="TN") {
834 : return true;
835 0 : } else if(residuename=="C") {
836 : return true;
837 0 : } else if(residuename=="C5") {
838 : return true;
839 0 : } else if(residuename=="C3") {
840 : return true;
841 0 : } else if(residuename=="CN") {
842 : return true;
843 0 : } else if(residuename=="DA") {
844 : return true;
845 0 : } else if(residuename=="DA5") {
846 : return true;
847 0 : } else if(residuename=="DA3") {
848 : return true;
849 0 : } else if(residuename=="DAN") {
850 : return true;
851 0 : } else if(residuename=="DG") {
852 : return true;
853 0 : } else if(residuename=="DG5") {
854 : return true;
855 0 : } else if(residuename=="DG3") {
856 : return true;
857 0 : } else if(residuename=="DGN") {
858 : return true;
859 0 : } else if(residuename=="DT") {
860 : return true;
861 0 : } else if(residuename=="DT5") {
862 : return true;
863 0 : } else if(residuename=="DT3") {
864 : return true;
865 0 : } else if(residuename=="DTN") {
866 : return true;
867 0 : } else if(residuename=="DC") {
868 : return true;
869 0 : } else if(residuename=="DC5") {
870 : return true;
871 0 : } else if(residuename=="DC3") {
872 : return true;
873 0 : } else if(residuename=="DCN") {
874 : return true;
875 : } else {
876 0 : return false;
877 : }
878 0 : } else if( type=="rna" ) {
879 0 : if(residuename=="A") {
880 : return true;
881 0 : } else if(residuename=="A5") {
882 : return true;
883 0 : } else if(residuename=="A3") {
884 : return true;
885 0 : } else if(residuename=="AN") {
886 : return true;
887 0 : } else if(residuename=="G") {
888 : return true;
889 0 : } else if(residuename=="G5") {
890 : return true;
891 0 : } else if(residuename=="G3") {
892 : return true;
893 0 : } else if(residuename=="GN") {
894 : return true;
895 0 : } else if(residuename=="U") {
896 : return true;
897 0 : } else if(residuename=="U5") {
898 : return true;
899 0 : } else if(residuename=="U3") {
900 : return true;
901 0 : } else if(residuename=="UN") {
902 : return true;
903 0 : } else if(residuename=="C") {
904 : return true;
905 0 : } else if(residuename=="C5") {
906 : return true;
907 0 : } else if(residuename=="C3") {
908 : return true;
909 0 : } else if(residuename=="CN") {
910 : return true;
911 0 : } else if(residuename=="RA") {
912 : return true;
913 0 : } else if(residuename=="RA5") {
914 : return true;
915 0 : } else if(residuename=="RA3") {
916 : return true;
917 0 : } else if(residuename=="RAN") {
918 : return true;
919 0 : } else if(residuename=="RG") {
920 : return true;
921 0 : } else if(residuename=="RG5") {
922 : return true;
923 0 : } else if(residuename=="RG3") {
924 : return true;
925 0 : } else if(residuename=="RGN") {
926 : return true;
927 0 : } else if(residuename=="RU") {
928 : return true;
929 0 : } else if(residuename=="RU5") {
930 : return true;
931 0 : } else if(residuename=="RU3") {
932 : return true;
933 0 : } else if(residuename=="RUN") {
934 : return true;
935 0 : } else if(residuename=="RC") {
936 : return true;
937 0 : } else if(residuename=="RC5") {
938 : return true;
939 0 : } else if(residuename=="RC3") {
940 : return true;
941 0 : } else if(residuename=="RCN") {
942 : return true;
943 : } else {
944 0 : return false;
945 : }
946 0 : } else if( type=="water" ) {
947 0 : if(residuename=="SOL") {
948 : return true;
949 : }
950 0 : if(residuename=="WAT") {
951 : return true;
952 : }
953 0 : return false;
954 0 : } else if( type=="ion" ) {
955 0 : if(residuename=="IB+") {
956 : return true;
957 : }
958 0 : if(residuename=="CA") {
959 : return true;
960 : }
961 0 : if(residuename=="CL") {
962 : return true;
963 : }
964 0 : if(residuename=="NA") {
965 : return true;
966 : }
967 0 : if(residuename=="MG") {
968 : return true;
969 : }
970 0 : if(residuename=="K") {
971 : return true;
972 : }
973 0 : if(residuename=="RB") {
974 : return true;
975 : }
976 0 : if(residuename=="CS") {
977 : return true;
978 : }
979 0 : if(residuename=="LI") {
980 : return true;
981 : }
982 0 : if(residuename=="ZN") {
983 : return true;
984 : }
985 0 : return false;
986 : }
987 : return false;
988 : }
989 :
990 : }
991 :
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