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 :
23 : #define cutOffNB 0.60 // buffer distance for neighbour-lists
24 : #define cutOffDist 0.50 // cut off distance for non-bonded pairwise forces
25 : #define cutOnDist 0.32 // cut off distance for non-bonded pairwise forces
26 : #define cutOffNB2 cutOffNB*cutOffNB // squared buffer distance for neighbour-lists
27 : #define cutOffDist2 cutOffDist*cutOffDist
28 : #define cutOnDist2 cutOnDist*cutOnDist
29 : #define invswitch 1.0/((cutOffDist2-cutOnDist2)*(cutOffDist2-cutOnDist2)*(cutOffDist2-cutOnDist2))
30 : #define cutOffDist4 cutOffDist2*cutOffDist2
31 : #define cutMixed cutOffDist2*cutOffDist2*cutOffDist2 -3.*cutOffDist2*cutOffDist2*cutOnDist2
32 :
33 : #include <string>
34 : #include <fstream>
35 : #include <iterator>
36 : #include <sstream>
37 :
38 : #include "MetainferenceBase.h"
39 : #include "core/ActionRegister.h"
40 : #include "tools/Pbc.h"
41 : #include "tools/PDB.h"
42 : #include "tools/Torsion.h"
43 : #include "tools/Communicator.h"
44 :
45 : namespace PLMD {
46 : namespace isdb {
47 :
48 : //+PLUMEDOC ISDB_COLVAR CS2BACKBONE
49 : /*
50 : Calculates the backbone chemical shifts for a protein.
51 :
52 : The functional form is that of CamShift \cite Kohlhoff:2009us. The chemical shift
53 : of the selected nuclei can be saved as components. Alternatively one can calculate either
54 : the CAMSHIFT score (useful as a collective variable \cite Granata:2013dk or as a scoring
55 : function \cite Robustelli:2010dn) or a \ref METAINFERENCE score (using DOSCORE).
56 : For these two latter cases experimental chemical shifts must be provided.
57 :
58 : CS2BACKBONE calculation can be relatively heavy because it often uses a large number of atoms, it can
59 : be run in parallel using MPI and \ref Openmp.
60 :
61 : As a general rule, when using \ref CS2BACKBONE or other experimental restraints it may be better to
62 : increase the accuracy of the constraint algorithm due to the increased strain on the bonded structure.
63 : In the case of GROMACS it is safer to use lincs-iter=2 and lincs-order=6.
64 :
65 : In general the system for which chemical shifts are calculated must be completely included in
66 : ATOMS and a TEMPLATE pdb file for the same atoms should be provided as well in the folder DATADIR.
67 : The system is made automatically whole unless NOPBC is used, in particular if the system is made
68 : by multiple chains it is usually better to use NOPBC and make the molecule whole \ref WHOLEMOLECULES
69 : selecting an appropriate order of the atoms. The pdb file is needed to the generate a simple topology of the protein.
70 : For histidine residues in protonation states different from D the HIE/HSE HIP/HSP name should be used.
71 : GLH and ASH can be used for the alternative protonation of GLU and ASP. Non-standard amino acids and other
72 : molecules are not yet supported, but in principle they can be named UNK. If multiple chains are present
73 : the chain identifier must be in the standard PDB format, together with the TER keyword at the end of each chain.
74 : Termini groups like ACE or NME should be removed from the TEMPLATE pdb because they are not recognized by
75 : CS2BACKBONE.
76 :
77 : Atoms indices in the TEMPLATE file should be numbered from 1 to N where N is the number of atoms used in ATOMS.
78 : This is not a problem for simple cases where atoms goes from 1 to N but is instead something to be carefull in case
79 : that a terminal group is removed from the PDB file.
80 :
81 : In addition to a pdb file one needs to provide a list of chemical shifts to be calculated using one
82 : file per nucleus type (CAshifts.dat, CBshifts.dat, Cshifts.dat, Hshifts.dat, HAshifts.dat, Nshifts.dat),
83 : add only the files for the nuclei you need, but each file should include all protein residues.
84 : A chemical shift for a nucleus is calculated if a value greater than 0 is provided.
85 : For practical purposes the value can correspond to the experimental value.
86 : Residues numbers should match that used in the pdb file, but must be positive, so double check the pdb.
87 : The first and last residue of each chain should be preceded by a # character.
88 :
89 : \verbatim
90 : CAshifts.dat:
91 : #1 0.0
92 : 2 55.5
93 : 3 58.4
94 : .
95 : .
96 : #last 0.0
97 : #first of second chain
98 : .
99 : #last of second chain
100 : \endverbatim
101 :
102 : The default behavior is to store the values for the active nuclei in components (ca-#, cb-#,
103 : co-#, ha-#, hn-#, nh-# and expca-#, expcb-#, expco-#, expha-#, exphn-#, exp-nh#) with NOEXP it is possible
104 : to only store the back-calculated values, where # includes a chain and residue number.
105 :
106 : One additional file is always needed in the folder DATADIR: camshift.db. This file includes all the parameters needed to
107 : calculate the chemical shifts and can be found in regtest/isdb/rt-cs2backbone/data/ .
108 :
109 : Additional material and examples can be also found in the tutorial \ref isdb-1 as well as in the cs2backbone regtests
110 : in the isdb folder.
111 :
112 : \par Examples
113 :
114 : In this first example the chemical shifts are used to calculate a collective variable to be used
115 : in NMR driven Metadynamics \cite Granata:2013dk :
116 :
117 : \plumedfile
118 : #SETTINGS AUXFOLDER=regtest/isdb/rt-cs2backbone/data
119 : whole: GROUP ATOMS=2612-2514:-1,961-1:-1,2466-962:-1,2513-2467:-1
120 : WHOLEMOLECULES ENTITY0=whole
121 : cs: CS2BACKBONE ATOMS=1-2612 DATADIR=data/ TEMPLATE=template.pdb CAMSHIFT NOPBC
122 : metad: METAD ARG=cs HEIGHT=0.5 SIGMA=0.1 PACE=200 BIASFACTOR=10
123 : PRINT ARG=cs,metad.bias FILE=COLVAR STRIDE=100
124 : \endplumedfile
125 :
126 : In this second example the chemical shifts are used as replica-averaged restrained as in \cite Camilloni:2012je \cite Camilloni:2013hs .
127 :
128 : \plumedfile
129 : #SETTINGS AUXFOLDER=regtest/isdb/rt-cs2backbone/data NREPLICAS=2
130 : cs: CS2BACKBONE ATOMS=1-174 DATADIR=data/
131 : encs: ENSEMBLE ARG=(cs\.hn-.*),(cs\.nh-.*)
132 : stcs: STATS ARG=encs.* SQDEVSUM PARARG=(cs\.exphn-.*),(cs\.expnh-.*)
133 : RESTRAINT ARG=stcs.sqdevsum AT=0 KAPPA=0 SLOPE=24
134 :
135 : PRINT ARG=(cs\.hn-.*),(cs\.nh-.*) FILE=RESTRAINT STRIDE=100
136 :
137 : \endplumedfile
138 :
139 : This third example show how to use chemical shifts to calculate a \ref METAINFERENCE score .
140 :
141 : \plumedfile
142 : #SETTINGS AUXFOLDER=regtest/isdb/rt-cs2backbone/data
143 : cs: CS2BACKBONE ATOMS=1-174 DATADIR=data/ SIGMA_MEAN0=1.0 DOSCORE
144 : csbias: BIASVALUE ARG=cs.score
145 :
146 : PRINT ARG=(cs\.hn-.*),(cs\.nh-.*) FILE=CS.dat STRIDE=1000
147 : PRINT ARG=cs.score FILE=BIAS STRIDE=100
148 : \endplumedfile
149 :
150 : */
151 : //+ENDPLUMEDOC
152 :
153 : class CS2BackboneDB {
154 : enum { STD, GLY, PRO};
155 : enum { HA_ATOM, H_ATOM, N_ATOM, CA_ATOM, CB_ATOM, C_ATOM };
156 : static const unsigned aa_kind = 3;
157 : static const unsigned atm_kind = 6;
158 : static const unsigned numXtraDists = 27;
159 :
160 : // ALA, ARG, ASN, ASP, CYS, GLU, GLN, GLY, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAL
161 : double c_aa[aa_kind][atm_kind][20];
162 : double c_aa_prev[aa_kind][atm_kind][20];
163 : double c_aa_succ[aa_kind][atm_kind][20];
164 : double co_bb[aa_kind][atm_kind][16];
165 : double co_sc_[aa_kind][atm_kind][20][20];
166 : double co_xd[aa_kind][atm_kind][numXtraDists];
167 : double co_sphere[aa_kind][atm_kind][2][8];
168 : // for ring current effects
169 : // Phe, Tyr, Trp_1, Trp_2, His
170 : double co_ring[aa_kind][atm_kind][5];
171 : // for dihedral angles
172 : // co * (a * cos(3 * omega + c) + b * cos(omega + d))
173 : double co_da[aa_kind][atm_kind][3];
174 : double pars_da[aa_kind][atm_kind][3][5];
175 :
176 : public:
177 :
178 10926 : inline unsigned kind(const std::string &s) {
179 10926 : if(s=="GLY") return GLY;
180 9324 : else if(s=="PRO") return PRO;
181 : return STD;
182 : }
183 :
184 10926 : inline unsigned atom_kind(const std::string &s) {
185 10926 : if(s=="HA")return HA_ATOM;
186 10872 : else if(s=="H") return H_ATOM;
187 8010 : else if(s=="N") return N_ATOM;
188 5148 : else if(s=="CA")return CA_ATOM;
189 2160 : else if(s=="CB")return CB_ATOM;
190 54 : else if(s=="C") return C_ATOM;
191 : return -1;
192 : }
193 :
194 : unsigned get_numXtraDists() {return numXtraDists;}
195 :
196 : //PARAMETERS
197 : inline double * CONSTAACURR(const unsigned a_kind, const unsigned at_kind) {return c_aa[a_kind][at_kind];}
198 : inline double * CONSTAANEXT(const unsigned a_kind, const unsigned at_kind) {return c_aa_succ[a_kind][at_kind];}
199 : inline double * CONSTAAPREV(const unsigned a_kind, const unsigned at_kind) {return c_aa_prev[a_kind][at_kind];}
200 : inline double * CONST_BB2(const unsigned a_kind, const unsigned at_kind) {return co_bb[a_kind][at_kind];}
201 : inline double * CONST_SC2(const unsigned a_kind, const unsigned at_kind, unsigned res_type) { return co_sc_[a_kind][at_kind][res_type];}
202 : inline double * CONST_XD(const unsigned a_kind, const unsigned at_kind) { return co_xd[a_kind][at_kind];}
203 : inline double * CO_SPHERE(const unsigned a_kind, const unsigned at_kind, unsigned exp_type) { return co_sphere[a_kind][at_kind][exp_type];}
204 : inline double * CO_RING(const unsigned a_kind, const unsigned at_kind) { return co_ring[a_kind][at_kind];}
205 : inline double * CO_DA(const unsigned a_kind, const unsigned at_kind) { return co_da[a_kind][at_kind];}
206 : inline double * PARS_DA(const unsigned a_kind, const unsigned at_kind, const unsigned ang_kind) { return pars_da[a_kind][at_kind][ang_kind];}
207 :
208 18 : void parse(const std::string &file, const double dscale) {
209 18 : std::ifstream in;
210 18 : in.open(file.c_str());
211 18 : if(!in) plumed_merror("Unable to open DB file: " + file);
212 :
213 : unsigned c_kind = 0;
214 : unsigned c_atom = 0;
215 : unsigned nline = 0;
216 :
217 396 : for(unsigned i=0; i<3; i++) for(unsigned j=0; j<6; j++) {
218 6804 : for(unsigned k=0; k<20; k++) {
219 6480 : c_aa[i][j][k]=0.;
220 6480 : c_aa_prev[i][j][k]=0.;
221 6480 : c_aa_succ[i][j][k]=0.;
222 136080 : for(unsigned m=0; m<20; m++) co_sc_[i][j][k][m]=0.;
223 : }
224 5508 : for(unsigned k=0; k<16; k++) {co_bb[i][j][k]=0.; }
225 2916 : for(unsigned k=0; k<8; k++) { co_sphere[i][j][0][k]=0.; co_sphere[i][j][1][k]=0.; }
226 1296 : for(unsigned k=0; k<3; k++) {
227 972 : co_da[i][j][k]=0.;
228 5832 : for(unsigned l=0; l<5; l++) pars_da[i][j][k][l]=0.;
229 : }
230 1944 : for(unsigned k=0; k<5; k++) co_ring[i][j][k]=0.;
231 9072 : for(unsigned k=0; k<numXtraDists; k++) co_xd[i][j][k]=0.;
232 : }
233 :
234 37710 : while(!in.eof()) {
235 : std::string line;
236 37692 : getline(in,line);
237 : ++nline;
238 37692 : if(line.compare(0,1,"#")==0) continue;
239 : std::vector<std::string> tok;
240 : std::vector<std::string> tmp;
241 40860 : tok = split(line,' ');
242 261828 : for(unsigned q=0; q<tok.size(); q++)
243 241398 : if(tok[q].size()) tmp.push_back(tok[q]);
244 20430 : tok = tmp;
245 20430 : if(tok.size()==0) continue;
246 20412 : if(tok[0]=="PAR") {
247 324 : c_kind = kind(tok[2]);
248 324 : c_atom = atom_kind(tok[1]);
249 324 : continue;
250 : }
251 20088 : else if(tok[0]=="WEIGHT") {
252 324 : continue;
253 : }
254 19764 : else if(tok[0]=="FLATBTM") {
255 324 : continue;
256 : }
257 19440 : else if (tok[0] == "SCALEHARM") {
258 324 : continue;
259 : }
260 19116 : else if (tok[0] == "TANHAMPLI") {
261 324 : continue;
262 : }
263 18792 : else if (tok[0] == "ENDHARMON") {
264 324 : continue;
265 : }
266 18468 : else if (tok[0] == "MAXRCDEVI") {
267 324 : continue;
268 : }
269 18144 : else if (tok[0] == "RANDCOIL") {
270 324 : continue;
271 : }
272 17820 : else if (tok[0] == "CONST") {
273 324 : continue;
274 : }
275 17496 : else if (tok[0] == "CONSTAA") {
276 324 : assign(c_aa[c_kind][c_atom],tok,1);
277 324 : continue;
278 : }
279 17172 : else if (tok[0] == "CONSTAA-1") {
280 324 : assign(c_aa_prev[c_kind][c_atom],tok,1);
281 324 : continue;
282 : }
283 16848 : else if (tok[0] == "CONSTAA+1") {
284 324 : assign(c_aa_succ[c_kind][c_atom],tok,1);
285 324 : continue;
286 : }
287 16524 : else if (tok[0] == "COBB1") {
288 324 : continue;
289 : }
290 16200 : else if (tok[0] == "COBB2") {
291 : //angstrom to nm
292 324 : assign(co_bb[c_kind][c_atom],tok,dscale);
293 324 : continue;
294 : }
295 15876 : else if (tok[0] == "SPHERE1") {
296 : // angstrom^-3 to nm^-3
297 324 : assign(co_sphere[c_kind][c_atom][0],tok,1./(dscale*dscale*dscale));
298 324 : continue;
299 : }
300 15552 : else if (tok[0] == "SPHERE2") {
301 : //angstrom to nm
302 324 : assign(co_sphere[c_kind][c_atom][1],tok,dscale);
303 324 : continue;
304 : }
305 15228 : else if (tok[0] == "DIHEDRALS") {
306 324 : assign(co_da[c_kind][c_atom],tok,1);
307 324 : continue;
308 : }
309 14904 : else if (tok[0] == "RINGS") {
310 : // angstrom^-3 to nm^-3
311 324 : assign(co_ring[c_kind][c_atom],tok,1./(dscale*dscale*dscale));
312 1944 : for(unsigned i=1; i<tok.size(); i++)
313 1620 : co_ring[c_kind][c_atom][i-1] *= 1000;
314 324 : continue;
315 324 : }
316 14580 : else if (tok[0] == "HBONDS") {
317 324 : continue;
318 : }
319 14256 : else if (tok[0] == "XTRADISTS") {
320 : //angstrom to nm
321 324 : assign(co_xd[c_kind][c_atom],tok,dscale);
322 324 : continue;
323 : }
324 13932 : else if(tok[0]=="DIHEDPHI") {
325 324 : assign(pars_da[c_kind][c_atom][0],tok,1);
326 324 : continue;
327 : }
328 13608 : else if(tok[0]=="DIHEDPSI") {
329 324 : assign(pars_da[c_kind][c_atom][1],tok,1);
330 324 : continue;
331 : }
332 13284 : else if(tok[0]=="DIHEDCHI1") {
333 324 : assign(pars_da[c_kind][c_atom][2],tok,1);
334 324 : continue;
335 : }
336 :
337 : bool ok = false;
338 : const std::string scIdent1 [] = {"COSCALA1", "COSCARG1", "COSCASN1", "COSCASP1", "COSCCYS1", "COSCGLN1", "COSCGLU1",
339 : "COSCGLY1", "COSCHIS1", "COSCILE1", "COSCLEU1", "COSCLYS1", "COSCMET1", "COSCPHE1",
340 : "COSCPRO1", "COSCSER1", "COSCTHR1", "COSCTRP1", "COSCTYR1", "COSCVAL1"
341 272160 : };
342 :
343 204120 : for(unsigned scC = 0; scC < 20; scC++) {
344 197640 : if(tok[0]==scIdent1[scC]) {
345 : ok = true;
346 : break;
347 : }
348 : }
349 285120 : if(ok) continue;
350 :
351 : const std::string scIdent2 [] = {"COSCALA2", "COSCARG2", "COSCASN2", "COSCASP2", "COSCCYS2", "COSCGLN2", "COSCGLU2",
352 : "COSCGLY2", "COSCHIS2", "COSCILE2", "COSCLEU2", "COSCLYS2", "COSCMET2", "COSCPHE2",
353 : "COSCPRO2", "COSCSER2", "COSCTHR2", "COSCTRP2", "COSCTYR2", "COSCVAL2"
354 136080 : };
355 :
356 68040 : for(unsigned scC = 0; scC < 20; scC++) {
357 68040 : if(tok[0]==scIdent2[scC]) {
358 : //angstrom to nm
359 6480 : assign(co_sc_[c_kind][c_atom][scC],tok,dscale);
360 : ok = true; break;
361 : }
362 : }
363 142560 : if(ok) continue;
364 :
365 0 : if(tok.size()) {
366 0 : std::string str_err = "DB WARNING: unrecognized token: " + tok[0];
367 0 : plumed_merror(str_err);
368 : }
369 428670 : }
370 18 : in.close();
371 18 : }
372 :
373 : private:
374 :
375 20430 : std::vector<std::string> &split(const std::string &s, char delim, std::vector<std::string> &elems) {
376 20430 : std::stringstream ss(s);
377 : std::string item;
378 261828 : while (getline(ss, item, delim)) {
379 241398 : elems.push_back(item);
380 : }
381 20430 : return elems;
382 20430 : }
383 :
384 20430 : std::vector<std::string> split(const std::string &s, char delim) {
385 : std::vector<std::string> elems;
386 20430 : split(s, delim, elems);
387 20430 : return elems;
388 0 : }
389 :
390 10368 : void assign(double * f, const std::vector<std::string> & v, const double scale) {
391 122796 : for(unsigned i=1; i<v.size(); i++) {
392 112428 : f[i-1] = scale*(atof(v[i].c_str()));
393 112428 : if(std::abs(f[i-1])<0.000001) f[i-1]=0.;
394 : }
395 10368 : }
396 : };
397 :
398 : class CS2Backbone : public MetainferenceBase {
399 : struct ChemicalShift {
400 : double exp_cs; // a reference chemical shifts
401 : Value *comp; // a pointer to the component
402 : unsigned res_kind; // residue type (STD/GLY/PRO)
403 : unsigned atm_kind; // nuclues (HA/CA/CB/CO/NH/HN)
404 : unsigned res_type_prev; // previous residue (ALA/VAL/..)
405 : unsigned res_type_curr; // current residue (ALA/VAL/..)
406 : unsigned res_type_next; // next residue (ALA/VAL/..)
407 : std::string res_name; // residue name
408 : std::string nucleus; // chemical shift
409 : bool has_chi1; // does we have a chi1
410 : unsigned csatoms; // fixed number of atoms used
411 : unsigned totcsatoms; // number of atoms used
412 : unsigned res_num; // residue number
413 : unsigned chain; // chain number
414 : unsigned ipos; // index of the atom for which we are calculating the chemical shifts
415 : std::vector<unsigned> bb; // atoms for the previous, current and next backbone
416 : std::vector<unsigned> side_chain;// atoms for the current sidechain
417 : std::vector<int> xd1; // additional couple of atoms
418 : std::vector<int> xd2; // additional couple of atoms
419 : std::vector<unsigned> box_nb; // non-bonded atoms
420 :
421 10602 : ChemicalShift():
422 10602 : exp_cs(0.),
423 10602 : comp(NULL),
424 10602 : res_kind(0),
425 10602 : atm_kind(0),
426 10602 : res_type_prev(0),
427 10602 : res_type_curr(0),
428 10602 : res_type_next(0),
429 10602 : res_name(""),
430 10602 : nucleus(""),
431 10602 : has_chi1(true),
432 10602 : csatoms(0),
433 10602 : totcsatoms(0),
434 10602 : res_num(0),
435 10602 : chain(0),
436 10602 : ipos(0)
437 : {
438 10602 : xd1.reserve(26);
439 10602 : xd2.reserve(26);
440 10602 : box_nb.reserve(150);
441 10602 : }
442 : };
443 :
444 : struct RingInfo {
445 : enum {R_PHE, R_TYR, R_TRP1, R_TRP2, R_HIS};
446 : unsigned rtype; // one out of five different types
447 : unsigned atom[6]; // up to six member per ring
448 : unsigned numAtoms; // number of ring members (5 or 6)
449 : Vector position; // center of ring coordinates
450 : Vector normVect; // ring plane normal std::vector
451 : Vector g[6]; // std::vector of the std::vectors used for normVect
452 : double lengthN2; // square of length of normVect
453 : double lengthNV; // length of normVect
454 360 : RingInfo():
455 360 : rtype(0),
456 360 : numAtoms(0),
457 360 : lengthN2(NAN),
458 2520 : lengthNV(NAN)
459 : {
460 2520 : for(unsigned i=0; i<6; i++) atom[i]=0;
461 360 : }
462 : };
463 :
464 : enum aa_t {ALA, ARG, ASN, ASP, CYS, GLN, GLU, GLY, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAL, UNK};
465 : enum sequence_t {Np, CAp, HAp, Cp, Op, Nc, Hc, CAc, HAc, Cc, Oc, Nn, Hn, CAn, HAn, Cn, CBc, CGc};
466 :
467 : CS2BackboneDB db;
468 : std::vector<ChemicalShift> chemicalshifts;
469 :
470 : std::vector<RingInfo> ringInfo;
471 : std::vector<unsigned> type;
472 : std::vector<unsigned> res_num;
473 : unsigned max_cs_atoms;
474 : unsigned box_nupdate;
475 : unsigned box_count;
476 : bool camshift;
477 : bool pbc;
478 : bool serial;
479 :
480 : void init_cs(const std::string &file, const std::string &k, const PDB &pdb);
481 : void update_neighb();
482 : void compute_ring_parameters();
483 : void init_types(const PDB &pdb);
484 : void init_rings(const PDB &pdb);
485 : aa_t frag2enum(const std::string &aa);
486 : std::vector<std::string> side_chain_atoms(const std::string &s);
487 : bool isSP2(const std::string & resType, const std::string & atomName);
488 : bool is_chi1_cx(const std::string & frg, const std::string & atm);
489 : void xdist_name_map(std::string & name);
490 :
491 : public:
492 :
493 : explicit CS2Backbone(const ActionOptions&);
494 : static void registerKeywords( Keywords& keys );
495 : void calculate() override;
496 : void update() override;
497 : };
498 :
499 : PLUMED_REGISTER_ACTION(CS2Backbone,"CS2BACKBONE")
500 :
501 20 : void CS2Backbone::registerKeywords( Keywords& keys ) {
502 20 : MetainferenceBase::registerKeywords( keys );
503 40 : keys.addFlag("NOPBC",false,"ignore the periodic boundary conditions when calculating distances");
504 40 : keys.addFlag("SERIAL",false,"Perform the calculation in serial - for debug purpose");
505 40 : keys.add("atoms","ATOMS","The atoms to be included in the calculation, e.g. the whole protein.");
506 40 : keys.add("compulsory","DATADIR","data/","The folder with the experimental chemical shifts.");
507 40 : keys.add("compulsory","TEMPLATE","template.pdb","A PDB file of the protein system.");
508 40 : keys.add("compulsory","NEIGH_FREQ","20","Period in step for neighbor list update.");
509 40 : keys.addFlag("CAMSHIFT",false,"Set to TRUE if you to calculate a single CamShift score.");
510 40 : keys.addFlag("NOEXP",false,"Set to TRUE if you don't want to have fixed components with the experimental values.");
511 40 : keys.addOutputComponent("ha","default","scalar","the calculated Ha hydrogen chemical shifts");
512 40 : keys.addOutputComponent("hn","default","scalar","the calculated H hydrogen chemical shifts");
513 40 : keys.addOutputComponent("nh","default","scalar","the calculated N nitrogen chemical shifts");
514 40 : keys.addOutputComponent("ca","default","scalar","the calculated Ca carbon chemical shifts");
515 40 : keys.addOutputComponent("cb","default","scalar","the calculated Cb carbon chemical shifts");
516 40 : keys.addOutputComponent("co","default","scalar","the calculated C' carbon chemical shifts");
517 40 : keys.addOutputComponent("expha","default","scalar","the experimental Ha hydrogen chemical shifts");
518 40 : keys.addOutputComponent("exphn","default","scalar","the experimental H hydrogen chemical shifts");
519 40 : keys.addOutputComponent("expnh","default","scalar","the experimental N nitrogen chemical shifts");
520 40 : keys.addOutputComponent("expca","default","scalar","the experimental Ca carbon chemical shifts");
521 40 : keys.addOutputComponent("expcb","default","scalar","the experimental Cb carbon chemical shifts");
522 40 : keys.addOutputComponent("expco","default","scalar","the experimental C' carbon chemical shifts");
523 40 : keys.setValueDescription("scalar","the backbone chemical shifts");
524 20 : }
525 :
526 18 : CS2Backbone::CS2Backbone(const ActionOptions&ao):
527 : PLUMED_METAINF_INIT(ao),
528 18 : max_cs_atoms(0),
529 18 : camshift(false),
530 18 : pbc(true),
531 18 : serial(false)
532 : {
533 : std::vector<AtomNumber> used_atoms;
534 18 : parseAtomList("ATOMS",used_atoms);
535 :
536 18 : parseFlag("CAMSHIFT",camshift);
537 18 : if(camshift&&getDoScore()) plumed_merror("It is not possible to use CAMSHIFT and DOSCORE at the same time");
538 :
539 18 : bool nopbc=!pbc;
540 18 : parseFlag("NOPBC",nopbc);
541 18 : pbc=!nopbc;
542 :
543 18 : parseFlag("SERIAL",serial);
544 :
545 18 : bool noexp=false;
546 36 : parseFlag("NOEXP",noexp);
547 :
548 : std::string stringa_data;
549 36 : parse("DATADIR",stringa_data);
550 :
551 : std::string stringa_template;
552 18 : parse("TEMPLATE",stringa_template);
553 :
554 18 : box_count=0;
555 18 : box_nupdate=20;
556 18 : parse("NEIGH_FREQ", box_nupdate);
557 :
558 18 : std::string stringadb = stringa_data + std::string("/camshift.db");
559 36 : std::string stringapdb = stringa_data + std::string("/") + stringa_template;
560 :
561 : /* Length conversion (parameters are tuned for angstrom) */
562 : double scale=1.;
563 18 : if(!usingNaturalUnits()) {
564 18 : scale = 10.*getUnits().getLength();
565 : }
566 :
567 18 : log.printf(" Initialization of the predictor ...\n");
568 18 : db.parse(stringadb,scale);
569 :
570 18 : PDB pdb;
571 18 : if( !pdb.read(stringapdb,usingNaturalUnits(),1./scale) ) plumed_merror("missing input file " + stringapdb);
572 :
573 : // first of all we build the list of chemical shifts we want to predict
574 18 : log.printf(" Reading experimental data ...\n"); log.flush();
575 36 : stringadb = stringa_data + std::string("/CAshifts.dat");
576 18 : log.printf(" Initializing CA shifts %s\n", stringadb.c_str());
577 18 : init_cs(stringadb, "CA", pdb);
578 36 : stringadb = stringa_data + std::string("/CBshifts.dat");
579 18 : log.printf(" Initializing CB shifts %s\n", stringadb.c_str());
580 18 : init_cs(stringadb, "CB", pdb);
581 36 : stringadb = stringa_data + std::string("/Cshifts.dat");
582 18 : log.printf(" Initializing C' shifts %s\n", stringadb.c_str());
583 18 : init_cs(stringadb, "C", pdb);
584 36 : stringadb = stringa_data + std::string("/HAshifts.dat");
585 18 : log.printf(" Initializing HA shifts %s\n", stringadb.c_str());
586 18 : init_cs(stringadb, "HA", pdb);
587 36 : stringadb = stringa_data + std::string("/Hshifts.dat");
588 18 : log.printf(" Initializing H shifts %s\n", stringadb.c_str());
589 18 : init_cs(stringadb, "H", pdb);
590 36 : stringadb = stringa_data + std::string("/Nshifts.dat");
591 18 : log.printf(" Initializing N shifts %s\n", stringadb.c_str());
592 36 : init_cs(stringadb, "N", pdb);
593 :
594 18 : if(chemicalshifts.size()==0) plumed_merror("There are no chemical shifts to calculate, there must be at least a not empty file (CA|CB|C|HA|H|N|shifts.dat)");
595 :
596 18 : init_types(pdb);
597 18 : init_rings(pdb);
598 :
599 18 : log<<" Bibliography "
600 36 : <<plumed.cite("Kohlhoff K, Robustelli P, Cavalli A, Salvatella A, Vendruscolo M, J. Am. Chem. Soc. 131, 13894 (2009)");
601 23 : if(camshift) log<<plumed.cite("Granata D, Camilloni C, Vendruscolo M, Laio A, Proc. Natl. Acad. Sci. USA 110, 6817 (2013)");
602 26 : else log<<plumed.cite("Camilloni C, Robustelli P, De Simone A, Cavalli A, Vendruscolo M, J. Am. Chem. Soc. 134, 3968 (2012)");
603 36 : log<<plumed.cite("Bonomi M, Camilloni C, Bioinformatics, 33, 3999 (2017)");
604 18 : log<<"\n";
605 :
606 18 : if(camshift) {
607 5 : noexp = true;
608 5 : addValueWithDerivatives();
609 5 : setNotPeriodic();
610 : } else {
611 7670 : for(unsigned cs=0; cs<chemicalshifts.size(); cs++) {
612 7657 : std::string num; Tools::convert(chemicalshifts[cs].res_num,num);
613 7657 : std::string chain_num; Tools::convert(chemicalshifts[cs].chain,chain_num);
614 7657 : if(getDoScore()) {
615 4712 : addComponent(chemicalshifts[cs].nucleus+chain_num+"-"+num);
616 4712 : componentIsNotPeriodic(chemicalshifts[cs].nucleus+chain_num+"-"+num);
617 2356 : chemicalshifts[cs].comp = getPntrToComponent(chemicalshifts[cs].nucleus+chain_num+"-"+num);
618 4712 : setParameter(chemicalshifts[cs].exp_cs);
619 : } else {
620 10602 : addComponentWithDerivatives(chemicalshifts[cs].nucleus+chain_num+"-"+num);
621 10602 : componentIsNotPeriodic(chemicalshifts[cs].nucleus+chain_num+"-"+num);
622 5301 : chemicalshifts[cs].comp = getPntrToComponent(chemicalshifts[cs].nucleus+chain_num+"-"+num);
623 : }
624 : }
625 13 : if(getDoScore()) Initialise(chemicalshifts.size());
626 : }
627 :
628 18 : if(!noexp) {
629 7670 : for(unsigned cs=0; cs<chemicalshifts.size(); cs++) {
630 7657 : std::string num; Tools::convert(chemicalshifts[cs].res_num,num);
631 7657 : std::string chain_num; Tools::convert(chemicalshifts[cs].chain,chain_num);
632 15314 : addComponent("exp"+chemicalshifts[cs].nucleus+chain_num+"-"+num);
633 15314 : componentIsNotPeriodic("exp"+chemicalshifts[cs].nucleus+chain_num+"-"+num);
634 15314 : Value* comp=getPntrToComponent("exp"+chemicalshifts[cs].nucleus+chain_num+"-"+num);
635 7657 : comp->set(chemicalshifts[cs].exp_cs);
636 : }
637 : }
638 :
639 18 : requestAtoms(used_atoms, false);
640 18 : setDerivatives();
641 18 : checkRead();
642 36 : }
643 :
644 108 : void CS2Backbone::init_cs(const std::string &file, const std::string &nucl, const PDB &pdb) {
645 : // number of chains
646 : std::vector<std::string> chains;
647 108 : pdb.getChainNames( chains );
648 : unsigned ichain=0;
649 :
650 108 : std::ifstream in;
651 108 : in.open(file.c_str());
652 108 : if(!in) return;
653 108 : std::istream_iterator<std::string> iter(in), end;
654 : unsigned begin=0;
655 :
656 108 : while(iter!=end) {
657 19008 : std::string tok = *iter;
658 : ++iter;
659 19008 : if(tok[0]=='#') {
660 : ++iter;
661 432 : if(begin==1) {
662 : begin=0;
663 216 : ichain++;
664 : } else begin=1;
665 432 : continue;
666 : }
667 : int ro = atoi(tok.c_str());
668 18576 : if(ro<0) plumed_merror("Residue numbers should be positive\n");
669 18576 : unsigned resnum = static_cast<unsigned> (ro);
670 : tok = *iter;
671 : ++iter;
672 : double cs = atof(tok.c_str());
673 18576 : if(cs==0) continue;
674 :
675 : unsigned fres, lres;
676 : std::string errmsg;
677 11070 : pdb.getResidueRange(chains[ichain], fres, lres, errmsg);
678 11070 : if(resnum==fres||resnum==lres) plumed_merror("First and Last residue of each chain should be annotated as # in " + file + " Remember that residue numbers should match");
679 :
680 : // check in the PDB for the chain/residue/atom and enable the chemical shift
681 11070 : std::string RES = pdb.getResidueName(resnum, chains[ichain]);
682 98766 : if(RES=="HIE"||RES=="HIP"||RES=="HIS"||RES=="HSP"||RES=="HSE"||RES=="CYS"||RES=="GLH"||RES=="ASH"||RES=="UNK") continue;
683 10944 : if(RES=="GLN"&&nucl=="CB") continue;
684 11322 : if(RES=="ILE"&&nucl=="CB") continue;
685 10998 : if(RES=="PRO"&&nucl=="N") continue;
686 10998 : if(RES=="PRO"&&nucl=="H") continue;
687 10998 : if(RES=="PRO"&&nucl=="CB") continue;
688 12240 : if(RES=="GLY"&&nucl=="HA") continue;
689 12240 : if(RES=="GLY"&&nucl=="CB") continue;
690 :
691 10602 : ChemicalShift tmp_cs;
692 :
693 10602 : tmp_cs.exp_cs = cs;
694 10602 : if(nucl=="CA") tmp_cs.nucleus = "ca-";
695 7668 : else if(nucl=="CB") tmp_cs.nucleus = "cb-";
696 5616 : else if(nucl=="C") tmp_cs.nucleus = "co-";
697 5616 : else if(nucl=="HA") tmp_cs.nucleus = "ha-";
698 5616 : else if(nucl=="H") tmp_cs.nucleus = "hn-";
699 2808 : else if(nucl=="N") tmp_cs.nucleus = "nh-";
700 10602 : tmp_cs.chain = ichain;
701 10602 : tmp_cs.res_num = resnum;
702 10602 : tmp_cs.res_type_curr = frag2enum(RES);
703 10602 : tmp_cs.res_type_prev = frag2enum(pdb.getResidueName(resnum-1, chains[ichain]));
704 10602 : tmp_cs.res_type_next = frag2enum(pdb.getResidueName(resnum+1, chains[ichain]));
705 : tmp_cs.res_name = RES;
706 10602 : tmp_cs.res_kind = db.kind(RES);
707 10602 : tmp_cs.atm_kind = db.atom_kind(nucl);
708 20556 : if(RES!="ALA"&&RES!="GLY") {tmp_cs.bb.resize(18); tmp_cs.has_chi1=true;}
709 2142 : else {tmp_cs.bb.resize(16); tmp_cs.has_chi1=false;}
710 :
711 10602 : std::vector<AtomNumber> res_atoms = pdb.getAtomsInResidue(resnum, chains[ichain]);
712 : // find the position of the nucleus and of the other backbone atoms as well as for phi/psi/chi
713 173268 : for(unsigned a=0; a<res_atoms.size(); a++) {
714 162666 : std::string AN = pdb.getAtomName(res_atoms[a]);
715 162666 : if(nucl=="HA"&&(AN=="HA"||AN=="HA1"||AN=="HA3")) tmp_cs.ipos = res_atoms[a].index();
716 244530 : else if(nucl=="H"&&(AN=="H"||AN=="HN")) tmp_cs.ipos = res_atoms[a].index();
717 202248 : else if(nucl=="N"&&AN=="N") tmp_cs.ipos = res_atoms[a].index();
718 200862 : else if(nucl=="CA"&&AN=="CA") tmp_cs.ipos = res_atoms[a].index();
719 188244 : else if(nucl=="CB"&&AN=="CB") tmp_cs.ipos = res_atoms[a].index();
720 152064 : else if(nucl=="C"&&AN=="C" ) tmp_cs.ipos = res_atoms[a].index();
721 : }
722 :
723 10602 : std::vector<AtomNumber> prev_res_atoms = pdb.getAtomsInResidue(resnum-1, chains[ichain]);
724 : // find the position of the previous residues backbone atoms
725 168498 : for(unsigned a=0; a<prev_res_atoms.size(); a++) {
726 157896 : std::string AN = pdb.getAtomName(prev_res_atoms[a]);
727 157896 : if(AN=="N") { tmp_cs.bb[Np] = prev_res_atoms[a].index(); }
728 147294 : else if(AN=="CA") { tmp_cs.bb[CAp] = prev_res_atoms[a].index(); }
729 390690 : else if(AN=="HA"||AN=="HA1"||AN=="HA3") { tmp_cs.bb[HAp] = prev_res_atoms[a].index(); }
730 126090 : else if(AN=="C" ) { tmp_cs.bb[Cp] = prev_res_atoms[a].index(); }
731 115488 : else if(AN=="O" ) { tmp_cs.bb[Op] = prev_res_atoms[a].index(); }
732 : }
733 :
734 173268 : for(unsigned a=0; a<res_atoms.size(); a++) {
735 162666 : std::string AN = pdb.getAtomName(res_atoms[a]);
736 162666 : if(AN=="N") { tmp_cs.bb[Nc] = res_atoms[a].index(); }
737 438282 : else if(AN=="H" ||AN=="HN"||(AN=="CD"&&RES=="PRO")) { tmp_cs.bb[Hc] = res_atoms[a].index(); }
738 141462 : else if(AN=="CA") { tmp_cs.bb[CAc] = res_atoms[a].index(); }
739 372870 : else if(AN=="HA"||AN=="HA1"||AN=="HA3") { tmp_cs.bb[HAc] = res_atoms[a].index(); }
740 120258 : else if(AN=="C" ) { tmp_cs.bb[Cc] = res_atoms[a].index(); }
741 109656 : else if(AN=="O" ) { tmp_cs.bb[Oc] = res_atoms[a].index(); }
742 :
743 318852 : if(RES!="ALA"&&RES!="GLY") {
744 145728 : if(AN=="CB") tmp_cs.bb[CBc] = res_atoms[a].index();
745 145728 : if(is_chi1_cx(RES,AN)) tmp_cs.bb[CGc] = res_atoms[a].index();
746 : }
747 : }
748 :
749 10602 : std::vector<AtomNumber> next_res_atoms = pdb.getAtomsInResidue(resnum+1, chains[ichain]);
750 10602 : std::string NRES = pdb.getResidueName(resnum+1, chains[ichain]);
751 : // find the position of the previous residues backbone atoms
752 168948 : for(unsigned a=0; a<next_res_atoms.size(); a++) {
753 158346 : std::string AN = pdb.getAtomName(next_res_atoms[a]);
754 158346 : if(AN=="N") { tmp_cs.bb[Nn] = next_res_atoms[a].index(); }
755 426096 : else if(AN=="H" ||AN=="HN"||(AN=="CD"&&NRES=="PRO")) { tmp_cs.bb[Hn] = next_res_atoms[a].index(); }
756 137142 : else if(AN=="CA") { tmp_cs.bb[CAn] = next_res_atoms[a].index(); }
757 360198 : else if(AN=="HA"||AN=="HA1"||AN=="HA3") { tmp_cs.bb[HAn] = next_res_atoms[a].index(); }
758 115938 : else if(AN=="C" ) { tmp_cs.bb[Cn] = next_res_atoms[a].index(); }
759 : }
760 :
761 : // set sidechain atoms
762 10602 : std::vector<std::string> sc_atm = side_chain_atoms(RES);
763 :
764 141084 : for(unsigned sc=0; sc<sc_atm.size(); sc++) {
765 2501208 : for(unsigned aa=0; aa<res_atoms.size(); aa++) {
766 2370726 : if(pdb.getAtomName(res_atoms[aa])==sc_atm[sc]) {
767 99162 : tmp_cs.side_chain.push_back(res_atoms[aa].index());
768 : }
769 : }
770 : }
771 :
772 : // find atoms for extra distances
773 286254 : const std::string atomsP1[] = {"H", "H", "H", "C", "C", "C", "O", "O", "O", "N", "N", "N", "O", "O", "O", "N", "N", "N", "CG", "CG", "CG", "CG", "CG", "CG", "CG", "CA"};
774 10602 : const int resOffsetP1[] = { 0, 0, 0, -1, -1, -1, 0, 0, 0, 1, 1, 1, -1, -1, -1, 0, 0, 0, 0, 0, 0, 0, 0, -1, 1, -1};
775 :
776 286254 : const std::string atomsP2[] = {"HA", "C", "CB", "HA", "C", "CB", "HA", "N", "CB", "HA", "N", "CB", "HA", "N", "CB", "HA", "N", "CB", "HA", "N", "C", "C", "N", "CA", "CA", "CA"};
777 10602 : const int resOffsetP2[] = { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -1, -1, -1, -1, -1, -1, 0, 0, 0, -1, 1, 0, 0, 1};
778 :
779 286254 : for(unsigned q=0; q<db.get_numXtraDists()-1; q++) {
780 : std::vector<AtomNumber> at1;
781 275652 : if(resOffsetP1[q]== 0) at1 = res_atoms;
782 275652 : if(resOffsetP1[q]==-1) at1 = prev_res_atoms;
783 275652 : if(resOffsetP1[q]==+1) at1 = next_res_atoms;
784 :
785 : std::vector<AtomNumber> at2;
786 275652 : if(resOffsetP2[q]== 0) at2 = res_atoms;
787 275652 : if(resOffsetP2[q]==-1) at2 = prev_res_atoms;
788 275652 : if(resOffsetP2[q]==+1) at2 = next_res_atoms;
789 :
790 275652 : int tmp1 = -1;
791 2197566 : for(unsigned a=0; a<at1.size(); a++) {
792 2181708 : std::string name = pdb.getAtomName(at1[a]);
793 2181708 : xdist_name_map(name);
794 :
795 2181708 : if(name==atomsP1[q]) {
796 259794 : tmp1 = at1[a].index();
797 : break;
798 : }
799 : }
800 :
801 275652 : int tmp2 = -1;
802 1427688 : for(unsigned a=0; a<at2.size(); a++) {
803 1418076 : std::string name = pdb.getAtomName(at2[a]);
804 1418076 : xdist_name_map(name);
805 :
806 1418076 : if(name==atomsP2[q]) {
807 266040 : tmp2 = at2[a].index();
808 : break;
809 : }
810 : }
811 :
812 275652 : tmp_cs.xd1.push_back(tmp1);
813 275652 : tmp_cs.xd2.push_back(tmp2);
814 : }
815 :
816 : // ready to add a new chemical shifts
817 10602 : tmp_cs.csatoms = 1 + 16 + tmp_cs.side_chain.size() + 2*tmp_cs.xd1.size();
818 20556 : if(tmp_cs.res_name!="ALA"&&tmp_cs.res_name!="GLY") tmp_cs.csatoms += 2;
819 10602 : chemicalshifts.push_back(tmp_cs);
820 593712 : }
821 :
822 108 : in.close();
823 108 : }
824 :
825 : // this assigns an atom-type to each atom of the pdb
826 18 : void CS2Backbone::init_types(const PDB &pdb) {
827 : enum atom_t {D_C, D_H, D_N, D_O, D_S, D_C2, D_N2, D_O2};
828 18 : std::vector<AtomNumber> aa = pdb.getAtomNumbers();
829 47034 : for(unsigned i=0; i<aa.size(); i++) {
830 47016 : unsigned frag = pdb.getResidueNumber(aa[i]);
831 47016 : std::string fragName = pdb.getResidueName(aa[i]);
832 47016 : std::string atom_name = pdb.getAtomName(aa[i]);
833 47016 : char atom_type = atom_name[0];
834 47016 : if(isdigit(atom_name[0])) atom_type = atom_name[1];
835 47016 : res_num.push_back(frag);
836 47016 : unsigned t = 0;
837 47016 : if (!isSP2(fragName, atom_name)) {
838 : if (atom_type == 'C') t = D_C;
839 468 : else if (atom_type == 'O') t = D_O;
840 23256 : else if (atom_type == 'H') t = D_H;
841 4032 : else if (atom_type == 'N') t = D_N;
842 162 : else if (atom_type == 'S') t = D_S;
843 0 : else plumed_merror("Unknown atom type: " + atom_name);
844 : } else {
845 10080 : if (atom_type == 'C') t = D_C2;
846 4104 : else if (atom_type == 'O') t = D_O2;
847 0 : else if (atom_type == 'N') t = D_N2;
848 0 : else plumed_merror("Unknown atom type: " + atom_name);
849 : }
850 47016 : type.push_back(t);
851 : }
852 18 : }
853 :
854 18 : void CS2Backbone::init_rings(const PDB &pdb)
855 : {
856 126 : const std::string pheTyr_n[] = {"CG","CD1","CE1","CZ","CE2","CD2"};
857 126 : const std::string trp1_n[] = {"CD2","CE2","CZ2","CH2","CZ3","CE3"};
858 108 : const std::string trp2_n[] = {"CG","CD1","NE1","CE2","CD2"};
859 108 : const std::string his_n[] = {"CG","ND1","CD2","CE1","NE2"};
860 :
861 : // number of chains
862 : std::vector<std::string> chains;
863 18 : pdb.getChainNames( chains );
864 : unsigned total_rings_atoms = 0;
865 :
866 : // cycle over chains
867 54 : for(unsigned i=0; i<chains.size(); i++) {
868 : unsigned start, end;
869 : std::string errmsg;
870 36 : pdb.getResidueRange( chains[i], start, end, errmsg );
871 : // cycle over residues
872 3168 : for(unsigned res=start; res<end; res++) {
873 3132 : std::string frg = pdb.getResidueName(res, chains[i]);
874 14364 : if(!((frg=="PHE")||(frg=="TYR")||(frg=="TRP")||
875 8370 : (frg=="HIS")||(frg=="HIP")||(frg=="HID")||
876 5580 : (frg=="HIE")||(frg=="HSD")||(frg=="HSE")||
877 : (frg=="HSP"))) continue;
878 :
879 342 : std::vector<AtomNumber> frg_atoms = pdb.getAtomsInResidue(res,chains[i]);
880 :
881 396 : if(frg=="PHE"||frg=="TYR") {
882 324 : RingInfo ri;
883 6840 : for(unsigned a=0; a<frg_atoms.size(); a++) {
884 : unsigned atm = frg_atoms[a].index();
885 38808 : for(unsigned aa=0; aa<6; aa++) {
886 34236 : if(pdb.getAtomName(frg_atoms[a])==pheTyr_n[aa]) {
887 1944 : ri.atom[aa] = atm;
888 1944 : break;
889 : }
890 : }
891 : }
892 324 : ri.numAtoms = 6;
893 324 : total_rings_atoms += 6;
894 324 : if(frg=="PHE") ri.rtype = RingInfo::R_PHE;
895 324 : if(frg=="TYR") ri.rtype = RingInfo::R_TYR;
896 324 : ringInfo.push_back(ri);
897 :
898 18 : } else if(frg=="TRP") {
899 : //First ring
900 18 : RingInfo ri;
901 450 : for(unsigned a=0; a<frg_atoms.size(); a++) {
902 : unsigned atm = frg_atoms[a].index();
903 2646 : for(unsigned aa=0; aa<6; aa++) {
904 2322 : if(pdb.getAtomName(frg_atoms[a])==trp1_n[aa]) {
905 108 : ri.atom[aa] = atm;
906 108 : break;
907 : }
908 : }
909 : }
910 18 : ri.numAtoms = 6;
911 : total_rings_atoms += 6;
912 18 : ri.rtype = RingInfo::R_TRP1;
913 18 : ringInfo.push_back(ri);
914 : //Second Ring
915 18 : RingInfo ri2;
916 450 : for(unsigned a=0; a<frg_atoms.size(); a++) {
917 : unsigned atm = frg_atoms[a].index();
918 2322 : for(unsigned aa=0; aa<5; aa++) {
919 1980 : if(pdb.getAtomName(frg_atoms[a])==trp2_n[aa]) {
920 90 : ri2.atom[aa] = atm;
921 90 : break;
922 : }
923 : }
924 : }
925 18 : ri2.numAtoms = 5;
926 18 : total_rings_atoms += 3;
927 18 : ri2.rtype = RingInfo::R_TRP2;
928 18 : ringInfo.push_back(ri2);
929 :
930 0 : } else if((frg=="HIS")||(frg=="HIP")||(frg=="HID")||
931 0 : (frg=="HIE")||(frg=="HSD")||(frg=="HSE")||
932 : (frg=="HSP")) {//HIS case
933 0 : RingInfo ri;
934 0 : for(unsigned a=0; a<frg_atoms.size(); a++) {
935 : unsigned atm = frg_atoms[a].index();
936 0 : for(unsigned aa=0; aa<5; aa++) {
937 0 : if(pdb.getAtomName(frg_atoms[a])==his_n[aa]) {
938 0 : ri.atom[aa] = atm;
939 0 : break;
940 : }
941 : }
942 : }
943 0 : ri.numAtoms = 5;
944 0 : total_rings_atoms += 3;
945 0 : ri.rtype = RingInfo::R_HIS;
946 0 : ringInfo.push_back(ri);
947 : } else {
948 0 : plumed_merror("Unknown Ring Fragment: " + frg);
949 : }
950 : }
951 : }
952 :
953 10620 : for(unsigned cs=0; cs<chemicalshifts.size(); cs++) chemicalshifts[cs].csatoms += total_rings_atoms;
954 486 : }
955 :
956 18 : void CS2Backbone::calculate()
957 : {
958 18 : if(pbc) makeWhole();
959 18 : if(getExchangeStep()) box_count=0;
960 18 : if(box_count==0) update_neighb();
961 18 : compute_ring_parameters();
962 :
963 18 : std::vector<double> camshift_sigma2(6);
964 18 : camshift_sigma2[0] = 0.08; // HA
965 18 : camshift_sigma2[1] = 0.30; // HN
966 18 : camshift_sigma2[2] = 9.00; // NH
967 18 : camshift_sigma2[3] = 1.30; // CA
968 18 : camshift_sigma2[4] = 1.56; // CB
969 18 : camshift_sigma2[5] = 1.70; // CO
970 :
971 : std::vector<Vector> cs_derivs;
972 : std::vector<Vector> aa_derivs;
973 : std::vector<unsigned> cs_atoms;
974 : std::vector<double> all_shifts;
975 :
976 18 : cs_derivs.resize(chemicalshifts.size()*max_cs_atoms,Vector(0,0,0));
977 18 : cs_atoms.resize(chemicalshifts.size()*max_cs_atoms,0);
978 18 : all_shifts.resize(chemicalshifts.size(),0);
979 18 : if(camshift||getDoScore()) aa_derivs.resize(getNumberOfAtoms(),Vector(0,0,0));
980 :
981 18 : unsigned stride = comm.Get_size();
982 18 : unsigned rank = comm.Get_rank();
983 18 : if(serial) {
984 : stride = 1;
985 : rank = 0;
986 : }
987 :
988 18 : unsigned nt=OpenMP::getNumThreads();
989 18 : if(nt*stride*2>chemicalshifts.size()) nt=1;
990 :
991 : // a single loop over all chemical shifts
992 18 : #pragma omp parallel num_threads(nt)
993 : {
994 : #pragma omp for schedule(dynamic)
995 : for(unsigned cs=rank; cs<chemicalshifts.size(); cs+=stride) {
996 : const unsigned kdx=cs*max_cs_atoms;
997 : const ChemicalShift *myfrag = &chemicalshifts[cs];
998 : const unsigned aa_kind = myfrag->res_kind;
999 : const unsigned at_kind = myfrag->atm_kind;
1000 :
1001 : double shift = db.CONSTAAPREV(aa_kind,at_kind)[myfrag->res_type_prev] +
1002 : db.CONSTAACURR(aa_kind,at_kind)[myfrag->res_type_curr] +
1003 : db.CONSTAANEXT(aa_kind,at_kind)[myfrag->res_type_next];
1004 :
1005 : const unsigned ipos = myfrag->ipos;
1006 : cs_atoms[kdx+0] = ipos;
1007 : unsigned atom_counter = 1;
1008 :
1009 : //BACKBONE (PREV CURR NEXT)
1010 : const double * CONST_BB2 = db.CONST_BB2(aa_kind,at_kind);
1011 : const unsigned bbsize = 16;
1012 : for(unsigned q=0; q<bbsize; q++) {
1013 : const double cb2q = CONST_BB2[q];
1014 : if(cb2q==0.) continue;
1015 : const unsigned jpos = myfrag->bb[q];
1016 : if(ipos==jpos) continue;
1017 : const Vector distance = delta(getPosition(jpos),getPosition(ipos));
1018 : const double d = distance.modulo();
1019 : const double fact = cb2q/d;
1020 :
1021 : shift += cb2q*d;
1022 : const Vector der = fact*distance;
1023 :
1024 : cs_derivs[kdx+0] += der;
1025 : cs_derivs[kdx+q+atom_counter] = -der;
1026 : cs_atoms[kdx+q+atom_counter] = jpos;
1027 : }
1028 :
1029 : atom_counter += bbsize;
1030 :
1031 : //DIHEDRAL ANGLES
1032 : const double *CO_DA = db.CO_DA(aa_kind,at_kind);
1033 : //Phi
1034 : {
1035 : const Vector d0 = delta(getPosition(myfrag->bb[Nc]), getPosition(myfrag->bb[Cp]));
1036 : const Vector d1 = delta(getPosition(myfrag->bb[CAc]), getPosition(myfrag->bb[Nc]));
1037 : const Vector d2 = delta(getPosition(myfrag->bb[Cc]), getPosition(myfrag->bb[CAc]));
1038 : Torsion t;
1039 : Vector dd0, dd1, dd2;
1040 : const double t_phi = t.compute(d0,d1,d2,dd0,dd1,dd2);
1041 : const double *PARS_DA = db.PARS_DA(aa_kind,at_kind,0);
1042 : const double val1 = 3.*t_phi+PARS_DA[3];
1043 : const double val2 = t_phi+PARS_DA[4];
1044 : shift += CO_DA[0]*(PARS_DA[0]*std::cos(val1)+PARS_DA[1]*std::cos(val2)+PARS_DA[2]);
1045 : const double fact = -CO_DA[0]*(+3.*PARS_DA[0]*std::sin(val1)+PARS_DA[1]*std::sin(val2));
1046 :
1047 : cs_derivs[kdx+Cp+1] += fact*dd0;
1048 : cs_derivs[kdx+Nc+1] += fact*(dd1-dd0);
1049 : cs_derivs[kdx+CAc+1]+= fact*(dd2-dd1);
1050 : cs_derivs[kdx+Cc+1] += -fact*dd2;
1051 : cs_atoms[kdx+Cp+1] = myfrag->bb[Cp];
1052 : cs_atoms[kdx+Nc+1] = myfrag->bb[Nc];
1053 : cs_atoms[kdx+CAc+1]= myfrag->bb[CAc];
1054 : cs_atoms[kdx+Cc+1] = myfrag->bb[Cc];
1055 : }
1056 :
1057 : //Psi
1058 : {
1059 : const Vector d0 = delta(getPosition(myfrag->bb[CAc]), getPosition(myfrag->bb[Nc]));
1060 : const Vector d1 = delta(getPosition(myfrag->bb[Cc]), getPosition(myfrag->bb[CAc]));
1061 : const Vector d2 = delta(getPosition(myfrag->bb[Nn]), getPosition(myfrag->bb[Cc]));
1062 : Torsion t;
1063 : Vector dd0, dd1, dd2;
1064 : const double t_psi = t.compute(d0,d1,d2,dd0,dd1,dd2);
1065 : const double *PARS_DA = db.PARS_DA(aa_kind,at_kind,1);
1066 : const double val1 = 3.*t_psi+PARS_DA[3];
1067 : const double val2 = t_psi+PARS_DA[4];
1068 : shift += CO_DA[1]*(PARS_DA[0]*std::cos(val1)+PARS_DA[1]*std::cos(val2)+PARS_DA[2]);
1069 : const double fact = -CO_DA[1]*(+3.*PARS_DA[0]*std::sin(val1)+PARS_DA[1]*std::sin(val2));
1070 :
1071 : cs_derivs[kdx+Nc+1] += fact*dd0;
1072 : cs_derivs[kdx+CAc+1] += fact*(dd1-dd0);
1073 : cs_derivs[kdx+Cc+1] += fact*(dd2-dd1);
1074 : cs_derivs[kdx+Nn+1] += -fact*dd2;
1075 : cs_atoms[kdx+Nc+1] = myfrag->bb[Nc];
1076 : cs_atoms[kdx+CAc+1]= myfrag->bb[CAc];
1077 : cs_atoms[kdx+Cc+1] = myfrag->bb[Cc];
1078 : cs_atoms[kdx+Nn+1] = myfrag->bb[Nn];
1079 : }
1080 :
1081 : //Chi
1082 : if(myfrag->has_chi1) {
1083 : const Vector d0 = delta(getPosition(myfrag->bb[CAc]), getPosition(myfrag->bb[Nc]));
1084 : const Vector d1 = delta(getPosition(myfrag->bb[CBc]), getPosition(myfrag->bb[CAc]));
1085 : const Vector d2 = delta(getPosition(myfrag->bb[CGc]), getPosition(myfrag->bb[CBc]));
1086 : Torsion t;
1087 : Vector dd0, dd1, dd2;
1088 : const double t_chi1 = t.compute(d0,d1,d2,dd0,dd1,dd2);
1089 : const double *PARS_DA = db.PARS_DA(aa_kind,at_kind,2);
1090 : const double val1 = 3.*t_chi1+PARS_DA[3];
1091 : const double val2 = t_chi1+PARS_DA[4];
1092 : shift += CO_DA[2]*(PARS_DA[0]*std::cos(val1)+PARS_DA[1]*std::cos(val2)+PARS_DA[2]);
1093 : const double fact = -CO_DA[2]*(+3.*PARS_DA[0]*std::sin(val1)+PARS_DA[1]*std::sin(val2));
1094 :
1095 : cs_derivs[kdx+Nc+1] += fact*dd0;
1096 : cs_derivs[kdx+CAc+1] += fact*(dd1-dd0);
1097 : cs_derivs[kdx+CBc+1] += fact*(dd2-dd1);
1098 : cs_derivs[kdx+CGc+1] += -fact*dd2;
1099 : cs_atoms[kdx+Nc+1] = myfrag->bb[Nc];
1100 : cs_atoms[kdx+CAc+1] = myfrag->bb[CAc];
1101 : cs_atoms[kdx+CBc+1] = myfrag->bb[CBc];
1102 : cs_atoms[kdx+CGc+1] = myfrag->bb[CGc];
1103 :
1104 : atom_counter += 2;
1105 : }
1106 : //END OF DIHE
1107 :
1108 : //SIDE CHAIN
1109 : const double * CONST_SC2 = db.CONST_SC2(aa_kind,at_kind,myfrag->res_type_curr);
1110 : const unsigned sidsize = myfrag->side_chain.size();
1111 : for(unsigned q=0; q<sidsize; q++) {
1112 : const double cs2q = CONST_SC2[q];
1113 : if(cs2q==0.) continue;
1114 : const unsigned jpos = myfrag->side_chain[q];
1115 : if(ipos==jpos) continue;
1116 : const Vector distance = delta(getPosition(jpos),getPosition(ipos));
1117 : const double d = distance.modulo();
1118 : const double fact = cs2q/d;
1119 :
1120 : shift += cs2q*d;
1121 : const Vector der = fact*distance;
1122 : cs_derivs[kdx+0] += der;
1123 : cs_derivs[kdx+q+atom_counter] = -der;
1124 : cs_atoms[kdx+q+atom_counter] = jpos;
1125 : }
1126 :
1127 : atom_counter += sidsize;
1128 :
1129 : //EXTRA DIST
1130 : const double * CONST_XD = db.CONST_XD(aa_kind,at_kind);
1131 : const unsigned xdsize=myfrag->xd1.size();
1132 : for(unsigned q=0; q<xdsize; q++) {
1133 : const double cxdq = CONST_XD[q];
1134 : if(cxdq==0.) continue;
1135 : if(myfrag->xd1[q]==-1||myfrag->xd2[q]==-1) continue;
1136 : const Vector distance = delta(getPosition(myfrag->xd1[q]),getPosition(myfrag->xd2[q]));
1137 : const double d = distance.modulo();
1138 : const double fact = cxdq/d;
1139 :
1140 : shift += cxdq*d;
1141 : const Vector der = fact*distance;
1142 : cs_derivs[kdx+2*q+atom_counter ] = der;
1143 : cs_derivs[kdx+2*q+atom_counter+1] = -der;
1144 : cs_atoms[kdx+2*q+atom_counter] = myfrag->xd2[q];
1145 : cs_atoms[kdx+2*q+atom_counter+1] = myfrag->xd1[q];
1146 : }
1147 :
1148 : atom_counter += 2*xdsize;
1149 :
1150 : //RINGS
1151 : const double *rc = db.CO_RING(aa_kind,at_kind);
1152 : const unsigned rsize = ringInfo.size();
1153 : // cycle over the list of rings
1154 : for(unsigned q=0; q<rsize; q++) {
1155 : // compute angle from ring middle point to current atom position
1156 : // get distance std::vector from query atom to ring center and normal std::vector to ring plane
1157 : const Vector n = ringInfo[q].normVect;
1158 : const double nL = ringInfo[q].lengthNV;
1159 : const double inL2 = ringInfo[q].lengthN2;
1160 :
1161 : const Vector d = delta(ringInfo[q].position, getPosition(ipos));
1162 : const double dL2 = d.modulo2();
1163 : double dL = std::sqrt(dL2);
1164 : const double idL3 = 1./(dL2*dL);
1165 :
1166 : const double dn = dotProduct(d,n);
1167 : const double dn2 = dn*dn;
1168 : const double dLnL = dL*nL;
1169 : const double dL_nL = dL/nL;
1170 :
1171 : const double ang2 = dn2*inL2/dL2;
1172 : const double u = 1.-3.*ang2;
1173 : const double cc = rc[ringInfo[q].rtype];
1174 :
1175 : shift += cc*u*idL3;
1176 :
1177 : const double fUU = -6.*dn*inL2;
1178 : const double fUQ = fUU/dL;
1179 : const Vector gradUQ = fUQ*(dL2*n - dn*d);
1180 : const Vector gradVQ = (3.*dL*u)*d;
1181 :
1182 : const double fact = cc*idL3*idL3;
1183 : cs_derivs[kdx+0] += fact*(gradUQ - gradVQ);
1184 :
1185 : const double fU = fUU/nL;
1186 : double OneOverN = 1./6.;
1187 : if(ringInfo[q].numAtoms==5) OneOverN=1./3.;
1188 : const Vector factor2 = OneOverN*n;
1189 : const Vector factor4 = (OneOverN/dL_nL)*d;
1190 :
1191 : const Vector gradV = -OneOverN*gradVQ;
1192 :
1193 : if(ringInfo[q].numAtoms==6) {
1194 : // update forces on ring atoms
1195 : for(unsigned at=0; at<6; at++) {
1196 : const Vector ab = crossProduct(d,ringInfo[q].g[at]);
1197 : const Vector c = crossProduct(n,ringInfo[q].g[at]);
1198 : const Vector factor3 = 0.5*dL_nL*c;
1199 : const Vector factor1 = 0.5*ab;
1200 : const Vector gradU = fU*( dLnL*(factor1 - factor2) -dn*(factor3 - factor4) );
1201 : cs_derivs[kdx+at+atom_counter] = fact*(gradU - gradV);
1202 : cs_atoms[kdx+at+atom_counter] = ringInfo[q].atom[at];
1203 : }
1204 : atom_counter += 6;
1205 : } else {
1206 : for(unsigned at=0; at<3; at++) {
1207 : const Vector ab = crossProduct(d,ringInfo[q].g[at]);
1208 : const Vector c = crossProduct(n,ringInfo[q].g[at]);
1209 : const Vector factor3 = dL_nL*c;
1210 : const Vector factor1 = ab;
1211 : const Vector gradU = fU*( dLnL*(factor1 - factor2) -dn*(factor3 - factor4) );
1212 : cs_derivs[kdx+at+atom_counter] = fact*(gradU - gradV);
1213 : }
1214 : cs_atoms[kdx+atom_counter] = ringInfo[q].atom[0];
1215 : cs_atoms[kdx+atom_counter+1] = ringInfo[q].atom[2];
1216 : cs_atoms[kdx+atom_counter+2] = ringInfo[q].atom[3];
1217 : atom_counter += 3;
1218 : }
1219 : }
1220 : //END OF RINGS
1221 :
1222 : //NON BOND
1223 : const double * CONST_CO_SPHERE3 = db.CO_SPHERE(aa_kind,at_kind,0);
1224 : const double * CONST_CO_SPHERE = db.CO_SPHERE(aa_kind,at_kind,1);
1225 : const unsigned boxsize = myfrag->box_nb.size();
1226 : for(unsigned q=0; q<boxsize; q++) {
1227 : const unsigned jpos = myfrag->box_nb[q];
1228 : const Vector distance = delta(getPosition(jpos),getPosition(ipos));
1229 : const double d2 = distance.modulo2();
1230 :
1231 : if(d2<cutOffDist2) {
1232 : double factor1 = std::sqrt(d2);
1233 : double dfactor1 = 1./factor1;
1234 : double factor3 = dfactor1*dfactor1*dfactor1;
1235 : double dfactor3 = -3.*factor3*dfactor1*dfactor1;
1236 :
1237 : if(d2>cutOnDist2) {
1238 : const double af = cutOffDist2 - d2;
1239 : const double bf = cutOffDist2 - 3.*cutOnDist2 + 2.*d2;
1240 : const double cf = invswitch*af;
1241 : const double df = cf*af*bf;
1242 : factor1 *= df;
1243 : factor3 *= df;
1244 :
1245 : const double d4 = d2*d2;
1246 : const double af1 = 15.*cutOnDist2*d2;
1247 : const double bf1 = -14.*d4;
1248 : const double cf1 = -3.*cutOffDist2*cutOnDist2 + cutOffDist2*d2;
1249 : const double df1 = af1+bf1+cf1;
1250 : dfactor1 *= cf*(cutOffDist4+df1);
1251 :
1252 : const double af3 = +2.*cutOffDist2*cutOnDist2;
1253 : const double bf3 = d2*(cutOffDist2+cutOnDist2);
1254 : const double cf3 = -2.*d4;
1255 : const double df3 = (af3+bf3+cf3)*d2;
1256 : dfactor3 *= invswitch*(cutMixed+df3);
1257 : }
1258 :
1259 : const unsigned t = type[jpos];
1260 : shift += factor1*CONST_CO_SPHERE[t] + factor3*CONST_CO_SPHERE3[t] ;
1261 : const double fact = dfactor1*CONST_CO_SPHERE[t]+dfactor3*CONST_CO_SPHERE3[t];
1262 : const Vector der = fact*distance;
1263 :
1264 : cs_derivs[kdx+0] += der;
1265 : cs_derivs[kdx+q+atom_counter] = -der;
1266 : cs_atoms[kdx+q+atom_counter] = jpos;
1267 : }
1268 : }
1269 : //END NON BOND
1270 :
1271 : atom_counter += boxsize;
1272 : all_shifts[cs] = shift;
1273 : }
1274 : }
1275 :
1276 18 : ++box_count;
1277 18 : if(box_count == box_nupdate) box_count = 0;
1278 :
1279 18 : if(!camshift) {
1280 13 : if(!serial) {
1281 13 : if(!getDoScore()) {
1282 9 : comm.Sum(&cs_derivs[0][0], 3*cs_derivs.size());
1283 9 : comm.Sum(&cs_atoms[0], cs_atoms.size());
1284 : }
1285 13 : comm.Sum(&all_shifts[0], chemicalshifts.size());
1286 : }
1287 7670 : for(unsigned cs=0; cs<chemicalshifts.size(); cs++) {
1288 7657 : Value *comp = chemicalshifts[cs].comp;
1289 7657 : comp->set(all_shifts[cs]);
1290 7657 : if(getDoScore()) setCalcData(cs, all_shifts[cs]);
1291 : else {
1292 5301 : const unsigned kdx=cs*max_cs_atoms;
1293 5301 : Tensor csvirial;
1294 1270127 : for(unsigned i=0; i<chemicalshifts[cs].totcsatoms; i++) {
1295 1264826 : setAtomsDerivatives(comp,cs_atoms[kdx+i],cs_derivs[kdx+i]);
1296 1264826 : csvirial-=Tensor(getPosition(cs_atoms[kdx+i]),cs_derivs[kdx+i]);
1297 : }
1298 5301 : setBoxDerivatives(comp,csvirial);
1299 : }
1300 : }
1301 13 : if(!getDoScore()) return;
1302 : }
1303 :
1304 9 : double score = 0.;
1305 :
1306 : /* Metainference */
1307 9 : if(getDoScore()) {
1308 4 : score = getScore();
1309 1182 : for(unsigned cs=rank; cs<chemicalshifts.size(); cs+=stride) {
1310 1178 : const unsigned kdx=cs*max_cs_atoms;
1311 : const double fact = getMetaDer(cs);
1312 282215 : for(unsigned i=0; i<chemicalshifts[cs].totcsatoms; i++) {
1313 281037 : aa_derivs[cs_atoms[kdx+i]] += cs_derivs[kdx+i]*fact;
1314 : }
1315 : }
1316 : }
1317 :
1318 : /* camshift */
1319 9 : if(camshift) {
1320 1772 : for(unsigned cs=rank; cs<chemicalshifts.size(); cs+=stride) {
1321 1767 : const unsigned kdx=cs*max_cs_atoms;
1322 1767 : score += (all_shifts[cs] - chemicalshifts[cs].exp_cs)*(all_shifts[cs] - chemicalshifts[cs].exp_cs)/camshift_sigma2[chemicalshifts[cs].atm_kind];
1323 1767 : double fact = 2.0*(all_shifts[cs] - chemicalshifts[cs].exp_cs)/camshift_sigma2[chemicalshifts[cs].atm_kind];
1324 423482 : for(unsigned i=0; i<chemicalshifts[cs].totcsatoms; i++) {
1325 421715 : aa_derivs[cs_atoms[kdx+i]] += cs_derivs[kdx+i]*fact;
1326 : }
1327 : }
1328 : }
1329 :
1330 9 : if(!serial) {
1331 9 : comm.Sum(&aa_derivs[0][0], 3*aa_derivs.size());
1332 9 : if(camshift) comm.Sum(&score, 1);
1333 : }
1334 :
1335 9 : Tensor virial;
1336 13069 : for(unsigned i=rank; i<getNumberOfAtoms(); i+=stride) {
1337 13060 : virial += Tensor(getPosition(i), aa_derivs[i]);
1338 : }
1339 :
1340 9 : if(!serial) {
1341 9 : comm.Sum(&virial[0][0], 9);
1342 : }
1343 :
1344 : /* calculate final derivatives */
1345 : Value* val;
1346 9 : if(getDoScore()) {
1347 4 : val=getPntrToComponent("score");
1348 4 : setScore(score);
1349 : } else {
1350 : val=getPntrToValue();
1351 5 : setValue(score);
1352 : }
1353 :
1354 : /* at this point we cycle over all atoms */
1355 23517 : for(unsigned i=0; i<getNumberOfAtoms(); i++) setAtomsDerivatives(val, i, aa_derivs[i]);
1356 9 : setBoxDerivatives(val,-virial);
1357 : }
1358 :
1359 18 : void CS2Backbone::update_neighb() {
1360 : // cycle over chemical shifts
1361 18 : unsigned nt=OpenMP::getNumThreads();
1362 18 : #pragma omp parallel for num_threads(nt)
1363 : for(unsigned cs=0; cs<chemicalshifts.size(); cs++) {
1364 : const unsigned boxsize = getNumberOfAtoms();
1365 : chemicalshifts[cs].box_nb.clear();
1366 : chemicalshifts[cs].box_nb.reserve(150);
1367 : const unsigned res_curr = res_num[chemicalshifts[cs].ipos];
1368 : for(unsigned bat=0; bat<boxsize; bat++) {
1369 : const unsigned res_dist = std::abs(static_cast<int>(res_curr-res_num[bat]));
1370 : if(res_dist<2) continue;
1371 : const Vector distance = delta(getPosition(bat),getPosition(chemicalshifts[cs].ipos));
1372 : const double d2=distance.modulo2();
1373 : if(d2<cutOffNB2) chemicalshifts[cs].box_nb.push_back(bat);
1374 : }
1375 : chemicalshifts[cs].totcsatoms = chemicalshifts[cs].csatoms + chemicalshifts[cs].box_nb.size();
1376 : }
1377 18 : max_cs_atoms=0;
1378 10620 : for(unsigned cs=0; cs<chemicalshifts.size(); cs++) {
1379 10602 : if(chemicalshifts[cs].totcsatoms>max_cs_atoms) max_cs_atoms = chemicalshifts[cs].totcsatoms;
1380 : }
1381 18 : }
1382 :
1383 18 : void CS2Backbone::compute_ring_parameters() {
1384 378 : for(unsigned i=0; i<ringInfo.size(); i++) {
1385 360 : const unsigned size = ringInfo[i].numAtoms;
1386 360 : if(size==6) {
1387 342 : ringInfo[i].g[0] = delta(getPosition(ringInfo[i].atom[4]),getPosition(ringInfo[i].atom[2]));
1388 342 : ringInfo[i].g[1] = delta(getPosition(ringInfo[i].atom[5]),getPosition(ringInfo[i].atom[3]));
1389 342 : ringInfo[i].g[2] = delta(getPosition(ringInfo[i].atom[0]),getPosition(ringInfo[i].atom[4]));
1390 342 : ringInfo[i].g[3] = delta(getPosition(ringInfo[i].atom[1]),getPosition(ringInfo[i].atom[5]));
1391 342 : ringInfo[i].g[4] = delta(getPosition(ringInfo[i].atom[2]),getPosition(ringInfo[i].atom[0]));
1392 342 : ringInfo[i].g[5] = delta(getPosition(ringInfo[i].atom[3]),getPosition(ringInfo[i].atom[1]));
1393 : // ring center
1394 342 : Vector midP = getPosition(ringInfo[i].atom[0]);
1395 2052 : for(unsigned j=1; j<size; j++) midP += getPosition(ringInfo[i].atom[j]);
1396 342 : ringInfo[i].position = midP/6.;
1397 : // compute normal std::vector to plane
1398 342 : Vector n1 = crossProduct(ringInfo[i].g[2], -ringInfo[i].g[4]);
1399 342 : Vector n2 = crossProduct(ringInfo[i].g[5], -ringInfo[i].g[1]);
1400 342 : ringInfo[i].normVect = 0.5*(n1 + n2);
1401 : } else {
1402 18 : ringInfo[i].g[0] = delta(getPosition(ringInfo[i].atom[3]),getPosition(ringInfo[i].atom[2]));
1403 18 : ringInfo[i].g[1] = delta(getPosition(ringInfo[i].atom[0]),getPosition(ringInfo[i].atom[3]));
1404 18 : ringInfo[i].g[2] = delta(getPosition(ringInfo[i].atom[2]),getPosition(ringInfo[i].atom[0]));
1405 : // ring center
1406 18 : ringInfo[i].position = (getPosition(ringInfo[i].atom[0])+getPosition(ringInfo[i].atom[2])+getPosition(ringInfo[i].atom[3]))/3.;
1407 : // ring plane normal std::vector
1408 18 : ringInfo[i].normVect = crossProduct(ringInfo[i].g[1],-ringInfo[i].g[2]);
1409 :
1410 : }
1411 : // calculate squared length and length of normal std::vector
1412 360 : ringInfo[i].lengthN2 = 1./ringInfo[i].normVect.modulo2();
1413 360 : ringInfo[i].lengthNV = 1./std::sqrt(ringInfo[i].lengthN2);
1414 : }
1415 18 : }
1416 :
1417 31806 : CS2Backbone::aa_t CS2Backbone::frag2enum(const std::string &aa) {
1418 : aa_t type = ALA;
1419 31806 : if (aa == "ALA") type = ALA;
1420 29934 : else if (aa == "ARG") type = ARG;
1421 28548 : else if (aa == "ASN") type = ASN;
1422 26910 : else if (aa == "ASP") type = ASP;
1423 25380 : else if (aa == "ASH") type = ASP;
1424 25380 : else if (aa == "CYS") type = CYS;
1425 24858 : else if (aa == "CYM") type = CYS;
1426 24858 : else if (aa == "GLN") type = GLN;
1427 24390 : else if (aa == "GLU") type = GLU;
1428 22068 : else if (aa == "GLH") type = GLU;
1429 22068 : else if (aa == "GLY") type = GLY;
1430 16974 : else if (aa == "HIS") type = HIS;
1431 16974 : else if (aa == "HSE") type = HIS;
1432 16974 : else if (aa == "HIE") type = HIS;
1433 16974 : else if (aa == "HSP") type = HIS;
1434 16974 : else if (aa == "HIP") type = HIS;
1435 16974 : else if (aa == "HSD") type = HIS;
1436 16974 : else if (aa == "HID") type = HIS;
1437 16974 : else if (aa == "ILE") type = ILE;
1438 15174 : else if (aa == "LEU") type = LEU;
1439 13536 : else if (aa == "LYS") type = LYS;
1440 10746 : else if (aa == "MET") type = MET;
1441 9936 : else if (aa == "PHE") type = PHE;
1442 6876 : else if (aa == "PRO") type = PRO;
1443 5940 : else if (aa == "SER") type = SER;
1444 4302 : else if (aa == "THR") type = THR;
1445 2196 : else if (aa == "TRP") type = TRP;
1446 1980 : else if (aa == "TYR") type = TYR;
1447 1602 : else if (aa == "VAL") type = VAL;
1448 0 : else if (aa == "UNK") type = UNK;
1449 0 : else plumed_merror("Error converting std::string " + aa + " into amino acid index: not a valid 3-letter code");
1450 31806 : return type;
1451 : }
1452 :
1453 10602 : std::vector<std::string> CS2Backbone::side_chain_atoms(const std::string &s) {
1454 : std::vector<std::string> sc;
1455 :
1456 10602 : if(s=="ALA") {
1457 648 : sc.push_back( "CB" );
1458 648 : sc.push_back( "HB1" );
1459 648 : sc.push_back( "HB2" );
1460 648 : sc.push_back( "HB3" );
1461 648 : return sc;
1462 9954 : } else if(s=="ARG") {
1463 468 : sc.push_back( "CB" );
1464 468 : sc.push_back( "CG" );
1465 468 : sc.push_back( "CD" );
1466 468 : sc.push_back( "NE" );
1467 468 : sc.push_back( "CZ" );
1468 468 : sc.push_back( "NH1" );
1469 468 : sc.push_back( "NH2" );
1470 468 : sc.push_back( "NH3" );
1471 468 : sc.push_back( "HB1" );
1472 468 : sc.push_back( "HB2" );
1473 468 : sc.push_back( "HB3" );
1474 468 : sc.push_back( "HG1" );
1475 468 : sc.push_back( "HG2" );
1476 468 : sc.push_back( "HG3" );
1477 468 : sc.push_back( "HD1" );
1478 468 : sc.push_back( "HD2" );
1479 468 : sc.push_back( "HD3" );
1480 468 : sc.push_back( "HE" );
1481 468 : sc.push_back( "HH11" );
1482 468 : sc.push_back( "HH12" );
1483 468 : sc.push_back( "HH21" );
1484 468 : sc.push_back( "HH22" );
1485 468 : sc.push_back( "1HH1" );
1486 468 : sc.push_back( "2HH1" );
1487 468 : sc.push_back( "1HH2" );
1488 468 : sc.push_back( "2HH2" );
1489 468 : return sc;
1490 9486 : } else if(s=="ASN") {
1491 594 : sc.push_back( "CB" );
1492 594 : sc.push_back( "CG" );
1493 594 : sc.push_back( "OD1" );
1494 594 : sc.push_back( "ND2" );
1495 594 : sc.push_back( "HB1" );
1496 594 : sc.push_back( "HB2" );
1497 594 : sc.push_back( "HB3" );
1498 594 : sc.push_back( "HD21" );
1499 594 : sc.push_back( "HD22" );
1500 594 : sc.push_back( "1HD2" );
1501 594 : sc.push_back( "2HD2" );
1502 594 : return sc;
1503 17226 : } else if(s=="ASP"||s=="ASH") {
1504 558 : sc.push_back( "CB" );
1505 558 : sc.push_back( "CG" );
1506 558 : sc.push_back( "OD1" );
1507 558 : sc.push_back( "OD2" );
1508 558 : sc.push_back( "HB1" );
1509 558 : sc.push_back( "HB2" );
1510 558 : sc.push_back( "HB3" );
1511 558 : return sc;
1512 16668 : } else if(s=="CYS"||s=="CYM") {
1513 0 : sc.push_back( "CB" );
1514 0 : sc.push_back( "SG" );
1515 0 : sc.push_back( "HB1" );
1516 0 : sc.push_back( "HB2" );
1517 0 : sc.push_back( "HB3" );
1518 0 : sc.push_back( "HG1" );
1519 0 : sc.push_back( "HG" );
1520 0 : return sc;
1521 8334 : } else if(s=="GLN") {
1522 162 : sc.push_back( "CB" );
1523 162 : sc.push_back( "CG" );
1524 162 : sc.push_back( "CD" );
1525 162 : sc.push_back( "OE1" );
1526 162 : sc.push_back( "NE2" );
1527 162 : sc.push_back( "HB1" );
1528 162 : sc.push_back( "HB2" );
1529 162 : sc.push_back( "HB3" );
1530 162 : sc.push_back( "HG1" );
1531 162 : sc.push_back( "HG2" );
1532 162 : sc.push_back( "HG3" );
1533 162 : sc.push_back( "HE21" );
1534 162 : sc.push_back( "HE22" );
1535 162 : sc.push_back( "1HE2" );
1536 162 : sc.push_back( "2HE2" );
1537 162 : return sc;
1538 15552 : } else if(s=="GLU"||s=="GLH") {
1539 792 : sc.push_back( "CB" );
1540 792 : sc.push_back( "CG" );
1541 792 : sc.push_back( "CD" );
1542 792 : sc.push_back( "OE1" );
1543 792 : sc.push_back( "OE2" );
1544 792 : sc.push_back( "HB1" );
1545 792 : sc.push_back( "HB2" );
1546 792 : sc.push_back( "HB3" );
1547 792 : sc.push_back( "HG1" );
1548 792 : sc.push_back( "HG2" );
1549 792 : sc.push_back( "HG3" );
1550 792 : return sc;
1551 7380 : } else if(s=="GLY") {
1552 1494 : sc.push_back( "HA2" );
1553 1494 : return sc;
1554 41202 : } else if(s=="HIS"||s=="HSE"||s=="HIE"||s=="HSD"||s=="HID"||s=="HIP"||s=="HSP") {
1555 0 : sc.push_back( "CB" );
1556 0 : sc.push_back( "CG" );
1557 0 : sc.push_back( "ND1" );
1558 0 : sc.push_back( "CD2" );
1559 0 : sc.push_back( "CE1" );
1560 0 : sc.push_back( "NE2" );
1561 0 : sc.push_back( "HB1" );
1562 0 : sc.push_back( "HB2" );
1563 0 : sc.push_back( "HB3" );
1564 0 : sc.push_back( "HD1" );
1565 0 : sc.push_back( "HD2" );
1566 0 : sc.push_back( "HE1" );
1567 0 : sc.push_back( "HE2" );
1568 0 : return sc;
1569 5886 : } else if(s=="ILE") {
1570 540 : sc.push_back( "CB" );
1571 540 : sc.push_back( "CG1" );
1572 540 : sc.push_back( "CG2" );
1573 540 : sc.push_back( "CD" );
1574 540 : sc.push_back( "HB" );
1575 540 : sc.push_back( "HG11" );
1576 540 : sc.push_back( "HG12" );
1577 540 : sc.push_back( "HG21" );
1578 540 : sc.push_back( "HG22" );
1579 540 : sc.push_back( "HG23" );
1580 540 : sc.push_back( "1HG1" );
1581 540 : sc.push_back( "2HG1" );
1582 540 : sc.push_back( "1HG2" );
1583 540 : sc.push_back( "2HG2" );
1584 540 : sc.push_back( "3HG2" );
1585 540 : sc.push_back( "HD1" );
1586 540 : sc.push_back( "HD2" );
1587 540 : sc.push_back( "HD3" );
1588 540 : return sc;
1589 5346 : } else if(s=="LEU") {
1590 648 : sc.push_back( "CB" );
1591 648 : sc.push_back( "CG" );
1592 648 : sc.push_back( "CD1" );
1593 648 : sc.push_back( "CD2" );
1594 648 : sc.push_back( "HB1" );
1595 648 : sc.push_back( "HB2" );
1596 648 : sc.push_back( "HB3" );
1597 648 : sc.push_back( "HG" );
1598 648 : sc.push_back( "HD11" );
1599 648 : sc.push_back( "HD12" );
1600 648 : sc.push_back( "HD13" );
1601 648 : sc.push_back( "HD21" );
1602 648 : sc.push_back( "HD22" );
1603 648 : sc.push_back( "HD23" );
1604 648 : sc.push_back( "1HD1" );
1605 648 : sc.push_back( "2HD1" );
1606 648 : sc.push_back( "3HD1" );
1607 648 : sc.push_back( "1HD2" );
1608 648 : sc.push_back( "2HD2" );
1609 648 : sc.push_back( "3HD2" );
1610 648 : return sc;
1611 4698 : } else if(s=="LYS") {
1612 1008 : sc.push_back( "CB" );
1613 1008 : sc.push_back( "CG" );
1614 1008 : sc.push_back( "CD" );
1615 1008 : sc.push_back( "CE" );
1616 1008 : sc.push_back( "NZ" );
1617 1008 : sc.push_back( "HB1" );
1618 1008 : sc.push_back( "HB2" );
1619 1008 : sc.push_back( "HB3" );
1620 1008 : sc.push_back( "HG1" );
1621 1008 : sc.push_back( "HG2" );
1622 1008 : sc.push_back( "HG3" );
1623 1008 : sc.push_back( "HD1" );
1624 1008 : sc.push_back( "HD2" );
1625 1008 : sc.push_back( "HD3" );
1626 1008 : sc.push_back( "HE1" );
1627 1008 : sc.push_back( "HE2" );
1628 1008 : sc.push_back( "HE3" );
1629 1008 : sc.push_back( "HZ1" );
1630 1008 : sc.push_back( "HZ2" );
1631 1008 : sc.push_back( "HZ3" );
1632 1008 : return sc;
1633 3690 : } else if(s=="MET") {
1634 288 : sc.push_back( "CB" );
1635 288 : sc.push_back( "CG" );
1636 288 : sc.push_back( "SD" );
1637 288 : sc.push_back( "CE" );
1638 288 : sc.push_back( "HB1" );
1639 288 : sc.push_back( "HB2" );
1640 288 : sc.push_back( "HB3" );
1641 288 : sc.push_back( "HG1" );
1642 288 : sc.push_back( "HG2" );
1643 288 : sc.push_back( "HG3" );
1644 288 : sc.push_back( "HE1" );
1645 288 : sc.push_back( "HE2" );
1646 288 : sc.push_back( "HE3" );
1647 288 : return sc;
1648 3402 : } else if(s=="PHE") {
1649 1098 : sc.push_back( "CB" );
1650 1098 : sc.push_back( "CG" );
1651 1098 : sc.push_back( "CD1" );
1652 1098 : sc.push_back( "CD2" );
1653 1098 : sc.push_back( "CE1" );
1654 1098 : sc.push_back( "CE2" );
1655 1098 : sc.push_back( "CZ" );
1656 1098 : sc.push_back( "HB1" );
1657 1098 : sc.push_back( "HB2" );
1658 1098 : sc.push_back( "HB3" );
1659 1098 : sc.push_back( "HD1" );
1660 1098 : sc.push_back( "HD2" );
1661 1098 : sc.push_back( "HD3" );
1662 1098 : sc.push_back( "HE1" );
1663 1098 : sc.push_back( "HE2" );
1664 1098 : sc.push_back( "HE3" );
1665 1098 : sc.push_back( "HZ" );
1666 1098 : return sc;
1667 2304 : } else if(s=="PRO") {
1668 108 : sc.push_back( "CB" );
1669 108 : sc.push_back( "CG" );
1670 108 : sc.push_back( "CD" );
1671 108 : sc.push_back( "HB1" );
1672 108 : sc.push_back( "HB2" );
1673 108 : sc.push_back( "HB3" );
1674 108 : sc.push_back( "HG1" );
1675 108 : sc.push_back( "HG2" );
1676 108 : sc.push_back( "HG3" );
1677 108 : sc.push_back( "HD1" );
1678 108 : sc.push_back( "HD2" );
1679 108 : sc.push_back( "HD3" );
1680 108 : return sc;
1681 2196 : } else if(s=="SER") {
1682 630 : sc.push_back( "CB" );
1683 630 : sc.push_back( "OG" );
1684 630 : sc.push_back( "HB1" );
1685 630 : sc.push_back( "HB2" );
1686 630 : sc.push_back( "HB3" );
1687 630 : sc.push_back( "HG1" );
1688 630 : sc.push_back( "HG" );
1689 630 : return sc;
1690 1566 : } else if(s=="THR") {
1691 774 : sc.push_back( "CB" );
1692 774 : sc.push_back( "OG1" );
1693 774 : sc.push_back( "CG2" );
1694 774 : sc.push_back( "HB" );
1695 774 : sc.push_back( "HG1" );
1696 774 : sc.push_back( "HG21" );
1697 774 : sc.push_back( "HG22" );
1698 774 : sc.push_back( "HG23" );
1699 774 : sc.push_back( "1HG2" );
1700 774 : sc.push_back( "2HG2" );
1701 774 : sc.push_back( "3HG2" );
1702 774 : return sc;
1703 792 : } else if(s=="TRP") {
1704 72 : sc.push_back( "CB" );
1705 72 : sc.push_back( "CG" );
1706 72 : sc.push_back( "CD1" );
1707 72 : sc.push_back( "CD2" );
1708 72 : sc.push_back( "NE1" );
1709 72 : sc.push_back( "CE2" );
1710 72 : sc.push_back( "CE3" );
1711 72 : sc.push_back( "CZ2" );
1712 72 : sc.push_back( "CZ3" );
1713 72 : sc.push_back( "CH2" );
1714 72 : sc.push_back( "HB1" );
1715 72 : sc.push_back( "HB2" );
1716 72 : sc.push_back( "HB3" );
1717 72 : sc.push_back( "HD1" );
1718 72 : sc.push_back( "HE1" );
1719 72 : sc.push_back( "HE3" );
1720 72 : sc.push_back( "HZ2" );
1721 72 : sc.push_back( "HZ3" );
1722 72 : sc.push_back( "HH2" );
1723 72 : return sc;
1724 720 : } else if(s=="TYR") {
1725 144 : sc.push_back( "CB" );
1726 144 : sc.push_back( "CG" );
1727 144 : sc.push_back( "CD1" );
1728 144 : sc.push_back( "CD2" );
1729 144 : sc.push_back( "CE1" );
1730 144 : sc.push_back( "CE2" );
1731 144 : sc.push_back( "CZ" );
1732 144 : sc.push_back( "OH" );
1733 144 : sc.push_back( "HB1" );
1734 144 : sc.push_back( "HB2" );
1735 144 : sc.push_back( "HB3" );
1736 144 : sc.push_back( "HD1" );
1737 144 : sc.push_back( "HD2" );
1738 144 : sc.push_back( "HD3" );
1739 144 : sc.push_back( "HE1" );
1740 144 : sc.push_back( "HE2" );
1741 144 : sc.push_back( "HE3" );
1742 144 : sc.push_back( "HH" );
1743 144 : return sc;
1744 576 : } else if(s=="VAL") {
1745 576 : sc.push_back( "CB" );
1746 576 : sc.push_back( "CG1" );
1747 576 : sc.push_back( "CG2" );
1748 576 : sc.push_back( "HB" );
1749 576 : sc.push_back( "HG11" );
1750 576 : sc.push_back( "HG12" );
1751 576 : sc.push_back( "HG13" );
1752 576 : sc.push_back( "HG21" );
1753 576 : sc.push_back( "HG22" );
1754 576 : sc.push_back( "HG23" );
1755 576 : sc.push_back( "1HG1" );
1756 576 : sc.push_back( "2HG1" );
1757 576 : sc.push_back( "3HG1" );
1758 576 : sc.push_back( "1HG2" );
1759 576 : sc.push_back( "2HG2" );
1760 576 : sc.push_back( "3HG2" );
1761 576 : return sc;
1762 0 : } else plumed_merror("Sidechain atoms unknown: " + s);
1763 0 : }
1764 :
1765 47016 : bool CS2Backbone::isSP2(const std::string & resType, const std::string & atomName) {
1766 : bool sp2 = false;
1767 47016 : if (atomName == "C") return true;
1768 43848 : if (atomName == "O") return true;
1769 :
1770 40716 : if(resType == "TRP") {
1771 396 : if (atomName == "CG") sp2 = true;
1772 378 : else if (atomName == "CD1") sp2 = true;
1773 360 : else if (atomName == "CD2") sp2 = true;
1774 342 : else if (atomName == "CE2") sp2 = true;
1775 324 : else if (atomName == "CE3") sp2 = true;
1776 306 : else if (atomName == "CZ2") sp2 = true;
1777 288 : else if (atomName == "CZ3") sp2 = true;
1778 270 : else if (atomName == "CH2") sp2 = true;
1779 40320 : } else if (resType == "ASP") {
1780 1656 : if (atomName == "CG") sp2 = true;
1781 1494 : else if (atomName == "OD1") sp2 = true;
1782 1332 : else if (atomName == "OD2") sp2 = true;
1783 38664 : } else if (resType == "GLU") {
1784 2844 : if (atomName == "CD") sp2 = true;
1785 2628 : else if (atomName == "OE1") sp2 = true;
1786 2412 : else if (atomName == "OE2") sp2 = true;
1787 35820 : } else if (resType == "ARG") {
1788 2772 : if (atomName == "CZ") sp2 = true;
1789 33048 : } else if (resType == "HIS") {
1790 0 : if (atomName == "CG") sp2 = true;
1791 0 : else if (atomName == "ND1") sp2 = true;
1792 0 : else if (atomName == "CD2") sp2 = true;
1793 0 : else if (atomName == "CE1") sp2 = true;
1794 0 : else if (atomName == "NE2") sp2 = true;
1795 33048 : } else if (resType == "PHE") {
1796 5184 : if (atomName == "CG") sp2 = true;
1797 4896 : else if (atomName == "CD1") sp2 = true;
1798 4608 : else if (atomName == "CD2") sp2 = true;
1799 4320 : else if (atomName == "CE1") sp2 = true;
1800 4032 : else if (atomName == "CE2") sp2 = true;
1801 3744 : else if (atomName == "CZ") sp2 = true;
1802 27864 : } else if (resType == "TYR") {
1803 684 : if (atomName == "CG") sp2 = true;
1804 648 : else if (atomName == "CD1") sp2 = true;
1805 612 : else if (atomName == "CD2") sp2 = true;
1806 576 : else if (atomName == "CE1") sp2 = true;
1807 540 : else if (atomName == "CE2") sp2 = true;
1808 504 : else if (atomName == "CZ") sp2 = true;
1809 27180 : } else if (resType == "ASN") {
1810 1944 : if (atomName == "CG") sp2 = true;
1811 1782 : else if (atomName == "OD1") sp2 = true;
1812 25236 : } else if (resType == "GLN") {
1813 810 : if (atomName == "CD") sp2 = true;
1814 756 : else if (atomName == "OE1") sp2 = true;
1815 : }
1816 :
1817 : return sp2;
1818 : }
1819 :
1820 145728 : bool CS2Backbone::is_chi1_cx(const std::string & frg, const std::string & atm) {
1821 145728 : if(atm=="CG") return true;
1822 139788 : if((frg == "CYS")&&(atm =="SG")) return true;
1823 288792 : if(((frg == "ILE")||(frg == "VAL"))&&(atm == "CG1")) return true;
1824 145602 : if((frg == "SER")&&(atm == "OG")) return true;
1825 148878 : if((frg == "THR")&&(atm == "OG1")) return true;
1826 :
1827 : return false;
1828 : }
1829 :
1830 3599784 : void CS2Backbone::xdist_name_map(std::string & name) {
1831 7199568 : if((name == "OT1")||(name == "OC1")) name = "O";
1832 10799352 : else if ((name == "HN") || (name == "HT1") || (name == "H1")) name = "H";
1833 7139232 : else if ((name == "CG1")|| (name == "OG")||
1834 7159572 : (name == "SG") || (name == "OG1")) name = "CG";
1835 7040070 : else if ((name == "HA1")|| (name == "HA3")) name = "HA";
1836 3599784 : }
1837 :
1838 18 : void CS2Backbone::update() {
1839 : // write status file
1840 18 : if(getWstride()>0&& (getStep()%getWstride()==0 || getCPT()) ) writeStatus();
1841 18 : }
1842 :
1843 : }
1844 : }
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