Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2016-2023 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 "MetainferenceBase.h"
23 : #include "core/ActionRegister.h"
24 : #include "tools/Pbc.h"
25 : #include "tools/Torsion.h"
26 :
27 : namespace PLMD {
28 : namespace isdb {
29 :
30 : //+PLUMEDOC ISDB_COLVAR JCOUPLING
31 : /*
32 : Calculates 3J coupling constants for a dihedral angle.
33 :
34 : The J-coupling between two atoms is given by the Karplus relation:
35 :
36 : \f[
37 : ^3J(\theta)=A\cos^2(\theta+\Delta\theta)+B\cos(\theta+\Delta\theta)+C
38 : \f]
39 :
40 : where \f$A\f$, \f$B\f$ and \f$C\f$ are the Karplus parameters and \f$\Delta\theta\f$ is an additional constant
41 : added on to the dihedral angle \f$\theta\f$. The Karplus parameters are determined empirically and are dependent
42 : on the type of J-coupling.
43 :
44 : This collective variable computes the J-couplings for a set of atoms defining a dihedral angle. You can specify
45 : the atoms involved using the \ref MOLINFO notation. You can also specify the experimental couplings using the
46 : COUPLING keywords. These will be included in the output. You must choose the type of
47 : coupling using the type keyword, you can also supply custom Karplus parameters using TYPE=CUSTOM and the A, B, C
48 : and SHIFT keywords. You will need to make sure you are using the correct dihedral angle:
49 :
50 : - Ha-N: \f$\psi\f$
51 : - Ha-HN: \f$\phi\f$
52 : - N-C\f$\gamma\f$: \f$\chi_1\f$
53 : - CO-C\f$\gamma\f$: \f$\chi_1\f$
54 :
55 : J-couplings can be used to calculate a Metainference score using the internal keyword DOSCORE and all the options
56 : of \ref METAINFERENCE .
57 :
58 : \par Examples
59 :
60 : In the following example we calculate the Ha-N J-coupling from a set of atoms involved in
61 : dihedral \f$\psi\f$ angles in the peptide backbone. We also add the experimental data points and compute
62 : the correlation and other measures and finally print the results.
63 :
64 : \plumedfile
65 : #SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
66 : MOLINFO MOLTYPE=protein STRUCTURE=peptide.pdb
67 : WHOLEMOLECULES ENTITY0=1-111
68 :
69 : JCOUPLING ...
70 : TYPE=HAN
71 : ATOMS1=@psi-2 COUPLING1=-0.49
72 : ATOMS2=@psi-4 COUPLING2=-0.54
73 : ATOMS3=@psi-5 COUPLING3=-0.53
74 : ATOMS4=@psi-7 COUPLING4=-0.39
75 : ATOMS5=@psi-8 COUPLING5=-0.39
76 : LABEL=jhan
77 : ... JCOUPLING
78 :
79 : jhanst: STATS ARG=(jhan\.j-.*) PARARG=(jhan\.exp-.*)
80 :
81 : PRINT ARG=jhanst.*,jhan.* FILE=COLVAR STRIDE=100
82 : \endplumedfile
83 :
84 : */
85 : //+ENDPLUMEDOC
86 :
87 : class JCoupling :
88 : public MetainferenceBase
89 : {
90 : private:
91 : bool pbc;
92 : enum { HAN, HAHN, CCG, NCG, CUSTOM };
93 : unsigned ncoupl_;
94 : double ka_;
95 : double kb_;
96 : double kc_;
97 : double kshift_;
98 :
99 : public:
100 : static void registerKeywords(Keywords& keys);
101 : explicit JCoupling(const ActionOptions&);
102 : void calculate() override;
103 : void update() override;
104 : };
105 :
106 : PLUMED_REGISTER_ACTION(JCoupling, "JCOUPLING")
107 :
108 8 : void JCoupling::registerKeywords(Keywords& keys) {
109 8 : MetainferenceBase::registerKeywords(keys);
110 16 : keys.addFlag("NOPBC",false,"ignore the periodic boundary conditions when calculating distances");
111 16 : keys.add("numbered", "ATOMS", "the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling. "
112 : "Keywords like ATOMS1, ATOMS2, ATOMS3,... should be listed and one J-coupling will be "
113 : "calculated for each ATOMS keyword you specify.");
114 16 : keys.reset_style("ATOMS", "atoms");
115 16 : keys.add("compulsory", "TYPE", "Type of J-coupling to compute (HAN,HAHN,CCG,NCG,CUSTOM)");
116 16 : keys.add("optional", "A", "Karplus parameter A");
117 16 : keys.add("optional", "B", "Karplus parameter B");
118 16 : keys.add("optional", "C", "Karplus parameter C");
119 16 : keys.add("optional", "SHIFT", "Angle shift in radians");
120 16 : keys.add("numbered", "COUPLING", "Add an experimental value for each coupling");
121 16 : keys.addOutputComponent("j", "default", "the calculated J-coupling");
122 16 : keys.addOutputComponent("exp", "COUPLING", "the experimental J-coupling");
123 8 : }
124 :
125 6 : JCoupling::JCoupling(const ActionOptions&ao):
126 : PLUMED_METAINF_INIT(ao),
127 6 : pbc(true)
128 : {
129 6 : bool nopbc = !pbc;
130 6 : parseFlag("NOPBC", nopbc);
131 6 : pbc =! nopbc;
132 :
133 : // Read in the atoms
134 : std::vector<AtomNumber> t, atoms;
135 6 : for (int i = 1; ; ++i) {
136 68 : parseAtomList("ATOMS", i, t );
137 34 : if (t.empty()) {
138 : break;
139 : }
140 :
141 28 : if (t.size() != 4) {
142 : std::string ss;
143 0 : Tools::convert(i, ss);
144 0 : error("ATOMS" + ss + " keyword has the wrong number of atoms");
145 : }
146 :
147 : // This makes the distance calculation easier later on (see Torsion implementation)
148 28 : atoms.push_back(t[0]);
149 28 : atoms.push_back(t[1]);
150 28 : atoms.push_back(t[1]);
151 28 : atoms.push_back(t[2]);
152 28 : atoms.push_back(t[2]);
153 28 : atoms.push_back(t[3]);
154 28 : t.resize(0);
155 28 : }
156 :
157 : // We now have 6 atoms per datapoint
158 6 : ncoupl_ = atoms.size()/6;
159 :
160 : // Parse J-Coupling type, this will determine the Karplus parameters
161 : unsigned jtype_ = CUSTOM;
162 : std::string string_type;
163 12 : parse("TYPE", string_type);
164 6 : if(string_type == "HAN") {
165 : jtype_ = HAN;
166 5 : } else if(string_type == "HAHN") {
167 : jtype_ = HAHN;
168 2 : } else if(string_type == "CCG") {
169 : jtype_ = CCG;
170 1 : } else if(string_type == "NCG") {
171 : jtype_ = NCG;
172 0 : } else if(string_type == "CUSTOM") {
173 : jtype_ = CUSTOM;
174 : } else {
175 0 : error("Unknown J-coupling type!");
176 : }
177 :
178 : // Optionally add an experimental value (like with RDCs)
179 : std::vector<double> coupl;
180 6 : coupl.resize( ncoupl_ );
181 : unsigned ntarget=0;
182 13 : for(unsigned i=0; i<ncoupl_; ++i) {
183 24 : if( !parseNumbered( "COUPLING", i+1, coupl[i] ) ) break;
184 7 : ntarget++;
185 : }
186 : bool addcoupling=false;
187 6 : if(ntarget!=ncoupl_ && ntarget!=0) error("found wrong number of COUPLING values");
188 6 : if(ntarget==ncoupl_) addcoupling=true;
189 6 : if(getDoScore()&&!addcoupling) error("with DOSCORE you need to set the COUPLING values");
190 :
191 : // For custom types we allow use of custom Karplus parameters
192 6 : if (jtype_ == CUSTOM) {
193 0 : parse("A", ka_);
194 0 : parse("B", kb_);
195 0 : parse("C", kc_);
196 0 : parse("SHIFT", kshift_);
197 : }
198 :
199 6 : log << " Bibliography ";
200 12 : log<<plumed.cite("Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)");
201 :
202 : // Set Karplus parameters
203 6 : switch (jtype_) {
204 1 : case HAN:
205 1 : ka_ = -0.88;
206 1 : kb_ = -0.61;
207 1 : kc_ = -0.27;
208 1 : kshift_ = pi / 3.0;
209 2 : log << plumed.cite("Wang A C, Bax A, J. Am. Chem. Soc. 117, 1810 (1995)");
210 1 : log<<"\n";
211 1 : log.printf(" J-coupling type is HAN, with A: %f, B: %f, C: %f, angle shift: %f\n", ka_, kb_, kc_, kshift_);
212 : break;
213 3 : case HAHN:
214 3 : ka_ = 7.09;
215 3 : kb_ = -1.42;
216 3 : kc_ = 1.55;
217 3 : kshift_ = -pi / 3.0;
218 6 : log << plumed.cite("Hu J-S, Bax A, J. Am. Chem. Soc. 119, 6360 (1997)");
219 3 : log<<"\n";
220 3 : log.printf(" J-coupling type is HAHN, with A: %f, B: %f, C: %f, angle shift: %f\n", ka_, kb_, kc_, kshift_);
221 : break;
222 1 : case CCG:
223 1 : ka_ = 2.31;
224 1 : kb_ = -0.87;
225 1 : kc_ = 0.55;
226 1 : kshift_ = (2.0 * pi) / 3.0;
227 2 : log << plumed.cite("Perez C, Löhr F, Rüterjans H, Schmidt J, J. Am. Chem. Soc. 123, 7081 (2001)");
228 1 : log<<"\n";
229 1 : log.printf(" J-coupling type is CCG, with A: %f, B: %f, C: %f, angle shift: %f\n", ka_, kb_, kc_, kshift_);
230 : break;
231 1 : case NCG:
232 1 : ka_ = 1.29;
233 1 : kb_ = -0.49;
234 1 : kc_ = 0.37;
235 1 : kshift_ = 0.0;
236 2 : log << plumed.cite("Perez C, Löhr F, Rüterjans H, Schmidt J, J. Am. Chem. Soc. 123, 7081 (2001)");
237 1 : log<<"\n";
238 1 : log.printf(" J-coupling type is NCG, with A: %f, B: %f, C: %f, angle shift: %f\n", ka_, kb_, kc_, kshift_);
239 : break;
240 0 : case CUSTOM:
241 0 : log<<"\n";
242 0 : log.printf(" J-coupling type is custom, with A: %f, B: %f, C: %f, angle shift: %f\n", ka_, kb_, kc_, kshift_);
243 : break;
244 : }
245 :
246 34 : for (unsigned i = 0; i < ncoupl_; ++i) {
247 28 : log.printf(" The %uth J-Coupling is calculated from atoms : %d %d %d %d.",
248 28 : i+1, atoms[6*i].serial(), atoms[6*i+1].serial(), atoms[6*i+3].serial(), atoms[6*i+5].serial());
249 28 : if (addcoupling) {
250 7 : log.printf(" Experimental J-Coupling is %f.", coupl[i]);
251 : }
252 28 : log.printf("\n");
253 : }
254 :
255 6 : if (pbc) {
256 0 : log.printf(" using periodic boundary conditions\n");
257 : } else {
258 6 : log.printf(" without periodic boundary conditions\n");
259 : }
260 :
261 6 : if(!getDoScore()) {
262 26 : for (unsigned i = 0; i < ncoupl_; i++) {
263 21 : std::string num; Tools::convert(i, num);
264 42 : addComponentWithDerivatives("j-" + num);
265 42 : componentIsNotPeriodic("j-" + num);
266 : }
267 : } else {
268 8 : for (unsigned i = 0; i < ncoupl_; i++) {
269 7 : std::string num; Tools::convert(i, num);
270 14 : addComponent("j-" + num);
271 14 : componentIsNotPeriodic("j-" + num);
272 : }
273 : }
274 :
275 6 : if (addcoupling||getDoScore()) {
276 8 : for (unsigned i = 0; i < ncoupl_; i++) {
277 7 : std::string num; Tools::convert(i, num);
278 14 : addComponent("exp-" + num);
279 7 : componentIsNotPeriodic("exp-" + num);
280 7 : Value* comp = getPntrToComponent("exp-" + num);
281 7 : comp->set(coupl[i]);
282 : }
283 : }
284 :
285 6 : requestAtoms(atoms, false);
286 6 : if(getDoScore()) {
287 1 : setParameters(coupl);
288 1 : Initialise(ncoupl_);
289 : }
290 6 : setDerivatives();
291 6 : checkRead();
292 6 : }
293 :
294 16 : void JCoupling::calculate()
295 : {
296 16 : if (pbc) makeWhole();
297 16 : std::vector<Vector> deriv(ncoupl_*6);
298 16 : std::vector<double> j(ncoupl_,0.);
299 :
300 16 : #pragma omp parallel num_threads(OpenMP::getNumThreads())
301 : {
302 : #pragma omp for
303 : // Loop through atoms, with steps of 6 atoms (one iteration per datapoint)
304 : for (unsigned r=0; r<ncoupl_; r++) {
305 : // Index is the datapoint index
306 : unsigned a0 = 6*r;
307 :
308 : // 6 atoms -> 3 vectors
309 : Vector d0 = delta(getPosition(a0+1), getPosition(a0));
310 : Vector d1 = delta(getPosition(a0+3), getPosition(a0+2));
311 : Vector d2 = delta(getPosition(a0+5), getPosition(a0+4));
312 :
313 : // Calculate dihedral with 3 vectors, get the derivatives
314 : Vector dd0, dd1, dd2;
315 : PLMD::Torsion t;
316 : double torsion = t.compute(d0, d1, d2, dd0, dd1, dd2);
317 :
318 : // Calculate the Karplus relation and its derivative
319 : double theta = torsion + kshift_;
320 : double cos_theta = std::cos(theta);
321 : double sin_theta = std::sin(theta);
322 : j[r] = ka_*cos_theta*cos_theta + kb_*cos_theta + kc_;
323 : double derj = -2.*ka_*sin_theta*cos_theta - kb_*sin_theta;
324 :
325 : dd0 *= derj;
326 : dd1 *= derj;
327 : dd2 *= derj;
328 :
329 : if(getDoScore()) setCalcData(r, j[r]);
330 : deriv[a0] = dd0;
331 : deriv[a0+1] = -dd0;
332 : deriv[a0+2] = dd1;
333 : deriv[a0+3] = -dd1;
334 : deriv[a0+4] = dd2;
335 : deriv[a0+5] = -dd2;
336 : }
337 : }
338 :
339 16 : if(getDoScore()) {
340 : /* Metainference */
341 6 : double score = getScore();
342 6 : setScore(score);
343 :
344 : /* calculate final derivatives */
345 6 : Tensor virial;
346 6 : Value* val=getPntrToComponent("score");
347 48 : for (unsigned r=0; r<ncoupl_; r++) {
348 42 : const unsigned a0 = 6*r;
349 42 : setAtomsDerivatives(val, a0, deriv[a0]*getMetaDer(r));
350 42 : setAtomsDerivatives(val, a0+1, deriv[a0+1]*getMetaDer(r));
351 42 : setAtomsDerivatives(val, a0+2, deriv[a0+2]*getMetaDer(r));
352 42 : setAtomsDerivatives(val, a0+3, deriv[a0+3]*getMetaDer(r));
353 42 : setAtomsDerivatives(val, a0+4, deriv[a0+4]*getMetaDer(r));
354 42 : setAtomsDerivatives(val, a0+5, deriv[a0+5]*getMetaDer(r));
355 42 : virial-=Tensor(getPosition(a0), deriv[a0]*getMetaDer(r));
356 42 : virial-=Tensor(getPosition(a0+1), deriv[a0+1]*getMetaDer(r));
357 42 : virial-=Tensor(getPosition(a0+2), deriv[a0+2]*getMetaDer(r));
358 42 : virial-=Tensor(getPosition(a0+3), deriv[a0+3]*getMetaDer(r));
359 42 : virial-=Tensor(getPosition(a0+4), deriv[a0+4]*getMetaDer(r));
360 42 : virial-=Tensor(getPosition(a0+5), deriv[a0+5]*getMetaDer(r));
361 : }
362 6 : setBoxDerivatives(val, virial);
363 : } else {
364 66 : for (unsigned r=0; r<ncoupl_; r++) {
365 56 : const unsigned a0 = 6*r;
366 56 : std::string num; Tools::convert(r,num);
367 56 : Value* val=getPntrToComponent("j-"+num);
368 56 : val->set(j[r]);
369 56 : setAtomsDerivatives(val, a0, deriv[a0]);
370 56 : setAtomsDerivatives(val, a0+1, deriv[a0+1]);
371 56 : setAtomsDerivatives(val, a0+2, deriv[a0+2]);
372 56 : setAtomsDerivatives(val, a0+3, deriv[a0+3]);
373 56 : setAtomsDerivatives(val, a0+4, deriv[a0+4]);
374 56 : setAtomsDerivatives(val, a0+5, deriv[a0+5]);
375 56 : Tensor virial;
376 56 : virial-=Tensor(getPosition(a0), deriv[a0]);
377 56 : virial-=Tensor(getPosition(a0+1), deriv[a0+1]);
378 56 : virial-=Tensor(getPosition(a0+2), deriv[a0+2]);
379 56 : virial-=Tensor(getPosition(a0+3), deriv[a0+3]);
380 56 : virial-=Tensor(getPosition(a0+4), deriv[a0+4]);
381 56 : virial-=Tensor(getPosition(a0+5), deriv[a0+5]);
382 56 : setBoxDerivatives(val, virial);
383 : }
384 : }
385 16 : }
386 :
387 16 : void JCoupling::update() {
388 : // write status file
389 16 : if(getWstride()>0&& (getStep()%getWstride()==0 || getCPT()) ) writeStatus();
390 16 : }
391 :
392 : }
393 : }
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