Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2016-2019 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 : using namespace std;
28 :
29 : namespace PLMD {
30 : namespace isdb {
31 :
32 : //+PLUMEDOC ISDB_COLVAR JCOUPLING
33 : /*
34 : Calculates \f$^3J\f$ coupling constants for a dihedral angle.
35 :
36 : The J-coupling between two atoms is given by the Karplus relation:
37 :
38 : \f[
39 : ^3J(\theta)=A\cos^2(\theta+\Delta\theta)+B\cos(\theta+\Delta\theta)+C
40 : \f]
41 :
42 : where \f$A\f$, \f$B\f$ and \f$C\f$ are the Karplus parameters and \f$\Delta\theta\f$ is an additional constant
43 : added on to the dihedral angle \f$\theta\f$. The Karplus parameters are determined empirically and are dependent
44 : on the type of J-coupling.
45 :
46 : This collective variable computes the J-couplings for a set of atoms defining a dihedral angle. You can specify
47 : the atoms involved using the \ref MOLINFO notation. You can also specify the experimental couplings using the
48 : COUPLING keywords. These will be included in the output. You must choose the type of
49 : coupling using the type keyword, you can also supply custom Karplus parameters using TYPE=CUSTOM and the A, B, C
50 : and SHIFT keywords. You will need to make sure you are using the correct dihedral angle:
51 :
52 : - Ha-N: \f$\psi\f$
53 : - Ha-HN: \f$\phi\f$
54 : - N-C\f$\gamma\f$: \f$\chi_1\f$
55 : - CO-C\f$\gamma\f$: \f$\chi_1\f$
56 :
57 : J-couplings can be used to calculate a Metainference score using the internal keyword DOSCORE and all the options
58 : of \ref METAINFERENCE .
59 :
60 : \par Examples
61 :
62 : In the following example we calculate the Ha-N J-coupling from a set of atoms involved in
63 : dihedral \f$\psi\f$ angles in the peptide backbone. We also add the experimental data points and compute
64 : the correlation and other measures and finally print the results.
65 :
66 : \plumedfile
67 : #SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
68 : MOLINFO MOLTYPE=protein STRUCTURE=peptide.pdb
69 : WHOLEMOLECULES ENTITY0=1-111
70 :
71 : JCOUPLING ...
72 : TYPE=HAN
73 : ATOMS1=@psi-2 COUPLING1=-0.49
74 : ATOMS2=@psi-4 COUPLING2=-0.54
75 : ATOMS3=@psi-5 COUPLING3=-0.53
76 : ATOMS4=@psi-7 COUPLING4=-0.39
77 : ATOMS5=@psi-8 COUPLING5=-0.39
78 : LABEL=jhan
79 : ... JCOUPLING
80 :
81 : jhanst: STATS ARG=(jhan\.j-.*) PARARG=(jhan\.exp-.*)
82 :
83 : PRINT ARG=jhanst.*,jhan.* FILE=COLVAR STRIDE=100
84 : \endplumedfile
85 :
86 : */
87 : //+ENDPLUMEDOC
88 :
89 12 : class JCoupling :
90 : public MetainferenceBase
91 : {
92 : private:
93 : bool pbc;
94 : enum { HAN, HAHN, CCG, NCG, CUSTOM };
95 : unsigned ncoupl_;
96 : double ka_;
97 : double kb_;
98 : double kc_;
99 : double kshift_;
100 :
101 : public:
102 : static void registerKeywords(Keywords& keys);
103 : explicit JCoupling(const ActionOptions&);
104 : void calculate() override;
105 : void update() override;
106 : };
107 :
108 7844 : PLUMED_REGISTER_ACTION(JCoupling, "JCOUPLING")
109 :
110 7 : void JCoupling::registerKeywords(Keywords& keys) {
111 7 : componentsAreNotOptional(keys);
112 7 : MetainferenceBase::registerKeywords(keys);
113 21 : keys.addFlag("NOPBC",false,"ignore the periodic boundary conditions when calculating distances");
114 : keys.add("numbered", "ATOMS", "the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling. "
115 : "Keywords like ATOMS1, ATOMS2, ATOMS3,... should be listed and one J-coupling will be "
116 28 : "calculated for each ATOMS keyword you specify.");
117 21 : keys.reset_style("ATOMS", "atoms");
118 28 : keys.add("compulsory", "TYPE", "Type of J-coupling to compute (HAN,HAHN,CCG,NCG,CUSTOM)");
119 28 : keys.add("optional", "A", "Karplus parameter A");
120 28 : keys.add("optional", "B", "Karplus parameter B");
121 28 : keys.add("optional", "C", "Karplus parameter C");
122 28 : keys.add("optional", "SHIFT", "Angle shift in radians");
123 28 : keys.add("numbered", "COUPLING", "Add an experimental value for each coupling");
124 28 : keys.addOutputComponent("j", "default", "the calculated J-coupling");
125 28 : keys.addOutputComponent("exp", "COUPLING", "the experimental J-coupling");
126 7 : }
127 :
128 6 : JCoupling::JCoupling(const ActionOptions&ao):
129 : PLUMED_METAINF_INIT(ao),
130 6 : pbc(true)
131 : {
132 6 : bool nopbc = !pbc;
133 12 : parseFlag("NOPBC", nopbc);
134 6 : pbc =! nopbc;
135 :
136 : // Read in the atoms
137 : vector<AtomNumber> t, atoms;
138 28 : for (int i = 1; ; ++i) {
139 68 : parseAtomList("ATOMS", i, t );
140 34 : if (t.empty()) {
141 : break;
142 : }
143 :
144 28 : if (t.size() != 4) {
145 : std::string ss;
146 0 : Tools::convert(i, ss);
147 0 : error("ATOMS" + ss + " keyword has the wrong number of atoms");
148 : }
149 :
150 : // This makes the distance calculation easier later on (see Torsion implementation)
151 28 : atoms.push_back(t[0]);
152 28 : atoms.push_back(t[1]);
153 28 : atoms.push_back(t[1]);
154 28 : atoms.push_back(t[2]);
155 28 : atoms.push_back(t[2]);
156 28 : atoms.push_back(t[3]);
157 28 : t.resize(0);
158 28 : }
159 :
160 : // We now have 6 atoms per datapoint
161 6 : ncoupl_ = atoms.size()/6;
162 :
163 : // Parse J-Coupling type, this will determine the Karplus parameters
164 : unsigned jtype_ = CUSTOM;
165 : string string_type;
166 12 : parse("TYPE", string_type);
167 6 : if(string_type == "HAN") {
168 : jtype_ = HAN;
169 5 : } else if(string_type == "HAHN") {
170 : jtype_ = HAHN;
171 2 : } else if(string_type == "CCG") {
172 : jtype_ = CCG;
173 1 : } else if(string_type == "NCG") {
174 : jtype_ = NCG;
175 0 : } else if(string_type == "CUSTOM") {
176 : jtype_ = CUSTOM;
177 : } else {
178 0 : error("Unknown J-coupling type!");
179 : }
180 :
181 : // Optionally add an experimental value (like with RDCs)
182 : vector<double> coupl;
183 6 : coupl.resize( ncoupl_ );
184 : unsigned ntarget=0;
185 13 : for(unsigned i=0; i<ncoupl_; ++i) {
186 36 : if( !parseNumbered( "COUPLING", i+1, coupl[i] ) ) break;
187 7 : ntarget++;
188 : }
189 : bool addcoupling=false;
190 6 : if(ntarget!=ncoupl_ && ntarget!=0) error("found wrong number of COUPLING values");
191 6 : if(ntarget==ncoupl_) addcoupling=true;
192 6 : if(getDoScore()&&!addcoupling) error("with DOSCORE you need to set the COUPLING values");
193 :
194 : // For custom types we allow use of custom Karplus parameters
195 6 : if (jtype_ == CUSTOM) {
196 0 : parse("A", ka_);
197 0 : parse("B", kb_);
198 0 : parse("C", kc_);
199 0 : parse("SHIFT", kshift_);
200 : }
201 :
202 6 : log << " Bibliography ";
203 :
204 : // Set Karplus parameters
205 6 : switch (jtype_) {
206 : case HAN:
207 1 : ka_ = -0.88;
208 1 : kb_ = -0.61;
209 1 : kc_ = -0.27;
210 1 : kshift_ = pi / 3.0;
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 3 : log << plumed.cite("Wang A C, Bax A, J. Am. Chem. Soc. 117, 1810 (1995)");
213 1 : break;
214 : case HAHN:
215 3 : ka_ = 7.09;
216 3 : kb_ = -1.42;
217 3 : kc_ = 1.55;
218 3 : kshift_ = -pi / 3.0;
219 3 : log.printf("J-coupling type is HAHN, with A: %f, B: %f, C: %f, angle shift: %f\n", ka_, kb_, kc_, kshift_);
220 9 : log << plumed.cite("Hu J-S, Bax A, J. Am. Chem. Soc. 119, 6360 (1997)");
221 3 : break;
222 : 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 1 : log.printf("J-coupling type is CCG, with A: %f, B: %f, C: %f, angle shift: %f\n", ka_, kb_, kc_, kshift_);
228 3 : log << plumed.cite("Perez C, Löhr F, Rüterjans H, Schmidt J, J. Am. Chem. Soc. 123, 7081 (2001)");
229 1 : break;
230 : case NCG:
231 1 : ka_ = 1.29;
232 1 : kb_ = -0.49;
233 1 : kc_ = 0.37;
234 1 : kshift_ = 0.0;
235 1 : log.printf("J-coupling type is NCG, with A: %f, B: %f, C: %f, angle shift: %f\n", ka_, kb_, kc_, kshift_);
236 3 : log << plumed.cite("Perez C, Löhr F, Rüterjans H, Schmidt J, J. Am. Chem. Soc. 123, 7081 (2001)");
237 1 : break;
238 : case CUSTOM:
239 0 : log.printf("J-coupling type is custom, with A: %f, B: %f, C: %f, angle shift: %f\n", ka_, kb_, kc_, kshift_);
240 : break;
241 : }
242 18 : log<<plumed.cite("Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)");
243 6 : log<<"\n";
244 :
245 34 : for (unsigned i = 0; i < ncoupl_; ++i) {
246 : log.printf(" The %uth J-Coupling is calculated from atoms : %d %d %d %d.",
247 140 : i+1, atoms[2*i].serial(), atoms[2*i+1].serial(), atoms[2*i+2].serial(), atoms[2*i+3].serial());
248 28 : if (addcoupling) {
249 14 : log.printf(" Experimental J-Coupling is %f.", coupl[i]);
250 : }
251 28 : log.printf("\n");
252 : }
253 :
254 6 : if (pbc) {
255 0 : log.printf(" using periodic boundary conditions\n");
256 : } else {
257 6 : log.printf(" without periodic boundary conditions\n");
258 : }
259 :
260 6 : if(!getDoScore()) {
261 21 : for (unsigned i = 0; i < ncoupl_; i++) {
262 21 : std::string num; Tools::convert(i, num);
263 42 : addComponentWithDerivatives("j-" + num);
264 42 : componentIsNotPeriodic("j-" + num);
265 : }
266 : } else {
267 7 : for (unsigned i = 0; i < ncoupl_; i++) {
268 7 : std::string num; Tools::convert(i, num);
269 14 : addComponent("j-" + num);
270 14 : componentIsNotPeriodic("j-" + num);
271 : }
272 : }
273 :
274 11 : if (addcoupling||getDoScore()) {
275 7 : for (unsigned i = 0; i < ncoupl_; i++) {
276 7 : std::string num; Tools::convert(i, num);
277 14 : addComponent("exp-" + num);
278 14 : componentIsNotPeriodic("exp-" + num);
279 14 : Value* comp = getPntrToComponent("exp-" + num);
280 14 : comp->set(coupl[i]);
281 : }
282 : }
283 :
284 6 : requestAtoms(atoms, false);
285 6 : if(getDoScore()) {
286 1 : setParameters(coupl);
287 1 : Initialise(ncoupl_);
288 : }
289 6 : setDerivatives();
290 6 : checkRead();
291 6 : }
292 :
293 16 : void JCoupling::calculate()
294 : {
295 16 : if (pbc) makeWhole();
296 16 : vector<Vector> deriv(ncoupl_*6);
297 16 : vector<double> j(ncoupl_,0.);
298 :
299 46 : #pragma omp parallel num_threads(OpenMP::getNumThreads())
300 : {
301 30 : #pragma omp for
302 : // Loop through atoms, with steps of 6 atoms (one iteration per datapoint)
303 : for (unsigned r=0; r<ncoupl_; r++) {
304 : // Index is the datapoint index
305 98 : unsigned a0 = 6*r;
306 :
307 : // 6 atoms -> 3 vectors
308 294 : Vector d0 = delta(getPosition(a0+1), getPosition(a0));
309 294 : Vector d1 = delta(getPosition(a0+3), getPosition(a0+2));
310 294 : Vector d2 = delta(getPosition(a0+5), getPosition(a0+4));
311 :
312 : // Calculate dihedral with 3 vectors, get the derivatives
313 98 : Vector dd0, dd1, dd2;
314 : PLMD::Torsion t;
315 98 : double torsion = t.compute(d0, d1, d2, dd0, dd1, dd2);
316 :
317 : // Calculate the Karplus relation and its derivative
318 98 : double theta = torsion + kshift_;
319 98 : double cos_theta = cos(theta);
320 98 : double sin_theta = sin(theta);
321 196 : j[r] = ka_*cos_theta*cos_theta + kb_*cos_theta + kc_;
322 98 : double derj = -2.*ka_*sin_theta*cos_theta - kb_*sin_theta;
323 :
324 98 : dd0 *= derj;
325 97 : dd1 *= derj;
326 98 : dd2 *= derj;
327 :
328 182 : if(getDoScore()) setCalcData(r, j[r]);
329 196 : deriv[a0] = dd0;
330 196 : deriv[a0+1] = -dd0;
331 196 : deriv[a0+2] = dd1;
332 196 : deriv[a0+3] = -dd1;
333 196 : deriv[a0+4] = dd2;
334 196 : deriv[a0+5] = -dd2;
335 : }
336 : }
337 :
338 16 : if(getDoScore()) {
339 : /* Metainference */
340 6 : double score = getScore();
341 : setScore(score);
342 :
343 : /* calculate final derivatives */
344 6 : Tensor virial;
345 12 : Value* val=getPntrToComponent("score");
346 48 : for (unsigned r=0; r<ncoupl_; r++) {
347 42 : const unsigned a0 = 6*r;
348 84 : setAtomsDerivatives(val, a0, deriv[a0]*getMetaDer(r));
349 84 : setAtomsDerivatives(val, a0+1, deriv[a0+1]*getMetaDer(r));
350 84 : setAtomsDerivatives(val, a0+2, deriv[a0+2]*getMetaDer(r));
351 84 : setAtomsDerivatives(val, a0+3, deriv[a0+3]*getMetaDer(r));
352 84 : setAtomsDerivatives(val, a0+4, deriv[a0+4]*getMetaDer(r));
353 84 : setAtomsDerivatives(val, a0+5, deriv[a0+5]*getMetaDer(r));
354 84 : virial-=Tensor(getPosition(a0), deriv[a0]*getMetaDer(r));
355 84 : virial-=Tensor(getPosition(a0+1), deriv[a0+1]*getMetaDer(r));
356 84 : virial-=Tensor(getPosition(a0+2), deriv[a0+2]*getMetaDer(r));
357 84 : virial-=Tensor(getPosition(a0+3), deriv[a0+3]*getMetaDer(r));
358 84 : virial-=Tensor(getPosition(a0+4), deriv[a0+4]*getMetaDer(r));
359 84 : virial-=Tensor(getPosition(a0+5), deriv[a0+5]*getMetaDer(r));
360 : }
361 6 : setBoxDerivatives(val, virial);
362 : } else {
363 56 : for (unsigned r=0; r<ncoupl_; r++) {
364 56 : const unsigned a0 = 6*r;
365 56 : string num; Tools::convert(r,num);
366 112 : Value* val=getPntrToComponent("j-"+num);
367 112 : val->set(j[r]);
368 112 : setAtomsDerivatives(val, a0, deriv[a0]);
369 112 : setAtomsDerivatives(val, a0+1, deriv[a0+1]);
370 112 : setAtomsDerivatives(val, a0+2, deriv[a0+2]);
371 112 : setAtomsDerivatives(val, a0+3, deriv[a0+3]);
372 112 : setAtomsDerivatives(val, a0+4, deriv[a0+4]);
373 112 : setAtomsDerivatives(val, a0+5, deriv[a0+5]);
374 56 : Tensor virial;
375 112 : virial-=Tensor(getPosition(a0), deriv[a0]);
376 112 : virial-=Tensor(getPosition(a0+1), deriv[a0+1]);
377 112 : virial-=Tensor(getPosition(a0+2), deriv[a0+2]);
378 112 : virial-=Tensor(getPosition(a0+3), deriv[a0+3]);
379 112 : virial-=Tensor(getPosition(a0+4), deriv[a0+4]);
380 112 : virial-=Tensor(getPosition(a0+5), deriv[a0+5]);
381 56 : setBoxDerivatives(val, virial);
382 : }
383 : }
384 16 : }
385 :
386 16 : void JCoupling::update() {
387 : // write status file
388 32 : if(getWstride()>0&& (getStep()%getWstride()==0 || getCPT()) ) writeStatus();
389 16 : }
390 :
391 : }
392 5874 : }
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