Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2014-2023 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/NeighborList.h"
25 : #include "tools/Pbc.h"
26 : #include <memory>
27 :
28 : namespace PLMD {
29 : namespace isdb {
30 :
31 : //+PLUMEDOC ISDB_COLVAR NOE
32 : /*
33 : Calculates NOE intensities as sums of 1/r^6, also averaging over multiple equivalent atoms
34 : or ambiguous NOE.
35 :
36 : Each NOE is defined by two groups containing the same number of atoms, distances are
37 : calculated in pairs, transformed in 1/r^6, summed and saved as components.
38 :
39 : \f[
40 : NOE() = (\frac{1}{N_{eq}}\sum_j^{N_{eq}} (\frac{1}{r_j^6}))
41 : \f]
42 :
43 : NOE can be used to calculate a Metainference score over one or more replicas using the intrinsic implementation
44 : of \ref METAINFERENCE that is activated by DOSCORE.
45 :
46 : \par Examples
47 : In the following examples three noes are defined, the first is calculated based on the distances
48 : of atom 1-2 and 3-2; the second is defined by the distance 5-7 and the third by the distances
49 : 4-15,4-16,8-15,8-16. \ref METAINFERENCE is activated using DOSCORE.
50 :
51 : \plumedfile
52 : NOE ...
53 : GROUPA1=1,3 GROUPB1=2,2 NOEDIST1=0.6
54 : GROUPA2=5 GROUPB2=7 NOEDIST2=0.6
55 : GROUPA3=4,4,8,8 GROUPB3=15,16,15,16 NOEDIST3=0.6
56 : DOSCORE
57 : SIGMA_MEAN0=1
58 : LABEL=noes
59 : ... NOE
60 :
61 : PRINT ARG=noes.* FILE=colvar
62 : \endplumedfile
63 :
64 : */
65 : //+ENDPLUMEDOC
66 :
67 : class NOE :
68 : public MetainferenceBase {
69 : private:
70 : bool pbc;
71 : std::vector<unsigned> nga;
72 : std::unique_ptr<NeighborList> nl;
73 : unsigned tot_size;
74 : public:
75 : static void registerKeywords( Keywords& keys );
76 : explicit NOE(const ActionOptions&);
77 : void calculate() override;
78 : void update() override;
79 : };
80 :
81 : PLUMED_REGISTER_ACTION(NOE,"NOE")
82 :
83 19 : void NOE::registerKeywords( Keywords& keys ) {
84 19 : MetainferenceBase::registerKeywords(keys);
85 19 : keys.addFlag("NOPBC",false,"ignore the periodic boundary conditions when calculating distances");
86 19 : keys.add("numbered","GROUPA","the atoms involved in each of the contacts you wish to calculate. "
87 : "Keywords like GROUPA1, GROUPA2, GROUPA3,... should be listed and one contact will be "
88 : "calculated for each ATOM keyword you specify.");
89 19 : keys.add("numbered","GROUPB","the atoms involved in each of the contacts you wish to calculate. "
90 : "Keywords like GROUPB1, GROUPB2, GROUPB3,... should be listed and one contact will be "
91 : "calculated for each ATOM keyword you specify.");
92 38 : keys.reset_style("GROUPA","atoms");
93 38 : keys.reset_style("GROUPB","atoms");
94 19 : keys.add("numbered","NOEDIST","Add an experimental value for each NOE.");
95 38 : keys.addOutputComponent("noe","default","scalar","the # NOE");
96 38 : keys.addOutputComponent("exp","NOEDIST","scalar","the # NOE experimental distance");
97 19 : }
98 :
99 17 : NOE::NOE(const ActionOptions&ao):
100 : PLUMED_METAINF_INIT(ao),
101 17 : pbc(true) {
102 17 : bool nopbc=!pbc;
103 17 : parseFlag("NOPBC",nopbc);
104 17 : pbc=!nopbc;
105 :
106 : // Read in the atoms
107 : std::vector<AtomNumber> t, ga_lista, gb_lista;
108 34 : for(int i=1;; ++i ) {
109 102 : parseAtomList("GROUPA", i, t );
110 51 : if( t.empty() ) {
111 : break;
112 : }
113 85 : for(unsigned j=0; j<t.size(); j++) {
114 51 : ga_lista.push_back(t[j]);
115 : }
116 34 : nga.push_back(t.size());
117 34 : t.resize(0);
118 34 : }
119 : std::vector<unsigned> ngb;
120 34 : for(int i=1;; ++i ) {
121 102 : parseAtomList("GROUPB", i, t );
122 51 : if( t.empty() ) {
123 : break;
124 : }
125 85 : for(unsigned j=0; j<t.size(); j++) {
126 51 : gb_lista.push_back(t[j]);
127 : }
128 34 : ngb.push_back(t.size());
129 34 : if(ngb[i-1]!=nga[i-1]) {
130 0 : error("The same number of atoms is expected for the same GROUPA-GROUPB couple");
131 : }
132 34 : t.resize(0);
133 34 : }
134 17 : if(nga.size()!=ngb.size()) {
135 0 : error("There should be the same number of GROUPA and GROUPB keywords");
136 : }
137 : // Create neighbour lists
138 34 : nl=Tools::make_unique<NeighborList>(ga_lista,gb_lista,false,true,pbc,getPbc(),comm);
139 :
140 : // Optionally add an experimental value (like with RDCs)
141 : std::vector<double> noedist;
142 17 : noedist.resize( nga.size() );
143 : unsigned ntarget=0;
144 43 : for(unsigned i=0; i<nga.size(); ++i) {
145 60 : if( !parseNumbered( "NOEDIST", i+1, noedist[i] ) ) {
146 : break;
147 : }
148 26 : ntarget++;
149 : }
150 : bool addexp=false;
151 17 : if(ntarget!=nga.size() && ntarget!=0) {
152 0 : error("found wrong number of NOEDIST values");
153 : }
154 17 : if(ntarget==nga.size()) {
155 : addexp=true;
156 : }
157 17 : if(getDoScore()&&!addexp) {
158 0 : error("with DOSCORE you need to set the NOEDIST values");
159 : }
160 :
161 : // Output details of all contacts
162 : unsigned index=0;
163 51 : for(unsigned i=0; i<nga.size(); ++i) {
164 34 : log.printf(" The %uth NOE is calculated using %u equivalent couples of atoms\n", i, nga[i]);
165 85 : for(unsigned j=0; j<nga[i]; j++) {
166 51 : log.printf(" couple %u is %d %d.\n", j, ga_lista[index].serial(), gb_lista[index].serial() );
167 51 : index++;
168 : }
169 : }
170 17 : tot_size = index;
171 :
172 17 : if(pbc) {
173 17 : log.printf(" using periodic boundary conditions\n");
174 : } else {
175 0 : log.printf(" without periodic boundary conditions\n");
176 : }
177 :
178 34 : log << " Bibliography" << plumed.cite("Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)") << "\n";
179 :
180 17 : if(!getDoScore()) {
181 27 : for(unsigned i=0; i<nga.size(); i++) {
182 : std::string num;
183 18 : Tools::convert(i,num);
184 36 : addComponentWithDerivatives("noe-"+num);
185 36 : componentIsNotPeriodic("noe-"+num);
186 : }
187 9 : if(addexp) {
188 15 : for(unsigned i=0; i<nga.size(); i++) {
189 : std::string num;
190 10 : Tools::convert(i,num);
191 20 : addComponent("exp-"+num);
192 10 : componentIsNotPeriodic("exp-"+num);
193 10 : Value* comp=getPntrToComponent("exp-"+num);
194 10 : comp->set(noedist[i]);
195 : }
196 : }
197 : } else {
198 24 : for(unsigned i=0; i<nga.size(); i++) {
199 : std::string num;
200 16 : Tools::convert(i,num);
201 32 : addComponent("noe-"+num);
202 32 : componentIsNotPeriodic("noe-"+num);
203 : }
204 24 : for(unsigned i=0; i<nga.size(); i++) {
205 : std::string num;
206 16 : Tools::convert(i,num);
207 32 : addComponent("exp-"+num);
208 16 : componentIsNotPeriodic("exp-"+num);
209 16 : Value* comp=getPntrToComponent("exp-"+num);
210 16 : comp->set(noedist[i]);
211 : }
212 : }
213 :
214 17 : requestAtoms(nl->getFullAtomList(), false);
215 17 : if(getDoScore()) {
216 8 : setParameters(noedist);
217 8 : Initialise(nga.size());
218 : }
219 17 : setDerivatives();
220 17 : checkRead();
221 17 : }
222 :
223 528 : void NOE::calculate() {
224 528 : const unsigned ngasz=nga.size();
225 528 : std::vector<Vector> deriv(tot_size, Vector{0,0,0});
226 :
227 528 : #pragma omp parallel for num_threads(OpenMP::getNumThreads())
228 : for(unsigned i=0; i<ngasz; i++) {
229 : Tensor dervir;
230 : double noe=0;
231 : unsigned index=0;
232 : for(unsigned k=0; k<i; k++) {
233 : index+=nga[k];
234 : }
235 : std::string num;
236 : Tools::convert(i,num);
237 : Value* val=getPntrToComponent("noe-"+num);
238 : // cycle over equivalent atoms
239 : for(unsigned j=0; j<nga[i]; j++) {
240 : const unsigned i0=nl->getClosePair(index+j).first;
241 : const unsigned i1=nl->getClosePair(index+j).second;
242 :
243 : Vector distance;
244 : if(pbc) {
245 : distance=pbcDistance(getPosition(i0),getPosition(i1));
246 : } else {
247 : distance=delta(getPosition(i0),getPosition(i1));
248 : }
249 :
250 : const double ir2=1./distance.modulo2();
251 : const double ir6=ir2*ir2*ir2;
252 : const double ir8=6*ir6*ir2;
253 :
254 : noe += ir6;
255 : deriv[index+j] = ir8*distance;
256 : if(!getDoScore()) {
257 : dervir += Tensor(distance, deriv[index+j]);
258 : setAtomsDerivatives(val, i0, deriv[index+j]);
259 : setAtomsDerivatives(val, i1, -deriv[index+j]);
260 : }
261 : }
262 : val->set(noe);
263 : if(!getDoScore()) {
264 : setBoxDerivatives(val, dervir);
265 : } else {
266 : setCalcData(i, noe);
267 : }
268 : }
269 :
270 528 : if(getDoScore()) {
271 : /* Metainference */
272 96 : Tensor dervir;
273 96 : double score = getScore();
274 96 : setScore(score);
275 :
276 : /* calculate final derivatives */
277 96 : Value* val=getPntrToComponent("score");
278 288 : for(unsigned i=0; i<ngasz; i++) {
279 : unsigned index=0;
280 288 : for(unsigned k=0; k<i; k++) {
281 96 : index+=nga[k];
282 : }
283 : // cycle over equivalent atoms
284 480 : for(unsigned j=0; j<nga[i]; j++) {
285 288 : const unsigned i0=nl->getClosePair(index+j).first;
286 288 : const unsigned i1=nl->getClosePair(index+j).second;
287 :
288 288 : Vector distance;
289 288 : if(pbc) {
290 288 : distance=pbcDistance(getPosition(i0),getPosition(i1));
291 : } else {
292 0 : distance=delta(getPosition(i0),getPosition(i1));
293 : }
294 :
295 288 : dervir += Tensor(distance,deriv[index+j]*getMetaDer(i));
296 288 : setAtomsDerivatives(val, i0, deriv[index+j]*getMetaDer(i));
297 288 : setAtomsDerivatives(val, i1, -deriv[index+j]*getMetaDer(i));
298 : }
299 : }
300 96 : setBoxDerivatives(val, dervir);
301 : }
302 528 : }
303 :
304 204 : void NOE::update() {
305 : // write status file
306 204 : if(getWstride()>0&& (getStep()%getWstride()==0 || getCPT()) ) {
307 17 : writeStatus();
308 : }
309 204 : }
310 :
311 : }
312 : }
|
