Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2012-2023 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 "SecondaryStructureBase.h"
23 : #include "core/ActionShortcut.h"
24 : #include "core/ActionRegister.h"
25 :
26 : namespace PLMD {
27 : namespace secondarystructure {
28 :
29 : //+PLUMEDOC COLVAR PARABETARMSD
30 : /*
31 : Probe the parallel beta sheet content of your protein structure.
32 :
33 : Two protein segments containing three contiguous residues can form a parallel beta sheet.
34 : Although if the two segments are part of the same protein chain they must be separated by
35 : a minimum of 3 residues to make room for the turn. This colvar thus generates the set of
36 : all possible six residue sections that could conceivably form a parallel beta sheet
37 : and calculates the [DRMSD](DRMSD.md) or [RMSD](RMSD.md) distance between the configuration in which the residues find themselves
38 : and an idealized parallel beta sheet structure. These distances can be calculated by either
39 : aligning the instantaneous structure with the reference structure and measuring each
40 : atomic displacement or by calculating differences between the set of inter-atomic
41 : distances in the reference and instantaneous structures.
42 :
43 : This colvar is based on the reference in the bibliography below. The authors of
44 : this paper use the set of distances from the parallel beta sheet configurations to measure
45 : the number of segments whose configuration resembles a parallel beta sheet. This is done by calculating
46 : the following sum of functions of the rmsd distances:
47 :
48 : $$
49 : s = \sum_i \frac{ 1 - \left(\frac{r_i-d_0}{r_0}\right)^n } { 1 - \left(\frac{r_i-d_0}{r_0}\right)^m }
50 : $$
51 :
52 : where the sum runs over all possible segments of parallel beta sheet. By default the
53 : NN, MM and D_0 parameters are set equal to those used in the paper cited below. The R_0
54 : parameter must be set by the user - the value used in the paper cited below was 0.08 nm.
55 :
56 : If you change the function in the above sum you can calculate quantities such as the average
57 : distance from a structure composed of only parallel beta sheets or the distance between the set of
58 : residues that is closest to a parallel beta sheet and the reference configuration. To do these sorts of
59 : calculations you can use the AVERAGE and MIN keywords. In addition you can use the LESS_THAN
60 : keyword if you would like to change the form of the switching function. If you use any of these
61 : options you no longer need to specify NN, R_0, MM and D_0.
62 :
63 : The following input calculates the number of six residue segments of
64 : protein that are in an parallel beta sheet configuration.
65 :
66 : ```plumed
67 : #SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
68 : MOLINFO STRUCTURE=regtest/basic/rt32/helix.pdb
69 : pb: PARABETARMSD RESIDUES=all STRANDS_CUTOFF=1 R_0=0.1
70 : PRINT ARG=pb FILE=colvar
71 : ```
72 :
73 : Here the same is done use [RMSD](RMSD.md) instead of [DRMSD](DRMSD.md), which is normally faster.
74 :
75 : ```plumed
76 : #SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
77 : MOLINFO STRUCTURE=regtest/basic/rt32/helix.pdb
78 : WHOLEMOLECULES ENTITY0=1-100
79 : hh: PARABETARMSD RESIDUES=all TYPE=OPTIMAL LESS_THAN={RATIONAL R_0=0.1 NN=8 MM=12} STRANDS_CUTOFF=1
80 : PRINT ARG=hh.lessthan FILE=colvar
81 : ```
82 :
83 : __YOUR CALCULATION WILL BE MUCH FASTER IF YOU USE THE `STRANDS_CUTOFF` KEYWORD.__ As you can see from the
84 : expanded version of the inputs above this keyword reduces the computational cost of the calculation by
85 : avoiding calculations of the RMSD values for segments that have the two strands of the beta sheet further apart
86 : than a cutoff.
87 :
88 : ## Periodic boundary conditions
89 :
90 : You can turn off periodic boundary conditions by using the NOPBC flag as shown below:
91 :
92 : ```plumed
93 : #SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
94 : MOLINFO STRUCTURE=regtest/basic/rt32/helix.pdb
95 : pb: PARABETARMSD RESIDUES=all STRANDS_CUTOFF=1 R_0=0.1 NOPBC
96 : PRINT ARG=pb FILE=colvar
97 : ```
98 :
99 : If you are using [DRMSD](DRMSD.md) to measure distances and you __don't__ use the NOPBC flag then
100 : all distances in the instaneous structure are evaluated in a way that takes the periodic boundary conditions
101 : into account. Using the NOPBC flag turns off this treatment.
102 :
103 : If you are using [RMSD](RMSD.md) to measure distances and you __don't__ use the NOPBC flag the the instaneous positions of
104 : each segment for which the RMSD is computed is reconstructed using the procedure outlined in the documentation for [WHOLEMOLECULES](WHOLEMOLECULES.md)
105 : before the RMSD is computed. Using the NOPBC flag turns off this treatment.
106 :
107 : */
108 : //+ENDPLUMEDOC
109 :
110 : class ParabetaRMSD : public ActionShortcut {
111 : public:
112 : static void registerKeywords( Keywords& keys );
113 : explicit ParabetaRMSD(const ActionOptions&);
114 : };
115 :
116 : PLUMED_REGISTER_ACTION(ParabetaRMSD,"PARABETARMSD")
117 :
118 100 : void ParabetaRMSD::registerKeywords( Keywords& keys ) {
119 100 : SecondaryStructureBase<Vector>::registerKeywords( keys );
120 100 : keys.remove("ATOMS");
121 100 : keys.remove("SEGMENT");
122 100 : keys.remove("STRUCTURE");
123 100 : keys.remove("MASK");
124 100 : keys.remove("ALIGN_STRANDS");
125 200 : keys.setValueDescription("scalar/vector","if LESS_THAN is present the RMSD distance between each residue and the ideal parallel beta sheet. If LESS_THAN is not present the number of residue segments where the structure is similar to a parallel beta sheet");
126 100 : keys.add("compulsory","STYLE","all","Parallel beta sheets can either form in a single chain or from a pair of chains. If STYLE=all all "
127 : "chain configuration with the appropriate geometry are counted. If STYLE=inter "
128 : "only sheet-like configurations involving two chains are counted, while if STYLE=intra "
129 : "only sheet-like configurations involving a single chain are counted");
130 100 : keys.add("optional","STRANDS_CUTOFF","If in a segment of protein the two strands are further apart then the calculation "
131 : "of the actual RMSD is skipped as the structure is very far from being beta-sheet like. "
132 : "This keyword speeds up the calculation enormously when you are using the LESS_THAN option. "
133 : "However, if you are using some other option, then this cannot be used");
134 100 : keys.needsAction("LOWEST");
135 100 : keys.needsAction("DISTANCE");
136 100 : keys.needsAction("CUSTOM");
137 100 : }
138 :
139 18 : ParabetaRMSD::ParabetaRMSD(const ActionOptions&ao):
140 : Action(ao),
141 18 : ActionShortcut(ao) {
142 : // Read in the input and create a string that describes how to compute the less than
143 : std::string ltmap;
144 18 : bool uselessthan=SecondaryStructureBase<Vector>::readShortcutWords( ltmap, this );
145 : // read in the backbone atoms
146 : std::vector<unsigned> chains;
147 : std::vector<std::string> all_atoms;
148 36 : SecondaryStructureBase<Vector>::readBackboneAtoms( this, plumed, "protein", chains, all_atoms );
149 :
150 : bool intra_chain(false), inter_chain(false);
151 : std::string style;
152 36 : parse("STYLE",style);
153 18 : if( Tools::caseInSensStringCompare(style, "all") ) {
154 : intra_chain=true;
155 : inter_chain=true;
156 1 : } else if( Tools::caseInSensStringCompare(style, "inter") ) {
157 : intra_chain=false;
158 : inter_chain=true;
159 0 : } else if( Tools::caseInSensStringCompare(style, "intra") ) {
160 : intra_chain=true;
161 : inter_chain=false;
162 : } else {
163 0 : error( style + " is not a valid directive for the STYLE keyword");
164 : }
165 :
166 18 : double strands_cutoff=-1.0;
167 36 : parse("STRANDS_CUTOFF",strands_cutoff);
168 : std::string scutoff_action;
169 18 : if( strands_cutoff>0 ) {
170 32 : scutoff_action=getShortcutLabel() + "_cut_dists: DISTANCE ";
171 : }
172 :
173 : // This constructs all conceivable sections of antibeta sheet in the backbone of the chains
174 : std::string seglist;
175 18 : unsigned jjkk=1;
176 18 : if( intra_chain ) {
177 : unsigned nprevious=0;
178 17 : std::vector<unsigned> nlist(30);
179 272 : for(unsigned i=0; i<chains.size(); ++i) {
180 255 : if( chains[i]<40 ) {
181 0 : error("segment of backbone is not long enough to form an antiparallel beta hairpin. Each backbone fragment must contain a minimum of 8 residues");
182 : }
183 : // Loop over all possible triples in each 8 residue segment of protein
184 255 : unsigned nres=chains[i]/5;
185 255 : if( chains[i]%5!=0 ) {
186 0 : error("backbone segment received does not contain a multiple of five residues");
187 : }
188 267 : for(unsigned ires=0; ires<nres-8; ires++) {
189 42 : for(unsigned jres=ires+6; jres<nres-2; jres++) {
190 480 : for(unsigned k=0; k<15; ++k) {
191 450 : nlist[k]=nprevious + ires*5+k;
192 450 : nlist[k+15]=nprevious + jres*5+k;
193 : }
194 : std::string nlstr, num;
195 30 : Tools::convert( nlist[0], nlstr );
196 30 : Tools::convert(jjkk, num);
197 30 : jjkk++;
198 60 : seglist += " SEGMENT" + num + "=" + nlstr;
199 900 : for(unsigned kk=1; kk<nlist.size(); ++kk ) {
200 870 : Tools::convert( nlist[kk], nlstr );
201 1740 : seglist += "," + nlstr;
202 : }
203 30 : if( strands_cutoff>0 ) {
204 20 : scutoff_action += " ATOMS" + num + "=" + all_atoms[nlist[6]] + "," + all_atoms[nlist[21]];
205 : }
206 : }
207 : }
208 255 : nprevious+=chains[i];
209 : }
210 : }
211 : // This constructs all conceivable sections of antibeta sheet that form between chains
212 18 : if( inter_chain ) {
213 18 : if( chains.size()==1 && !Tools::caseInSensStringCompare(style, "all") ) {
214 0 : error("there is only one chain defined so cannot use inter_chain option");
215 : }
216 18 : std::vector<unsigned> nlist(30);
217 273 : for(unsigned ichain=1; ichain<chains.size(); ++ichain) {
218 : unsigned iprev=0;
219 2550 : for(unsigned i=0; i<ichain; ++i) {
220 2295 : iprev+=chains[i];
221 : }
222 255 : unsigned inres=chains[ichain]/5;
223 255 : if( chains[ichain]%5!=0 ) {
224 0 : error("backbone segment received does not contain a multiple of five residues");
225 : }
226 1785 : for(unsigned ires=0; ires<inres-2; ++ires) {
227 15300 : for(unsigned jchain=0; jchain<ichain; ++jchain) {
228 : unsigned jprev=0;
229 87210 : for(unsigned i=0; i<jchain; ++i) {
230 73440 : jprev+=chains[i];
231 : }
232 13770 : unsigned jnres=chains[jchain]/5;
233 13770 : if( chains[jchain]%5!=0 ) {
234 0 : error("backbone segment received does not contain a multiple of five residues");
235 : }
236 96390 : for(unsigned jres=0; jres<jnres-2; ++jres) {
237 1321920 : for(unsigned k=0; k<15; ++k) {
238 1239300 : nlist[k]=iprev + ires*5+k;
239 1239300 : nlist[k+15]=jprev + jres*5+k;
240 : }
241 : std::string nlstr, num;
242 82620 : Tools::convert( nlist[0], nlstr );
243 82620 : Tools::convert(jjkk, num);
244 82620 : jjkk++;
245 165240 : seglist += " SEGMENT" + num + "=" + nlstr;
246 2478600 : for(unsigned kk=1; kk<nlist.size(); ++kk ) {
247 2395980 : Tools::convert( nlist[kk], nlstr );
248 4791960 : seglist += "," + nlstr;
249 : }
250 82620 : if( strands_cutoff>0 ) {
251 165240 : scutoff_action += " ATOMS" + num + "=" + all_atoms[nlist[6]] + "," + all_atoms[nlist[21]];
252 : }
253 : }
254 : }
255 : }
256 : }
257 : }
258 :
259 : // Build the reference structure ( in angstroms )
260 18 : std::vector<Vector> reference(30);
261 18 : reference[0]=Vector( 1.244, -4.620, -2.127); // N i
262 18 : reference[1]=Vector(-0.016, -4.500, -1.395); // CA
263 18 : reference[2]=Vector( 0.105, -5.089, 0.024); // CB
264 18 : reference[3]=Vector(-0.287, -3.000, -1.301); // C
265 18 : reference[4]=Vector( 0.550, -2.245, -0.822); // O
266 18 : reference[5]=Vector(-1.445, -2.551, -1.779); // N i+1
267 18 : reference[6]=Vector(-1.752, -1.130, -1.677); // CA
268 18 : reference[7]=Vector(-2.113, -0.550, -3.059); // CB
269 18 : reference[8]=Vector(-2.906, -0.961, -0.689); // C
270 18 : reference[9]=Vector(-3.867, -1.738, -0.695); // O
271 18 : reference[10]=Vector(-2.774, 0.034, 0.190); // N i+2
272 18 : reference[11]=Vector(-3.788, 0.331, 1.201); // CA
273 18 : reference[12]=Vector(-3.188, 0.300, 2.624); // CB
274 18 : reference[13]=Vector(-4.294, 1.743, 0.937); // C
275 18 : reference[14]=Vector(-3.503, 2.671, 0.821); // O
276 18 : reference[15]=Vector( 4.746, -2.363, 0.188); // N j
277 18 : reference[16]=Vector( 3.427, -1.839, 0.545); // CA
278 18 : reference[17]=Vector( 3.135, -1.958, 2.074); // CB
279 18 : reference[18]=Vector( 3.346, -0.365, 0.181); // C
280 18 : reference[19]=Vector( 4.237, 0.412, 0.521); // O
281 18 : reference[20]=Vector( 2.261, 0.013, -0.487); // N j+1
282 18 : reference[21]=Vector( 2.024, 1.401, -0.875); // CA
283 18 : reference[22]=Vector( 1.489, 1.514, -2.313); // CB
284 18 : reference[23]=Vector( 0.914, 1.902, 0.044); // C
285 18 : reference[24]=Vector(-0.173, 1.330, 0.052); // O
286 18 : reference[25]=Vector( 1.202, 2.940, 0.828); // N j+2
287 18 : reference[26]=Vector( 0.190, 3.507, 1.718); // CA
288 18 : reference[27]=Vector( 0.772, 3.801, 3.104); // CB
289 18 : reference[28]=Vector(-0.229, 4.791, 1.038); // C
290 18 : reference[29]=Vector( 0.523, 5.771, 0.996); // O
291 : // Store the secondary structure ( last number makes sure we convert to internal units nm )
292 : std::string ref0, ref1, ref2;
293 18 : Tools::convert( reference[0][0], ref0 );
294 18 : Tools::convert( reference[0][1], ref1 );
295 18 : Tools::convert( reference[0][2], ref2 );
296 36 : std::string structure=" STRUCTURE1=" + ref0 + "," + ref1 + "," + ref2;
297 540 : for(unsigned i=1; i<30; ++i) {
298 2088 : for(unsigned k=0; k<3; ++k) {
299 1566 : Tools::convert( reference[i][k], ref0 );
300 3132 : structure += "," + ref0;
301 : }
302 : }
303 :
304 18 : reference[0]=Vector(-1.439, -5.122, -1.144); // N i
305 18 : reference[1]=Vector(-0.816, -3.803, -1.013); // CA
306 18 : reference[2]=Vector( 0.099, -3.509, -2.206); // CB
307 18 : reference[3]=Vector(-1.928, -2.770, -0.952); // C
308 18 : reference[4]=Vector(-2.991, -2.970, -1.551); // O
309 18 : reference[5]=Vector(-1.698, -1.687, -0.215); // N i+1
310 18 : reference[6]=Vector(-2.681, -0.613, -0.143); // CA
311 18 : reference[7]=Vector(-3.323, -0.477, 1.267); // CB
312 18 : reference[8]=Vector(-1.984, 0.681, -0.574); // C
313 18 : reference[9]=Vector(-0.807, 0.921, -0.273); // O
314 18 : reference[10]=Vector(-2.716, 1.492, -1.329); // N i+2
315 18 : reference[11]=Vector(-2.196, 2.731, -1.883); // CA
316 18 : reference[12]=Vector(-2.263, 2.692, -3.418); // CB
317 18 : reference[13]=Vector(-2.989, 3.949, -1.433); // C
318 18 : reference[14]=Vector(-4.214, 3.989, -1.583); // O
319 18 : reference[15]=Vector( 2.464, -4.352, 2.149); // N j
320 18 : reference[16]=Vector( 3.078, -3.170, 1.541); // CA
321 18 : reference[17]=Vector( 3.398, -3.415, 0.060); // CB
322 18 : reference[18]=Vector( 2.080, -2.021, 1.639); // C
323 18 : reference[19]=Vector( 0.938, -2.178, 1.225); // O
324 18 : reference[20]=Vector( 2.525, -0.886, 2.183); // N j+1
325 18 : reference[21]=Vector( 1.692, 0.303, 2.346); // CA
326 18 : reference[22]=Vector( 1.541, 0.665, 3.842); // CB
327 18 : reference[23]=Vector( 2.420, 1.410, 1.608); // C
328 18 : reference[24]=Vector( 3.567, 1.733, 1.937); // O
329 18 : reference[25]=Vector( 1.758, 1.976, 0.600); // N j+2
330 18 : reference[26]=Vector( 2.373, 2.987, -0.238); // CA
331 18 : reference[27]=Vector( 2.367, 2.527, -1.720); // CB
332 18 : reference[28]=Vector( 1.684, 4.331, -0.148); // C
333 18 : reference[29]=Vector( 0.486, 4.430, -0.415); // O
334 : // Store the secondary structure ( last number makes sure we convert to internal units nm )
335 18 : Tools::convert( reference[0][0], ref0 );
336 18 : Tools::convert( reference[0][1], ref1 );
337 18 : Tools::convert( reference[0][2], ref2 );
338 36 : structure +=" STRUCTURE2=" + ref0 + "," + ref1 + "," + ref2;
339 540 : for(unsigned i=1; i<30; ++i) {
340 2088 : for(unsigned k=0; k<3; ++k) {
341 1566 : Tools::convert( reference[i][k], ref0 );
342 3132 : structure += "," + ref0;
343 : }
344 : }
345 :
346 18 : std::string nopbcstr="";
347 : bool nopbc;
348 18 : parseFlag("NOPBC",nopbc);
349 18 : if( nopbc ) {
350 : nopbcstr = " NOPBC";
351 : }
352 18 : std::string usegpustr="";
353 : {
354 : bool usegpu;
355 18 : parseFlag("USEGPU",usegpu);
356 18 : if( usegpu ) {
357 : usegpustr = " USEGPU";
358 : }
359 : }
360 : std::string type;
361 18 : parse("TYPE",type);
362 18 : std::string lab = getShortcutLabel() + "_low";
363 18 : if( uselessthan ) {
364 17 : lab = getShortcutLabel();
365 : }
366 18 : std::string atoms="ATOMS=" + all_atoms[0];
367 10980 : for(unsigned i=1; i<all_atoms.size(); ++i) {
368 21924 : atoms += "," + all_atoms[i];
369 : }
370 18 : std::string inputLine = getShortcutLabel() + "_both:";
371 18 : if( type=="DRMSD" ) {
372 : inputLine+=" SECONDARY_STRUCTURE_DRMSD BONDLENGTH=0.17";
373 : } else {
374 20 : inputLine+=" SECONDARY_STRUCTURE_RMSD TYPE=" +type;
375 : }
376 36 : inputLine+=" ALIGN_STRANDS " + seglist + structure
377 36 : + " " + atoms + nopbcstr + usegpustr;
378 :
379 18 : if( strands_cutoff>0 ) {
380 16 : readInputLine( scutoff_action );
381 : std::string str_cut;
382 16 : Tools::convert( strands_cutoff, str_cut );
383 48 : readInputLine( getShortcutLabel() + "_cut: CUSTOM ARG=" + getShortcutLabel()
384 32 : + "_cut_dists FUNC=step(" + str_cut + "-x) PERIODIC=NO");
385 32 : inputLine+=" MASK=" + getShortcutLabel() + "_cut";
386 16 : readInputLine(inputLine);
387 16 : if( ltmap.length()>0 ) {
388 : // Create the lowest line
389 48 : readInputLine( lab + ": LOWEST ARG=" + getShortcutLabel() + "_both.struct-1,"
390 48 : + getShortcutLabel() + "_both.struct-2 MASK=" + getShortcutLabel() + "_cut");
391 : // Create the less than object
392 48 : readInputLine( getShortcutLabel() + "_ltu: LESS_THAN ARG=" + lab
393 48 : + " SWITCH={" + ltmap +"} MASK=" + getShortcutLabel() + "_cut");
394 : // Multiply by the strands cutoff
395 32 : readInputLine( getShortcutLabel()
396 48 : + "_lt: CUSTOM ARG=" + getShortcutLabel() + "_ltu,"
397 48 : + getShortcutLabel() + "_cut"
398 : " FUNC=x*y PERIODIC=NO");
399 : }
400 : } else {
401 2 : readInputLine(inputLine);
402 2 : if( ltmap.length()>0 ) {
403 : // Create the lowest line
404 6 : readInputLine( lab + ": LOWEST ARG=" + getShortcutLabel() + "_both.struct-1,"
405 6 : + getShortcutLabel() + "_both.struct-2" );
406 : // Create the less than object
407 4 : readInputLine( getShortcutLabel() + "_lt: LESS_THAN ARG=" + lab + " SWITCH={" + ltmap +"}");
408 : }
409 : }
410 : // Create the less than object
411 18 : if( ltmap.length()>0 ) {
412 18 : if( uselessthan ) {
413 34 : readInputLine( getShortcutLabel() + "_lessthan: SUM ARG=" + getShortcutLabel() + "_lt PERIODIC=NO");
414 : } else {
415 2 : readInputLine( getShortcutLabel() + ": SUM ARG=" + getShortcutLabel() + "_lt PERIODIC=NO");
416 : }
417 : }
418 36 : }
419 :
420 : }
421 : }
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