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 "SecondaryStructureRMSD.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)
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 : */
89 : //+ENDPLUMEDOC
90 :
91 : class ParabetaRMSD : public ActionShortcut {
92 : public:
93 : static void registerKeywords( Keywords& keys );
94 : explicit ParabetaRMSD(const ActionOptions&);
95 : };
96 :
97 : PLUMED_REGISTER_ACTION(ParabetaRMSD,"PARABETARMSD")
98 :
99 100 : void ParabetaRMSD::registerKeywords( Keywords& keys ) {
100 100 : SecondaryStructureRMSD::registerKeywords( keys );
101 200 : 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");
102 100 : keys.remove("ATOMS");
103 100 : keys.remove("SEGMENT");
104 100 : keys.remove("BONDLENGTH");
105 100 : keys.remove("NO_ACTION_LOG");
106 100 : keys.remove("CUTOFF_ATOMS");
107 200 : keys.remove("STRUCTURE");
108 100 : 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 "
109 : "chain configuration with the appropriate geometry are counted. If STYLE=inter "
110 : "only sheet-like configurations involving two chains are counted, while if STYLE=intra "
111 : "only sheet-like configurations involving a single chain are counted");
112 100 : keys.needsAction("LOWEST");
113 100 : }
114 :
115 18 : ParabetaRMSD::ParabetaRMSD(const ActionOptions&ao):
116 : Action(ao),
117 18 : ActionShortcut(ao) {
118 : // Read in the input and create a string that describes how to compute the less than
119 : std::string ltmap;
120 18 : bool uselessthan=SecondaryStructureRMSD::readShortcutWords( ltmap, this );
121 : // read in the backbone atoms
122 : std::vector<unsigned> chains;
123 : std::string atoms;
124 36 : SecondaryStructureRMSD::readBackboneAtoms( this, plumed, "protein", chains, atoms );
125 :
126 : bool intra_chain(false), inter_chain(false);
127 : std::string seglist;
128 : std::string style;
129 18 : parse("STYLE",style);
130 18 : unsigned jjkk=1;
131 36 : if( Tools::caseInSensStringCompare(style, "all") ) {
132 : intra_chain=true;
133 : inter_chain=true;
134 2 : } else if( Tools::caseInSensStringCompare(style, "inter") ) {
135 : intra_chain=false;
136 : inter_chain=true;
137 0 : } else if( Tools::caseInSensStringCompare(style, "intra") ) {
138 : intra_chain=true;
139 : inter_chain=false;
140 : } else {
141 0 : error( style + " is not a valid directive for the STYLE keyword");
142 : }
143 :
144 : // This constructs all conceivable sections of antibeta sheet in the backbone of the chains
145 : if( intra_chain ) {
146 : unsigned nprevious=0;
147 17 : std::vector<unsigned> nlist(30);
148 272 : for(unsigned i=0; i<chains.size(); ++i) {
149 255 : if( chains[i]<40 ) {
150 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");
151 : }
152 : // Loop over all possible triples in each 8 residue segment of protein
153 255 : unsigned nres=chains[i]/5;
154 255 : if( chains[i]%5!=0 ) {
155 0 : error("backbone segment received does not contain a multiple of five residues");
156 : }
157 267 : for(unsigned ires=0; ires<nres-8; ires++) {
158 42 : for(unsigned jres=ires+6; jres<nres-2; jres++) {
159 480 : for(unsigned k=0; k<15; ++k) {
160 450 : nlist[k]=nprevious + ires*5+k;
161 450 : nlist[k+15]=nprevious + jres*5+k;
162 : }
163 : std::string nlstr, num;
164 30 : Tools::convert( nlist[0], nlstr );
165 30 : Tools::convert(jjkk, num);
166 30 : jjkk++;
167 60 : seglist += " SEGMENT" + num + "=" + nlstr;
168 900 : for(unsigned kk=1; kk<nlist.size(); ++kk ) {
169 870 : Tools::convert( nlist[kk], nlstr );
170 1740 : seglist += "," + nlstr;
171 : }
172 : }
173 : }
174 255 : nprevious+=chains[i];
175 : }
176 : }
177 : // This constructs all conceivable sections of antibeta sheet that form between chains
178 18 : if( inter_chain ) {
179 24 : if( chains.size()==1 && !Tools::caseInSensStringCompare(style, "all") ) {
180 0 : error("there is only one chain defined so cannot use inter_chain option");
181 : }
182 18 : std::vector<unsigned> nlist(30);
183 273 : for(unsigned ichain=1; ichain<chains.size(); ++ichain) {
184 : unsigned iprev=0;
185 2550 : for(unsigned i=0; i<ichain; ++i) {
186 2295 : iprev+=chains[i];
187 : }
188 255 : unsigned inres=chains[ichain]/5;
189 255 : if( chains[ichain]%5!=0 ) {
190 0 : error("backbone segment received does not contain a multiple of five residues");
191 : }
192 1785 : for(unsigned ires=0; ires<inres-2; ++ires) {
193 15300 : for(unsigned jchain=0; jchain<ichain; ++jchain) {
194 : unsigned jprev=0;
195 87210 : for(unsigned i=0; i<jchain; ++i) {
196 73440 : jprev+=chains[i];
197 : }
198 13770 : unsigned jnres=chains[jchain]/5;
199 13770 : if( chains[jchain]%5!=0 ) {
200 0 : error("backbone segment received does not contain a multiple of five residues");
201 : }
202 96390 : for(unsigned jres=0; jres<jnres-2; ++jres) {
203 1321920 : for(unsigned k=0; k<15; ++k) {
204 1239300 : nlist[k]=iprev + ires*5+k;
205 1239300 : nlist[k+15]=jprev + jres*5+k;
206 : }
207 : std::string nlstr, num;
208 82620 : Tools::convert( nlist[0], nlstr );
209 82620 : Tools::convert(jjkk, num);
210 82620 : jjkk++;
211 165240 : seglist += " SEGMENT" + num + "=" + nlstr;
212 2478600 : for(unsigned kk=1; kk<nlist.size(); ++kk ) {
213 2395980 : Tools::convert( nlist[kk], nlstr );
214 4791960 : seglist += "," + nlstr;
215 : }
216 : }
217 : }
218 : }
219 : }
220 : }
221 :
222 : // Build the reference structure ( in angstroms )
223 18 : std::vector<Vector> reference(30);
224 18 : reference[0]=Vector( 1.244, -4.620, -2.127); // N i
225 18 : reference[1]=Vector(-0.016, -4.500, -1.395); // CA
226 18 : reference[2]=Vector( 0.105, -5.089, 0.024); // CB
227 18 : reference[3]=Vector(-0.287, -3.000, -1.301); // C
228 18 : reference[4]=Vector( 0.550, -2.245, -0.822); // O
229 18 : reference[5]=Vector(-1.445, -2.551, -1.779); // N i+1
230 18 : reference[6]=Vector(-1.752, -1.130, -1.677); // CA
231 18 : reference[7]=Vector(-2.113, -0.550, -3.059); // CB
232 18 : reference[8]=Vector(-2.906, -0.961, -0.689); // C
233 18 : reference[9]=Vector(-3.867, -1.738, -0.695); // O
234 18 : reference[10]=Vector(-2.774, 0.034, 0.190); // N i+2
235 18 : reference[11]=Vector(-3.788, 0.331, 1.201); // CA
236 18 : reference[12]=Vector(-3.188, 0.300, 2.624); // CB
237 18 : reference[13]=Vector(-4.294, 1.743, 0.937); // C
238 18 : reference[14]=Vector(-3.503, 2.671, 0.821); // O
239 18 : reference[15]=Vector( 4.746, -2.363, 0.188); // N j
240 18 : reference[16]=Vector( 3.427, -1.839, 0.545); // CA
241 18 : reference[17]=Vector( 3.135, -1.958, 2.074); // CB
242 18 : reference[18]=Vector( 3.346, -0.365, 0.181); // C
243 18 : reference[19]=Vector( 4.237, 0.412, 0.521); // O
244 18 : reference[20]=Vector( 2.261, 0.013, -0.487); // N j+1
245 18 : reference[21]=Vector( 2.024, 1.401, -0.875); // CA
246 18 : reference[22]=Vector( 1.489, 1.514, -2.313); // CB
247 18 : reference[23]=Vector( 0.914, 1.902, 0.044); // C
248 18 : reference[24]=Vector(-0.173, 1.330, 0.052); // O
249 18 : reference[25]=Vector( 1.202, 2.940, 0.828); // N j+2
250 18 : reference[26]=Vector( 0.190, 3.507, 1.718); // CA
251 18 : reference[27]=Vector( 0.772, 3.801, 3.104); // CB
252 18 : reference[28]=Vector(-0.229, 4.791, 1.038); // C
253 18 : reference[29]=Vector( 0.523, 5.771, 0.996); // O
254 : // Store the secondary structure ( last number makes sure we convert to internal units nm )
255 : std::string ref0, ref1, ref2;
256 18 : Tools::convert( reference[0][0], ref0 );
257 18 : Tools::convert( reference[0][1], ref1 );
258 18 : Tools::convert( reference[0][2], ref2 );
259 36 : std::string structure=" STRUCTURE1=" + ref0 + "," + ref1 + "," + ref2;
260 540 : for(unsigned i=1; i<30; ++i) {
261 2088 : for(unsigned k=0; k<3; ++k) {
262 1566 : Tools::convert( reference[i][k], ref0 );
263 3132 : structure += "," + ref0;
264 : }
265 : }
266 :
267 18 : reference[0]=Vector(-1.439, -5.122, -1.144); // N i
268 18 : reference[1]=Vector(-0.816, -3.803, -1.013); // CA
269 18 : reference[2]=Vector( 0.099, -3.509, -2.206); // CB
270 18 : reference[3]=Vector(-1.928, -2.770, -0.952); // C
271 18 : reference[4]=Vector(-2.991, -2.970, -1.551); // O
272 18 : reference[5]=Vector(-1.698, -1.687, -0.215); // N i+1
273 18 : reference[6]=Vector(-2.681, -0.613, -0.143); // CA
274 18 : reference[7]=Vector(-3.323, -0.477, 1.267); // CB
275 18 : reference[8]=Vector(-1.984, 0.681, -0.574); // C
276 18 : reference[9]=Vector(-0.807, 0.921, -0.273); // O
277 18 : reference[10]=Vector(-2.716, 1.492, -1.329); // N i+2
278 18 : reference[11]=Vector(-2.196, 2.731, -1.883); // CA
279 18 : reference[12]=Vector(-2.263, 2.692, -3.418); // CB
280 18 : reference[13]=Vector(-2.989, 3.949, -1.433); // C
281 18 : reference[14]=Vector(-4.214, 3.989, -1.583); // O
282 18 : reference[15]=Vector( 2.464, -4.352, 2.149); // N j
283 18 : reference[16]=Vector( 3.078, -3.170, 1.541); // CA
284 18 : reference[17]=Vector( 3.398, -3.415, 0.060); // CB
285 18 : reference[18]=Vector( 2.080, -2.021, 1.639); // C
286 18 : reference[19]=Vector( 0.938, -2.178, 1.225); // O
287 18 : reference[20]=Vector( 2.525, -0.886, 2.183); // N j+1
288 18 : reference[21]=Vector( 1.692, 0.303, 2.346); // CA
289 18 : reference[22]=Vector( 1.541, 0.665, 3.842); // CB
290 18 : reference[23]=Vector( 2.420, 1.410, 1.608); // C
291 18 : reference[24]=Vector( 3.567, 1.733, 1.937); // O
292 18 : reference[25]=Vector( 1.758, 1.976, 0.600); // N j+2
293 18 : reference[26]=Vector( 2.373, 2.987, -0.238); // CA
294 18 : reference[27]=Vector( 2.367, 2.527, -1.720); // CB
295 18 : reference[28]=Vector( 1.684, 4.331, -0.148); // C
296 18 : reference[29]=Vector( 0.486, 4.430, -0.415); // O
297 : // Store the secondary structure ( last number makes sure we convert to internal units nm )
298 18 : Tools::convert( reference[0][0], ref0 );
299 18 : Tools::convert( reference[0][1], ref1 );
300 18 : Tools::convert( reference[0][2], ref2 );
301 36 : structure +=" STRUCTURE2=" + ref0 + "," + ref1 + "," + ref2;
302 540 : for(unsigned i=1; i<30; ++i) {
303 2088 : for(unsigned k=0; k<3; ++k) {
304 1566 : Tools::convert( reference[i][k], ref0 );
305 3132 : structure += "," + ref0;
306 : }
307 : }
308 :
309 : std::string strands_cutoff;
310 18 : parse("STRANDS_CUTOFF",strands_cutoff);
311 18 : std::string nopbcstr="";
312 : bool nopbc;
313 18 : parseFlag("NOPBC",nopbc);
314 18 : if( nopbc ) {
315 : nopbcstr = " NOPBC";
316 : }
317 18 : if( strands_cutoff.length()>0 ) {
318 32 : strands_cutoff=" CUTOFF_ATOMS=6,21 STRANDS_CUTOFF="+strands_cutoff;
319 : }
320 : std::string type;
321 18 : parse("TYPE",type);
322 18 : std::string lab = getShortcutLabel() + "_low";
323 18 : if( uselessthan ) {
324 17 : lab = getShortcutLabel();
325 : }
326 18 : if( seglist.length()==0 ) {
327 0 : error("no segments to investigate");
328 : }
329 36 : readInputLine( getShortcutLabel() + "_both: SECONDARY_STRUCTURE_RMSD BONDLENGTH=0.17" + seglist + structure + " " + atoms + " TYPE=" + type + strands_cutoff + nopbcstr );
330 18 : if( ltmap.length()>0 ) {
331 : // Create the lowest line
332 36 : readInputLine( lab + ": LOWEST ARG=" + getShortcutLabel() + "_both.struct-1," + getShortcutLabel() + "_both.struct-2" );
333 : // Create the less than object
334 18 : SecondaryStructureRMSD::expandShortcut( uselessthan, getShortcutLabel(), lab, ltmap, this );
335 : }
336 18 : }
337 :
338 : }
339 : }
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