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 ANTIBETARMSD
30 : /*
31 : Probe the antiparallel beta sheet content of your protein structure.
32 :
33 : Two protein segments containing three contiguous residues can form an antiparallel beta sheet.
34 : Although if the two segments are part of the same protein chain they must be separated by
35 : a minimum of 2 residues to make room for the turn. This colvar thus generates the set of
36 : all possible six residue sections that could conceivably form an antiparallel 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 antiparallel 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 ideas from the paper cited below. The authors of
44 : this paper use the set of distances from the anti parallel beta sheet configurations to measure
45 : the number of segments that have an configuration that resembles an anti 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 antiparallel 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 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 purely configuration composed of pure anti-parallel beta sheets or the distance between the set of
58 : residues that is closest to an anti-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 antiparallel beta sheet configuration.
65 :
66 : ```plumed
67 : #SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
68 : MOLINFO STRUCTURE=regtest/basic/rt32/helix.pdb
69 : ab: ANTIBETARMSD RESIDUES=all STRANDS_CUTOFF=1 R_0=0.1
70 : PRINT ARG=ab 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: ANTIBETARMSD 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 AntibetaRMSD : public ActionShortcut {
92 : public:
93 : static void registerKeywords( Keywords& keys );
94 : explicit AntibetaRMSD(const ActionOptions&);
95 : };
96 :
97 : PLUMED_REGISTER_ACTION(AntibetaRMSD,"ANTIBETARMSD")
98 :
99 101 : void AntibetaRMSD::registerKeywords( Keywords& keys ) {
100 101 : SecondaryStructureRMSD::registerKeywords( keys );
101 202 : keys.setValueDescription("scalar/vector","if LESS_THAN is present the RMSD distance between each residue and the ideal antiparallel beta sheet. If LESS_THAN is not present the number of residue segments where the structure is similar to an anti parallel beta sheet");
102 101 : keys.remove("ATOMS");
103 101 : keys.remove("SEGMENT");
104 101 : keys.remove("BONDLENGTH");
105 101 : keys.remove("NO_ACTION_LOG");
106 101 : keys.remove("CUTOFF_ATOMS");
107 202 : keys.remove("STRUCTURE");
108 101 : keys.add("compulsory","STYLE","all","Antiparallel 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");
112 101 : }
113 :
114 17 : AntibetaRMSD::AntibetaRMSD(const ActionOptions&ao):
115 : Action(ao),
116 17 : ActionShortcut(ao) {
117 : // Read in the input and create a string that describes how to compute the less than
118 : std::string ltmap;
119 17 : bool uselessthan=SecondaryStructureRMSD::readShortcutWords( ltmap, this );
120 : // read in the backbone atoms
121 : std::vector<unsigned> chains;
122 : std::string atoms;
123 34 : SecondaryStructureRMSD::readBackboneAtoms( this, plumed, "protein", chains, atoms );
124 :
125 : bool intra_chain(false), inter_chain(false);
126 : std::string style;
127 17 : parse("STYLE",style);
128 34 : if( Tools::caseInSensStringCompare(style, "all") ) {
129 : intra_chain=true;
130 : inter_chain=true;
131 4 : } else if( Tools::caseInSensStringCompare(style, "inter") ) {
132 : intra_chain=false;
133 : inter_chain=true;
134 2 : } else if( Tools::caseInSensStringCompare(style, "intra") ) {
135 : intra_chain=true;
136 : inter_chain=false;
137 : } else {
138 0 : error( style + " is not a valid directive for the STYLE keyword");
139 : }
140 :
141 : // This constructs all conceivable sections of antibeta sheet in the backbone of the chains
142 : std::string seglist;
143 17 : unsigned k=1;
144 17 : if( intra_chain ) {
145 : unsigned nprevious=0;
146 16 : std::vector<unsigned> nlist(30);
147 287 : for(unsigned i=0; i<chains.size(); ++i) {
148 271 : if( chains[i]<40 ) {
149 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");
150 : }
151 : // Loop over all possible triples in each 8 residue segment of protein
152 271 : unsigned nres=chains[i]/5;
153 271 : if( chains[i]%5!=0 ) {
154 0 : error("backbone segment received does not contain a multiple of five residues");
155 : }
156 546 : for(unsigned ires=0; ires<nres-7; ires++) {
157 560 : for(unsigned jres=ires+7; jres<nres; jres++) {
158 4560 : for(unsigned k=0; k<15; ++k) {
159 4275 : nlist[k]=nprevious + ires*5+k;
160 4275 : nlist[k+15]=nprevious + (jres-2)*5+k;
161 : }
162 : std::string nlstr, num;
163 285 : Tools::convert( nlist[0], nlstr );
164 285 : Tools::convert(k, num);
165 285 : k++;
166 570 : seglist += " SEGMENT" + num + "=" + nlstr;
167 8550 : for(unsigned kk=1; kk<nlist.size(); ++kk ) {
168 8265 : Tools::convert( nlist[kk], nlstr );
169 16530 : seglist += "," + nlstr;
170 : }
171 : }
172 : }
173 271 : nprevious+=chains[i];
174 : }
175 : }
176 17 : if( inter_chain ) {
177 17 : if( chains.size()==1 && style!="all" ) {
178 0 : error("there is only one chain defined so cannot use inter_chain option");
179 : }
180 16 : std::vector<unsigned> nlist(30);
181 255 : for(unsigned ichain=1; ichain<chains.size(); ++ichain) {
182 : unsigned iprev=0;
183 2382 : for(unsigned i=0; i<ichain; ++i) {
184 2143 : iprev+=chains[i];
185 : }
186 239 : unsigned inres=chains[ichain]/5;
187 239 : if( chains[ichain]%5!=0 ) {
188 0 : error("backbone segment received does not contain a multiple of five residues");
189 : }
190 1668 : for(unsigned ires=0; ires<inres-2; ++ires) {
191 14282 : for(unsigned jchain=0; jchain<ichain; ++jchain) {
192 : unsigned jprev=0;
193 81397 : for(unsigned i=0; i<jchain; ++i) {
194 68544 : jprev+=chains[i];
195 : }
196 12853 : unsigned jnres=chains[jchain]/5;
197 12853 : if( chains[jchain]%5!=0 ) {
198 0 : error("backbone segment received does not contain a multiple of five residues");
199 : }
200 89966 : for(unsigned jres=0; jres<jnres-2; ++jres) {
201 1233808 : for(unsigned k=0; k<15; ++k) {
202 1156695 : nlist[k]=iprev+ ires*5+k;
203 1156695 : nlist[k+15]=jprev+ jres*5+k;
204 : }
205 : std::string nlstr, num;
206 77113 : Tools::convert( nlist[0], nlstr );
207 77113 : Tools::convert(k, num);
208 77113 : k++;
209 154226 : seglist += " SEGMENT" + num + "=" + nlstr;
210 2313390 : for(unsigned kk=1; kk<nlist.size(); ++kk ) {
211 2236277 : Tools::convert( nlist[kk], nlstr );
212 4472554 : seglist += "," + nlstr;
213 : }
214 : }
215 : }
216 : }
217 : }
218 : }
219 :
220 : // Build the reference structure ( in angstroms )
221 17 : std::vector<Vector> reference(30);
222 17 : reference[0]=Vector( 2.263, -3.795, 1.722); // N i
223 17 : reference[1]=Vector( 2.493, -2.426, 2.263); // CA
224 17 : reference[2]=Vector( 3.847, -1.838, 1.761); // CB
225 17 : reference[3]=Vector( 1.301, -1.517, 1.921); // C
226 17 : reference[4]=Vector( 0.852, -1.504, 0.739); // O
227 17 : reference[5]=Vector( 0.818, -0.738, 2.917); // N i+1
228 17 : reference[6]=Vector(-0.299, 0.243, 2.748); // CA
229 17 : reference[7]=Vector(-1.421, -0.076, 3.757); // CB
230 17 : reference[8]=Vector( 0.273, 1.680, 2.854); // C
231 17 : reference[9]=Vector( 0.902, 1.993, 3.888); // O
232 17 : reference[10]=Vector( 0.119, 2.532, 1.813); // N i+2
233 17 : reference[11]=Vector( 0.683, 3.916, 1.680); // CA
234 17 : reference[12]=Vector( 1.580, 3.940, 0.395); // CB
235 17 : reference[13]=Vector(-0.394, 5.011, 1.630); // C
236 17 : reference[14]=Vector(-1.459, 4.814, 0.982); // O
237 17 : reference[15]=Vector(-2.962, 3.559, -1.359); // N j-2
238 17 : reference[16]=Vector(-2.439, 2.526, -2.287); // CA
239 17 : reference[17]=Vector(-1.189, 3.006, -3.087); // CB
240 17 : reference[18]=Vector(-2.081, 1.231, -1.520); // C
241 17 : reference[19]=Vector(-1.524, 1.324, -0.409); // O
242 17 : reference[20]=Vector(-2.326, 0.037, -2.095); // N j-1
243 17 : reference[21]=Vector(-1.858, -1.269, -1.554); // CA
244 17 : reference[22]=Vector(-3.053, -2.199, -1.291); // CB
245 17 : reference[23]=Vector(-0.869, -1.949, -2.512); // C
246 17 : reference[24]=Vector(-1.255, -2.070, -3.710); // O
247 17 : reference[25]=Vector( 0.326, -2.363, -2.072); // N j
248 17 : reference[26]=Vector( 1.405, -2.992, -2.872); // CA
249 17 : reference[27]=Vector( 2.699, -2.129, -2.917); // CB
250 17 : reference[28]=Vector( 1.745, -4.399, -2.330); // C
251 17 : reference[29]=Vector( 1.899, -4.545, -1.102); // O
252 : std::string ref0, ref1, ref2;
253 17 : Tools::convert( reference[0][0], ref0 );
254 17 : Tools::convert( reference[0][1], ref1 );
255 17 : Tools::convert( reference[0][2], ref2 );
256 34 : std::string structure=" STRUCTURE1=" + ref0 + "," + ref1 + "," + ref2;
257 510 : for(unsigned i=1; i<30; ++i) {
258 1972 : for(unsigned k=0; k<3; ++k) {
259 1479 : Tools::convert( reference[i][k], ref0 );
260 2958 : structure += "," + ref0;
261 : }
262 : }
263 :
264 : std::string strands_cutoff;
265 34 : parse("STRANDS_CUTOFF",strands_cutoff);
266 17 : if( strands_cutoff.length()>0 ) {
267 32 : strands_cutoff=" CUTOFF_ATOMS=6,21 STRANDS_CUTOFF="+strands_cutoff;
268 : }
269 : std::string type;
270 17 : parse("TYPE",type);
271 17 : std::string lab = getShortcutLabel() + "_rmsd";
272 17 : if( uselessthan ) {
273 17 : lab = getShortcutLabel();
274 : }
275 17 : std::string nopbcstr="";
276 : bool nopbc;
277 17 : parseFlag("NOPBC",nopbc);
278 17 : if( nopbc ) {
279 : nopbcstr = " NOPBC";
280 : }
281 17 : if( seglist.length()==0 ) {
282 0 : error("no segments to investigate");
283 : }
284 34 : readInputLine( lab + ": SECONDARY_STRUCTURE_RMSD BONDLENGTH=0.17" + seglist + structure + " " + atoms + " TYPE=" + type + strands_cutoff + nopbcstr );
285 : // Create the less than object
286 17 : if( ltmap.length()>0 ) {
287 17 : SecondaryStructureRMSD::expandShortcut( uselessthan, getShortcutLabel(), lab, ltmap, this );
288 : }
289 17 : }
290 :
291 : }
292 : }
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