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Fixed a bug in the pdb-writing code.
[gromacs.git] / src / tools / g_rmsdist.c
blob63f5a5c1fd0632d409b9102caa133f448a8a36a4
1 /*
2 * $Id$
3 *
4 * This source code is part of
5 *
6 * G R O M A C S
7 *
8 * GROningen MAchine for Chemical Simulations
9 *
10 * VERSION 3.1
11 * Copyright (c) 1991-2001, University of Groningen, The Netherlands
12 * This program is free software; you can redistribute it and/or
13 * modify it under the terms of the GNU General Public License
14 * as published by the Free Software Foundation; either version 2
15 * of the License, or (at your option) any later version.
16 *
17 * If you want to redistribute modifications, please consider that
18 * scientific software is very special. Version control is crucial -
19 * bugs must be traceable. We will be happy to consider code for
20 * inclusion in the official distribution, but derived work must not
21 * be called official GROMACS. Details are found in the README & COPYING
22 * files - if they are missing, get the official version at www.gromacs.org.
23 *
24 * To help us fund GROMACS development, we humbly ask that you cite
25 * the papers on the package - you can find them in the top README file.
26 *
27 * For more info, check our website at http://www.gromacs.org
28 *
29 * And Hey:
30 * GROtesk MACabre and Sinister
31 */
32 static char *SRCID_g_rmsdist_c = "$Id$";
33 #include <math.h>
34 #include <ctype.h>
35 #include "macros.h"
36 #include "smalloc.h"
37 #include "typedefs.h"
38 #include "names.h"
39 #include "copyrite.h"
40 #include "statutil.h"
41 #include "tpxio.h"
42 #include "string2.h"
43 #include "strdb.h"
44 #include "vec.h"
45 #include "macros.h"
46 #include "rdgroup.h"
47 #include "pbc.h"
48 #include "xvgr.h"
49 #include "futil.h"
50 #include "matio.h"
51 #include "assert.h"
52
53 static void calc_dist(int nind,atom_id index[],rvec x[],real **d)
54 {
55 int i,j;
56 real *xi;
57 rvec dx;
58
59 for(i=0; (i<nind-1); i++) {
60 xi=x[index[i]];
61 for(j=i+1; (j<nind); j++) {
62 pbc_dx(xi,x[index[j]],dx);
63 d[i][j]=norm(dx);
64 }
65 }
66 }
67
68 static void calc_dist_tot(int nind,atom_id index[], rvec x[],
69 real **d, real **dtot, real **dtot2,
70 bool bNMR, real **dtot1_3, real **dtot1_6)
71 {
72 int i,j;
73 real *xi;
74 real temp, temp2, temp1_3;
75 rvec dx;
76
77 for(i=0; (i<nind-1); i++) {
78 xi=x[index[i]];
79 for(j=i+1; (j<nind); j++) {
80 pbc_dx(xi,x[index[j]],dx);
81 temp2=dx[XX]*dx[XX]+dx[YY]*dx[YY]+dx[ZZ]*dx[ZZ];
82 temp =sqrt(temp2);
83 d[i][j]=temp;
84 dtot[i][j]+=temp;
85 dtot2[i][j]+=temp2;
86 if (bNMR) {
87 temp1_3 = 1.0/(temp*temp2);
88 dtot1_3[i][j] += temp1_3;
89 dtot1_6[i][j] += temp1_3*temp1_3;
90 }
91 }
92 }
93 }
94
95 static void calc_nmr(int nind, int nframes, real **dtot1_3, real **dtot1_6,
96 real *max1_3, real *max1_6)
97 {
98 int i,j;
99 real temp1_3,temp1_6;
100
101 for(i=0; (i<nind-1); i++) {
102 for(j=i+1; (j<nind); j++) {
103 temp1_3 = pow(dtot1_3[i][j]/nframes,-1.0/3.0);
104 temp1_6 = pow(dtot1_6[i][j]/nframes,-1.0/6.0);
105 if (temp1_3 > *max1_3) *max1_3 = temp1_3;
106 if (temp1_6 > *max1_6) *max1_6 = temp1_6;
107 dtot1_3[i][j] = temp1_3;
108 dtot1_6[i][j] = temp1_6;
109 dtot1_3[j][i] = temp1_3;
110 dtot1_6[j][i] = temp1_6;
111 }
112 }
113 }
114
115 static char Hnum[] = "123";
116
117 typedef struct {
118 int nr;
119 real r_3;
120 real r_6;
121 real i_3;
122 real i_6;
123 } t_noe;
124
125 typedef struct {
126 int anr;
127 int ianr;
128 int rnr;
129 char *aname;
130 char *rname;
131 } t_noe_gr;
132
133 typedef struct {
134 int rnr;
135 char *nname;
136 char *rname;
137 char *aname;
138 } t_equiv;
139
140 static int read_equiv(char *eq_fn, t_equiv ***equivptr)
141 {
142 FILE *fp;
143 char line[STRLEN],resname[10],atomname[10],*lp;
144 int neq, na, n, resnr;
145 t_equiv **equiv;
146
147 fp = ffopen(eq_fn,"r");
148 neq=0;
149 equiv=NULL;
150 while(get_a_line(fp,line,STRLEN)) {
151 lp=line;
152 /* this is not efficient, but I'm lazy */
153 srenew(equiv,neq+1);
154 equiv[neq]=NULL;
155 na=0;
156 if (sscanf(lp,"%s %n",atomname,&n)==1) {
157 lp+=n;
158 snew(equiv[neq], 1);
159 equiv[neq][0].nname=strdup(atomname);
160 while (sscanf(lp,"%d %s %s %n",&resnr,resname,atomname,&n)==3) {
161 /* this is not efficient, but I'm lazy (again) */
162 srenew(equiv[neq], na+1);
163 equiv[neq][na].rnr=resnr-1;
164 equiv[neq][na].rname=strdup(resname);
165 equiv[neq][na].aname=strdup(atomname);
166 if (na>0) equiv[neq][na].nname=NULL;
167 na++;
168 lp+=n;
169 }
170 }
171 /* make empty element as flag for end of array */
172 srenew(equiv[neq], na+1);
173 equiv[neq][na].rnr=NOTSET;
174 equiv[neq][na].rname=NULL;
175 equiv[neq][na].aname=NULL;
176
177 /* next */
178 neq++;
179 }
180 ffclose(fp);
181
182 *equivptr=equiv;
183
184 return neq;
185 }
186
187 static void dump_equiv(FILE *out, int neq, t_equiv **equiv)
188 {
189 int i,j;
190
191 fprintf(out,"Dumping equivalent list\n");
192 for (i=0; i<neq; i++) {
193 fprintf(out,"%s",equiv[i][0].nname);
194 for(j=0; equiv[i][j].rnr!=NOTSET; j++)
195 fprintf(out," %d %s %s",
196 equiv[i][j].rnr,equiv[i][j].rname,equiv[i][j].aname);
197 fprintf(out,"\n");
198 }
199 }
200
201 static bool is_equiv(int neq, t_equiv **equiv, char **nname,
202 int rnr1, char *rname1, char *aname1,
203 int rnr2, char *rname2, char *aname2)
204 {
205 int i,j;
206 bool bFound;
207
208 bFound=FALSE;
209 /* we can terminate each loop when bFound is true! */
210 for (i=0; i<neq && !bFound; i++) {
211 /* find first atom */
212 for(j=0; equiv[i][j].rnr!=NOTSET && !bFound; j++)
213 bFound = ( equiv[i][j].rnr==rnr1 &&
214 strcmp(equiv[i][j].rname, rname1)==0 &&
215 strcmp(equiv[i][j].aname, aname1)==0 );
216 if (bFound) {
217 /* find second atom */
218 bFound=FALSE;
219 for(j=0; equiv[i][j].rnr!=NOTSET && !bFound; j++)
220 bFound = ( equiv[i][j].rnr==rnr2 &&
221 strcmp(equiv[i][j].rname, rname2)==0 &&
222 strcmp(equiv[i][j].aname, aname2)==0 );
223 }
224 }
225 if (bFound)
226 *nname = strdup(equiv[i-1][0].nname);
227
228 return bFound;
229 }
230
231 static int analyze_noe_equivalent(char *eq_fn,
232 t_atoms *atoms, int isize, atom_id *index,
233 bool bSumH,
234 atom_id *noe_index, t_noe_gr *noe_gr)
235 {
236 FILE *fp;
237 int i, j, anmil, anmjl, rnri, rnrj, gi, groupnr, neq;
238 char *anmi, *anmj, **nnm;
239 bool bMatch,bEquiv;
240 t_equiv **equiv;
241
242 snew(nnm,isize);
243 if (bSumH) {
244 if (eq_fn) {
245 neq=read_equiv(eq_fn,&equiv);
246 if (debug) dump_equiv(debug,neq,equiv);
247 } else {
248 neq=0;
249 equiv=NULL;
250 }
251
252 groupnr=0;
253 for(i=0; i<isize; i++) {
254 if (equiv && i<isize-1) {
255 /* check explicit list of equivalent atoms */
256 do {
257 j=i+1;
258 rnri=atoms->atom[index[i]].resnr;
259 rnrj=atoms->atom[index[j]].resnr;
260 bEquiv =
261 is_equiv(neq, equiv, &nnm[i],
262 rnri, *atoms->resname[rnri], *atoms->atomname[index[i]],
263 rnrj, *atoms->resname[rnrj], *atoms->atomname[index[j]]);
264 if(nnm[i] && bEquiv)
265 nnm[j]=strdup(nnm[i]);
266 if (bEquiv) {
267 /* set index for matching atom */
268 noe_index[j]=groupnr;
269 /* skip matching atom */
270 i=j;
271 }
272 } while ( bEquiv && i<isize-1 );
273 } else
274 bEquiv=FALSE;
275 if (!bEquiv) {
276 /* look for triplets of consecutive atoms with name XX?,
277 X are any number of letters or digits and ? goes from 1 to 3
278 This is supposed to cover all CH3 groups and the like */
279 anmi = *atoms->atomname[index[i]];
280 anmil = strlen(anmi);
281 bMatch = i<isize-3 && anmi[anmil-1]=='1';
282 if (bMatch)
283 for(j=1; j<3; j++) {
284 anmj = *atoms->atomname[index[i+j]];
285 anmjl = strlen(anmj);
286 bMatch = bMatch && ( anmil==anmjl && anmj[anmjl-1]==Hnum[j] &&
287 strncmp(anmi, anmj, anmil-1)==0 );
288 }
289 /* set index for this atom */
290 noe_index[i]=groupnr;
291 if (bMatch) {
292 /* set index for next two matching atoms */
293 for(j=1; j<3; j++)
294 noe_index[i+j]=groupnr;
295 /* skip matching atoms */
296 i+=2;
297 }
298 }
299 groupnr++;
300 }
301 } else {
302 /* make index without looking for equivalent atoms */
303 for(i=0; i<isize; i++)
304 noe_index[i]=i;
305 groupnr=isize;
306 }
307 noe_index[isize]=groupnr;
308
309 if (debug)
310 /* dump new names */
311 for(i=0; i<isize; i++) {
312 rnri=atoms->atom[index[i]].resnr;
313 fprintf(debug,"%s %s %d -> %s\n",*atoms->atomname[index[i]],
314 *atoms->resname[rnri],rnri,nnm[i]?nnm[i]:"");
315 }
316
317 for(i=0; i<isize; i++) {
318 gi=noe_index[i];
319 if (!noe_gr[gi].aname) {
320 noe_gr[gi].ianr=i;
321 noe_gr[gi].anr=index[i];
322 if (nnm[i])
323 noe_gr[gi].aname=strdup(nnm[i]);
324 else {
325 noe_gr[gi].aname=strdup(*atoms->atomname[index[i]]);
326 if ( noe_index[i]==noe_index[i+1] )
327 noe_gr[gi].aname[strlen(noe_gr[gi].aname)-1]='*';
328 }
329 noe_gr[gi].rnr=atoms->atom[index[i]].resnr;
330 noe_gr[gi].rname=strdup(*atoms->resname[noe_gr[gi].rnr]);
331 /* dump group definitions */
332 if (debug) fprintf(debug,"%d %d %d %d %s %s %d\n",i,gi,
333 noe_gr[gi].ianr,noe_gr[gi].anr,noe_gr[gi].aname,
334 noe_gr[gi].rname,noe_gr[gi].rnr);
335 }
336 }
337 for(i=0; i<isize; i++)
338 sfree(nnm[i]);
339 sfree(nnm);
340
341 return groupnr;
342 }
343
344 /* #define NSCALE 3 */
345 /* static char *noe_scale[NSCALE+1] = { */
346 /* "strong", "medium", "weak", "none" */
347 /* }; */
348 #define NSCALE 6
349
350 static char *noe2scale(real r3, real r6, real rmax)
351 {
352 int i,s3, s6;
353 static char buf[NSCALE+1];
354
355 /* r goes from 0 to rmax
356 NSCALE*r/rmax goes from 0 to NSCALE
357 NSCALE - NSCALE*r/rmax goes from NSCALE to 0 */
358 s3 = NSCALE - min(NSCALE, (int)(NSCALE*r3/rmax));
359 s6 = NSCALE - min(NSCALE, (int)(NSCALE*r6/rmax));
360
361 for(i=0; i<s3; i++)
362 buf[i]='=';
363 for( ; i<s6; i++)
364 buf[i]='-';
365 buf[i]='\0';
366
367 return buf;
368 }
369
370 static void calc_noe(int isize, atom_id *noe_index,
371 real **dtot1_3, real **dtot1_6, int gnr, t_noe **noe)
372 {
373 int i, j, gi, gj;
374
375 /* make half matrix of noe-group distances from atom distances */
376 for(i=0; i<isize; i++) {
377 gi=noe_index[i];
378 for(j=i; j<isize; j++) {
379 gj=noe_index[j];
380 noe[gi][gj].nr++;
381 noe[gi][gj].i_3+=pow(dtot1_3[i][j],-3);
382 noe[gi][gj].i_6+=pow(dtot1_6[i][j],-6);
383 }
384 }
385
386 /* make averages */
387 for(i=0; i<gnr; i++)
388 for(j=i+1; j<gnr; j++) {
389 noe[i][j].r_3 = pow(noe[i][j].i_3/noe[i][j].nr,-1.0/3.0);
390 noe[i][j].r_6 = pow(noe[i][j].i_6/noe[i][j].nr,-1.0/6.0);
391 noe[j][i] = noe[i][j];
392 }
393 }
394
395 static void write_noe(FILE *fp,int gnr,t_noe **noe,t_noe_gr *noe_gr,real rmax)
396 {
397 int i,j;
398 real r3, r6, min3, min6;
399 char buf[10],b3[10],b6[10];
400 t_noe_gr gri, grj;
401
402 min3 = min6 = 1e6;
403 fprintf(fp,
404 ";%4s %3s %4s %4s%3s %4s %4s %4s %4s%3s %5s %5s %8s %2s %2s %s\n",
405 "ianr","anr","anm","rnm","rnr","ianr","anr","anm","rnm","rnr",
406 "1/r^3","1/r^6","intnsty","Dr","Da","scale");
407 for(i=0; i<gnr; i++) {
408 gri=noe_gr[i];
409 for(j=i+1; j<gnr; j++) {
410 grj=noe_gr[j];
411 r3 = noe[i][j].r_3;
412 r6 = noe[i][j].r_6;
413 min3 = min(r3,min3);
414 min6 = min(r6,min6);
415 if ( r3 < rmax || r6 < rmax ) {
416 if (grj.rnr == gri.rnr)
417 sprintf(buf,"%2d", grj.anr-gri.anr);
418 else
419 buf[0]='\0';
420 if ( r3 < rmax )
421 sprintf(b3,"%-5.3f",r3);
422 else
423 strcpy(b3,"-");
424 if ( r6 < rmax )
425 sprintf(b6,"%-5.3f",r6);
426 else
427 strcpy(b6,"-");
428 fprintf(fp,
429 "%4d %4d %4s %4s%3d %4d %4d %4s %4s%3d %5s %5s %8d %2d %2s %s\n",
430 gri.ianr+1, gri.anr+1, gri.aname, gri.rname, gri.rnr+1,
431 grj.ianr+1, grj.anr+1, grj.aname, grj.rname, grj.rnr+1,
432 b3, b6, (int)(noe[i][j].i_6+0.5), grj.rnr-gri.rnr, buf,
433 noe2scale(r3, r6, rmax));
434 }
435 }
436 }
437 #define MINI ((i==3)?min3:min6)
438 for(i=3; i<=6; i+=3)
439 if ( MINI > rmax )
440 fprintf(stdout,"NOTE: no 1/r^%d averaged distances found below %g, "
441 "smallest was %g\n", i, rmax, MINI );
442 else
443 fprintf(stdout,"Smallest 1/r^%d averaged distance was %g\n", i, MINI );
444 #undef MINI
445 }
446
447 static void calc_rms(int nind, int nframes,
448 real **dtot, real **dtot2,
449 real **rmsmat, real *rmsmax,
450 real **rmscmat, real *rmscmax,
451 real **meanmat, real *meanmax)
452 {
453 int i,j;
454 real mean, mean2, rms, rmsc;
455 /* N.B. dtot and dtot2 contain the total distance and the total squared
456 * distance respectively, BUT they return RMS and the scaled RMS resp.
457 */
458
459 *rmsmax=-1000;
460 *rmscmax=-1000;
461 *meanmax=-1000;
462
463 for(i=0; (i<nind-1); i++) {
464 for(j=i+1; (j<nind); j++) {
465 mean =dtot[i][j]/nframes;
466 mean2=dtot2[i][j]/nframes;
467 rms=sqrt(max(0,mean2-mean*mean));
468 rmsc=rms/mean;
469 if (mean > *meanmax) *meanmax=mean;
470 if (rms > *rmsmax ) *rmsmax =rms;
471 if (rmsc > *rmscmax) *rmscmax=rmsc;
472 meanmat[i][j]=meanmat[j][i]=mean;
473 rmsmat[i][j] =rmsmat[j][i] =rms;
474 rmscmat[i][j]=rmscmat[j][i]=rmsc;
475 }
476 }
477 }
478
479 real rms_diff(int natom,real **d,real **d_r)
480 {
481 int i,j;
482 real r,r2;
483
484 r2=0.0;
485 for(i=0; (i<natom-1); i++)
486 for(j=i+1; (j<natom); j++) {
487 r=d[i][j]-d_r[i][j];
488 r2+=r*r;
489 }
490 r2/=(natom*(natom-1))/2;
491
492 return sqrt(r2);
493 }
494
495 int main (int argc,char *argv[])
496 {
497 static char *desc[] = {
498 "g_rmsdist computes the root mean square deviation of atom distances,",
499 "which has the advantage that no fit is needed like in standard RMS",
500 "deviation as computed by g_rms.",
501 "The reference structure is taken from the structure file.",
502 "The rmsd at time t is calculated as the rms",
503 "of the differences in distance between atom-pairs in the reference",
504 "structure and the structure at time t.[PAR]",
505 "g_rmsdist can also produce matrices of the rms distances, rms distances",
506 "scaled with the mean distance and the mean distances and matrices with",
507 "NMR averaged distances (1/r^3 and 1/r^6 averaging). Finally, lists",
508 "of atom pairs with 1/r^3 and 1/r^6 averaged distance below the",
509 "maximum distance ([TT]-max[tt], which will default to 0.6 in this case)",
510 "can be generated, by default averaging over equivalent hydrogens",
511 "(all triplets of hydrogens named *[123]). Additionally a list of",
512 "equivalent atoms can be supplied ([TT]-equiv[tt]), each line containing",
513 "a set of equivalent atoms specified as residue number and name and",
514 "atom name; e.g.:[PAR]",
515 "[TT]3 SER HB1 3 SER HB2[tt][PAR]",
516 "Residue and atom names must exactly match those in the structure",
517 "file, including case. Specifying non-sequential atoms is undefined."
518
519 };
520
521 int natom,i,j,teller,gi,gj;
522 real t;
523
524 t_topology top;
525 t_atoms *atoms;
526 matrix box;
527 rvec *x;
528 FILE *fp;
529
530 int status,isize,gnr=0;
531 atom_id *index, *noe_index;
532 char *grpname;
533 real **d_r,**d,**dtot,**dtot2,**mean,**rms,**rmsc,*resnr;
534 real **dtot1_3=NULL,**dtot1_6=NULL;
535 real rmsnow,meanmax,rmsmax,rmscmax;
536 real max1_3,max1_6;
537 t_noe_gr *noe_gr=NULL;
538 t_noe **noe=NULL;
539 t_rgb rlo,rhi;
540 char buf[255];
541 bool bRMS, bScale, bMean, bNOE, bNMR3, bNMR6, bNMR;
542
543 static int nlevels=40;
544 static real scalemax=-1.0;
545 static bool bSumH=TRUE;
546 t_pargs pa[] = {
547 { "-nlevels", FALSE, etINT, {&nlevels},
548 "Discretize rms in # levels" },
549 { "-max", FALSE, etREAL, {&scalemax},
550 "Maximum level in matrices" },
551 { "-sumh", FALSE, etBOOL, {&bSumH},
552 "average distance over equivalent hydrogens" }
553 };
554 t_filenm fnm[] = {
555 { efTRX, "-f", NULL, ffREAD },
556 { efTPS, NULL, NULL, ffREAD },
557 { efNDX, NULL, NULL, ffOPTRD },
558 { efDAT, "-equiv","equiv", ffOPTRD },
559 { efXVG, NULL, "distrmsd", ffWRITE },
560 { efXPM, "-rms", "rmsdist", ffOPTWR },
561 { efXPM, "-scl", "rmsscale", ffOPTWR },
562 { efXPM, "-mean","rmsmean", ffOPTWR },
563 { efXPM, "-nmr3","nmr3", ffOPTWR },
564 { efXPM, "-nmr6","nmr6", ffOPTWR },
565 { efDAT, "-noe", "noe", ffOPTWR },
566 };
567 #define NFILE asize(fnm)
568
569 CopyRight(stderr,argv[0]);
570 parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE ,
571 NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
572
573 bRMS = opt2bSet("-rms", NFILE,fnm);
574 bScale= opt2bSet("-scl", NFILE,fnm);
575 bMean = opt2bSet("-mean",NFILE,fnm);
576 bNOE = opt2bSet("-noe", NFILE,fnm);
577 bNMR3 = opt2bSet("-nmr3",NFILE,fnm);
578 bNMR6 = opt2bSet("-nmr6",NFILE,fnm);
579 bNMR = bNMR3 || bNMR6 || bNOE;
580
581 /* check input */
582 if (bNOE && scalemax < 0) {
583 scalemax=0.6;
584 fprintf(stderr,"WARNING: using -noe without -max "
585 "makes no sense, setting -max to %g\n\n",scalemax);
586 }
587
588 /* get topology and index */
589 read_tps_conf(ftp2fn(efTPS,NFILE,fnm),buf,&top,&x,NULL,box,FALSE);
590 atoms=&(top.atoms);
591
592 get_index(atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&isize,&index,&grpname);
593
594 /* initialize arrays */
595 snew(d,isize);
596 snew(dtot,isize);
597 snew(dtot2,isize);
598 if (bNMR) {
599 snew(dtot1_3,isize);
600 snew(dtot1_6,isize);
601 }
602 snew(mean,isize);
603 snew(rms,isize);
604 snew(rmsc,isize);
605 snew(d_r,isize);
606 snew(resnr,isize);
607 for(i=0; (i<isize); i++) {
608 snew(d[i],isize);
609 snew(dtot[i],isize);
610 snew(dtot2[i],isize);
611 if (bNMR) {
612 snew(dtot1_3[i],isize);
613 snew(dtot1_6[i],isize);
614 }
615 snew(mean[i],isize);
616 snew(rms[i],isize);
617 snew(rmsc[i],isize);
618 snew(d_r[i],isize);
619 resnr[i]=i+1;
620 }
621
622 /*set box type*/
623 init_pbc(box);
624 calc_dist(isize,index,x,d_r);
625 sfree(x);
626
627 /*open output files*/
628 fp=xvgropen(ftp2fn(efXVG,NFILE,fnm),"RMS Deviation","Time (ps)","RMSD (nm)");
629 fprintf(fp,"@ subtitle \"of distances between %s atoms\"\n",grpname);
630
631 /*do a first step*/
632 natom=read_first_x(&status,ftp2fn(efTRX,NFILE,fnm),&t,&x,box);
633
634 do {
635 calc_dist_tot(isize,index,x,d,dtot,dtot2,bNMR,dtot1_3,dtot1_6);
636
637 rmsnow=rms_diff(isize,d,d_r);
638 fprintf(fp,"%g %g\n",t,rmsnow);
639 } while (read_next_x(status,&t,natom,x,box));
640 fprintf(stderr, "\n");
641
642 fclose(fp);
643 close_trj(status);
644
645 teller = nframes_read();
646 calc_rms(isize,teller,dtot,dtot2,mean,&meanmax,rms,&rmsmax,rmsc,&rmscmax);
647 fprintf(stderr,"rmsmax = %g, rmscmax = %g\n",rmsmax,rmscmax);
648
649 if (bNMR) {
650 max1_3=0;
651 max1_6=0;
652 calc_nmr(isize,teller,dtot1_3,dtot1_6,&max1_3,&max1_6);
653 }
654
655 if (scalemax > -1.0) {
656 rmsmax=scalemax;
657 rmscmax=scalemax;
658 meanmax=scalemax;
659 max1_3=scalemax;
660 max1_6=scalemax;
661 }
662
663 if (bNOE) {
664 /* make list of noe atom groups */
665 snew(noe_index, isize+1);
666 snew(noe_gr, isize);
667 gnr=analyze_noe_equivalent(opt2fn_null("-equiv",NFILE,fnm),
668 atoms, isize, index, bSumH, noe_index, noe_gr);
669 fprintf(stdout, "Found %d non-equivalent atom-groups in %d atoms\n",
670 gnr, isize);
671 /* make half matrix of of noe-group distances from atom distances */
672 snew(noe,gnr);
673 for(i=0; i<gnr; i++)
674 snew(noe[i],gnr);
675 calc_noe(isize, noe_index, dtot1_3, dtot1_6, gnr, noe);
676 }
677
678 rlo.r=1.0, rlo.g=1.0, rlo.b=1.0;
679 rhi.r=0.0, rhi.g=0.0, rhi.b=0.0;
680
681 if ( bRMS )
682 write_xpm(opt2FILE("-rms",NFILE,fnm,"w"),
683 "RMS of distance","RMS (nm)","Atom Index","Atom Index",
684 isize,isize,resnr,resnr,rms,0.0,rmsmax,rlo,rhi,&nlevels);
685
686 if ( bScale )
687 write_xpm(opt2FILE("-scl",NFILE,fnm,"w"),
688 "Relative RMS","RMS","Atom Index","Atom Index",
689 isize,isize,resnr,resnr,rmsc,0.0,rmscmax,rlo,rhi,&nlevels);
690
691 if ( bMean )
692 write_xpm(opt2FILE("-mean",NFILE,fnm,"w"),
693 "Mean Distance","Distance (nm)","Atom Index","Atom Index",
694 isize,isize,resnr,resnr,mean,0.0,meanmax,rlo,rhi,&nlevels);
695
696 if (bNMR3)
697 write_xpm(opt2FILE("-nmr3",NFILE,fnm,"w"),"1/r^3 averaged distances",
698 "Distance (nm)","Atom Index","Atom Index",
699 isize,isize,resnr,resnr,dtot1_3,0.0,max1_3,rlo,rhi,&nlevels);
700 if (bNMR6)
701 write_xpm(opt2FILE("-nmr6",NFILE,fnm,"w"),"1/r^6 averaged distances",
702 "Distance (nm)","Atom Index","Atom Index",
703 isize,isize,resnr,resnr,dtot1_6,0.0,max1_6,rlo,rhi,&nlevels);
704
705 if (bNOE)
706 write_noe(opt2FILE("-noe",NFILE,fnm,"w"), gnr, noe, noe_gr, scalemax);
707
708 do_view(ftp2fn(efXVG,NFILE,fnm),NULL);
709
710 thanx(stderr);
711 return 0;
712 }
The ultimate molecular dynamics simulation package