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48 #include "gromacs/commandline/pargs.h"
49 #include "gromacs/fileio/tpxio.h"
50 #include "gromacs/fileio/trxio.h"
52 #include "gromacs/fileio/strdb.h"
58 #include "gromacs/fileio/futil.h"
59 #include "gromacs/fileio/matio.h"
63 static void calc_dist(int nind, atom_id index[], rvec x[], int ePBC, matrix box,
72 set_pbc(&pbc, ePBC, box);
73 for (i = 0; (i < nind-1); i++)
76 for (j = i+1; (j < nind); j++)
78 pbc_dx(&pbc, xi, x[index[j]], dx);
80 d[i][j] = sqrt(temp2);
85 static void calc_dist_tot(int nind, atom_id index[], rvec x[],
87 real **d, real **dtot, real **dtot2,
88 gmx_bool bNMR, real **dtot1_3, real **dtot1_6)
92 real temp, temp2, temp1_3;
96 set_pbc(&pbc, ePBC, box);
97 for (i = 0; (i < nind-1); i++)
100 for (j = i+1; (j < nind); j++)
102 pbc_dx(&pbc, xi, x[index[j]], dx);
107 dtot2[i][j] += temp2;
110 temp1_3 = 1.0/(temp*temp2);
111 dtot1_3[i][j] += temp1_3;
112 dtot1_6[i][j] += temp1_3*temp1_3;
118 static void calc_nmr(int nind, int nframes, real **dtot1_3, real **dtot1_6,
119 real *max1_3, real *max1_6)
122 real temp1_3, temp1_6;
124 for (i = 0; (i < nind-1); i++)
126 for (j = i+1; (j < nind); j++)
128 temp1_3 = pow(dtot1_3[i][j]/nframes, -1.0/3.0);
129 temp1_6 = pow(dtot1_6[i][j]/nframes, -1.0/6.0);
130 if (temp1_3 > *max1_3)
134 if (temp1_6 > *max1_6)
138 dtot1_3[i][j] = temp1_3;
139 dtot1_6[i][j] = temp1_6;
140 dtot1_3[j][i] = temp1_3;
141 dtot1_6[j][i] = temp1_6;
146 static char Hnum[] = "123";
171 static int read_equiv(const char *eq_fn, t_equiv ***equivptr)
174 char line[STRLEN], resname[10], atomname[10], *lp;
175 int neq, na, n, resnr;
178 fp = gmx_ffopen(eq_fn, "r");
181 while (get_a_line(fp, line, STRLEN))
184 /* this is not efficient, but I'm lazy */
185 srenew(equiv, neq+1);
188 if (sscanf(lp, "%s %n", atomname, &n) == 1)
192 equiv[neq][0].nname = strdup(atomname);
193 while (sscanf(lp, "%d %s %s %n", &resnr, resname, atomname, &n) == 3)
195 /* this is not efficient, but I'm lazy (again) */
196 srenew(equiv[neq], na+1);
197 equiv[neq][na].rnr = resnr-1;
198 equiv[neq][na].rname = strdup(resname);
199 equiv[neq][na].aname = strdup(atomname);
202 equiv[neq][na].nname = NULL;
208 /* make empty element as flag for end of array */
209 srenew(equiv[neq], na+1);
210 equiv[neq][na].rnr = NOTSET;
211 equiv[neq][na].rname = NULL;
212 equiv[neq][na].aname = NULL;
224 static void dump_equiv(FILE *out, int neq, t_equiv **equiv)
228 fprintf(out, "Dumping equivalent list\n");
229 for (i = 0; i < neq; i++)
231 fprintf(out, "%s", equiv[i][0].nname);
232 for (j = 0; equiv[i][j].rnr != NOTSET; j++)
234 fprintf(out, " %d %s %s",
235 equiv[i][j].rnr, equiv[i][j].rname, equiv[i][j].aname);
241 static gmx_bool is_equiv(int neq, t_equiv **equiv, char **nname,
242 int rnr1, char *rname1, char *aname1,
243 int rnr2, char *rname2, char *aname2)
249 /* we can terminate each loop when bFound is true! */
250 for (i = 0; i < neq && !bFound; i++)
252 /* find first atom */
253 for (j = 0; equiv[i][j].rnr != NOTSET && !bFound; j++)
255 bFound = ( equiv[i][j].rnr == rnr1 &&
256 strcmp(equiv[i][j].rname, rname1) == 0 &&
257 strcmp(equiv[i][j].aname, aname1) == 0 );
261 /* find second atom */
263 for (j = 0; equiv[i][j].rnr != NOTSET && !bFound; j++)
265 bFound = ( equiv[i][j].rnr == rnr2 &&
266 strcmp(equiv[i][j].rname, rname2) == 0 &&
267 strcmp(equiv[i][j].aname, aname2) == 0 );
273 *nname = strdup(equiv[i-1][0].nname);
279 static int analyze_noe_equivalent(const char *eq_fn,
280 t_atoms *atoms, int isize, atom_id *index,
282 atom_id *noe_index, t_noe_gr *noe_gr)
285 int i, j, anmil, anmjl, rnri, rnrj, gi, groupnr, neq;
286 char *anmi, *anmj, **nnm;
287 gmx_bool bMatch, bEquiv;
295 neq = read_equiv(eq_fn, &equiv);
298 dump_equiv(debug, neq, equiv);
308 for (i = 0; i < isize; i++)
310 if (equiv && i < isize-1)
312 /* check explicit list of equivalent atoms */
316 rnri = atoms->atom[index[i]].resind;
317 rnrj = atoms->atom[index[j]].resind;
319 is_equiv(neq, equiv, &nnm[i],
320 rnri, *atoms->resinfo[rnri].name, *atoms->atomname[index[i]],
321 rnrj, *atoms->resinfo[rnrj].name, *atoms->atomname[index[j]]);
322 if (nnm[i] && bEquiv)
324 nnm[j] = strdup(nnm[i]);
328 /* set index for matching atom */
329 noe_index[j] = groupnr;
330 /* skip matching atom */
334 while (bEquiv && i < isize-1);
342 /* look for triplets of consecutive atoms with name XX?,
343 X are any number of letters or digits and ? goes from 1 to 3
344 This is supposed to cover all CH3 groups and the like */
345 anmi = *atoms->atomname[index[i]];
346 anmil = strlen(anmi);
347 bMatch = i < isize-3 && anmi[anmil-1] == '1';
350 for (j = 1; j < 3; j++)
352 anmj = *atoms->atomname[index[i+j]];
353 anmjl = strlen(anmj);
354 bMatch = bMatch && ( anmil == anmjl && anmj[anmjl-1] == Hnum[j] &&
355 strncmp(anmi, anmj, anmil-1) == 0 );
358 /* set index for this atom */
359 noe_index[i] = groupnr;
362 /* set index for next two matching atoms */
363 for (j = 1; j < 3; j++)
365 noe_index[i+j] = groupnr;
367 /* skip matching atoms */
376 /* make index without looking for equivalent atoms */
377 for (i = 0; i < isize; i++)
383 noe_index[isize] = groupnr;
388 for (i = 0; i < isize; i++)
390 rnri = atoms->atom[index[i]].resind;
391 fprintf(debug, "%s %s %d -> %s\n", *atoms->atomname[index[i]],
392 *atoms->resinfo[rnri].name, rnri, nnm[i] ? nnm[i] : "");
396 for (i = 0; i < isize; i++)
399 if (!noe_gr[gi].aname)
402 noe_gr[gi].anr = index[i];
405 noe_gr[gi].aname = strdup(nnm[i]);
409 noe_gr[gi].aname = strdup(*atoms->atomname[index[i]]);
410 if (noe_index[i] == noe_index[i+1])
412 noe_gr[gi].aname[strlen(noe_gr[gi].aname)-1] = '*';
415 noe_gr[gi].rnr = atoms->atom[index[i]].resind;
416 noe_gr[gi].rname = strdup(*atoms->resinfo[noe_gr[gi].rnr].name);
417 /* dump group definitions */
420 fprintf(debug, "%d %d %d %d %s %s %d\n", i, gi,
421 noe_gr[gi].ianr, noe_gr[gi].anr, noe_gr[gi].aname,
422 noe_gr[gi].rname, noe_gr[gi].rnr);
426 for (i = 0; i < isize; i++)
435 /* #define NSCALE 3 */
436 /* static char *noe_scale[NSCALE+1] = { */
437 /* "strong", "medium", "weak", "none" */
441 static char *noe2scale(real r3, real r6, real rmax)
444 static char buf[NSCALE+1];
446 /* r goes from 0 to rmax
447 NSCALE*r/rmax goes from 0 to NSCALE
448 NSCALE - NSCALE*r/rmax goes from NSCALE to 0 */
449 s3 = NSCALE - min(NSCALE, (int)(NSCALE*r3/rmax));
450 s6 = NSCALE - min(NSCALE, (int)(NSCALE*r6/rmax));
452 for (i = 0; i < s3; i++)
465 static void calc_noe(int isize, atom_id *noe_index,
466 real **dtot1_3, real **dtot1_6, int gnr, t_noe **noe)
470 /* make half matrix of noe-group distances from atom distances */
471 for (i = 0; i < isize; i++)
474 for (j = i; j < isize; j++)
478 noe[gi][gj].i_3 += pow(dtot1_3[i][j], -3);
479 noe[gi][gj].i_6 += pow(dtot1_6[i][j], -6);
484 for (i = 0; i < gnr; i++)
486 for (j = i+1; j < gnr; j++)
488 noe[i][j].r_3 = pow(noe[i][j].i_3/noe[i][j].nr, -1.0/3.0);
489 noe[i][j].r_6 = pow(noe[i][j].i_6/noe[i][j].nr, -1.0/6.0);
490 noe[j][i] = noe[i][j];
495 static void write_noe(FILE *fp, int gnr, t_noe **noe, t_noe_gr *noe_gr, real rmax)
498 real r3, r6, min3, min6;
499 char buf[10], b3[10], b6[10];
504 ";%4s %3s %4s %4s%3s %4s %4s %4s %4s%3s %5s %5s %8s %2s %2s %s\n",
505 "ianr", "anr", "anm", "rnm", "rnr", "ianr", "anr", "anm", "rnm", "rnr",
506 "1/r^3", "1/r^6", "intnsty", "Dr", "Da", "scale");
507 for (i = 0; i < gnr; i++)
510 for (j = i+1; j < gnr; j++)
515 min3 = min(r3, min3);
516 min6 = min(r6, min6);
517 if (r3 < rmax || r6 < rmax)
519 if (grj.rnr == gri.rnr)
521 sprintf(buf, "%2d", grj.anr-gri.anr);
529 sprintf(b3, "%-5.3f", r3);
537 sprintf(b6, "%-5.3f", r6);
544 "%4d %4d %4s %4s%3d %4d %4d %4s %4s%3d %5s %5s %8d %2d %2s %s\n",
545 gri.ianr+1, gri.anr+1, gri.aname, gri.rname, gri.rnr+1,
546 grj.ianr+1, grj.anr+1, grj.aname, grj.rname, grj.rnr+1,
547 b3, b6, (int)(noe[i][j].i_6+0.5), grj.rnr-gri.rnr, buf,
548 noe2scale(r3, r6, rmax));
552 #define MINI ((i == 3) ? min3 : min6)
553 for (i = 3; i <= 6; i += 3)
557 fprintf(stdout, "NOTE: no 1/r^%d averaged distances found below %g, "
558 "smallest was %g\n", i, rmax, MINI );
562 fprintf(stdout, "Smallest 1/r^%d averaged distance was %g\n", i, MINI );
568 static void calc_rms(int nind, int nframes,
569 real **dtot, real **dtot2,
570 real **rmsmat, real *rmsmax,
571 real **rmscmat, real *rmscmax,
572 real **meanmat, real *meanmax)
575 real mean, mean2, rms, rmsc;
576 /* N.B. dtot and dtot2 contain the total distance and the total squared
577 * distance respectively, BUT they return RMS and the scaled RMS resp.
584 for (i = 0; (i < nind-1); i++)
586 for (j = i+1; (j < nind); j++)
588 mean = dtot[i][j]/nframes;
589 mean2 = dtot2[i][j]/nframes;
590 rms = sqrt(max(0, mean2-mean*mean));
604 meanmat[i][j] = meanmat[j][i] = mean;
605 rmsmat[i][j] = rmsmat[j][i] = rms;
606 rmscmat[i][j] = rmscmat[j][i] = rmsc;
611 real rms_diff(int natom, real **d, real **d_r)
617 for (i = 0; (i < natom-1); i++)
619 for (j = i+1; (j < natom); j++)
621 r = d[i][j]-d_r[i][j];
625 r2 /= (natom*(natom-1))/2;
630 int gmx_rmsdist(int argc, char *argv[])
632 const char *desc[] = {
633 "[THISMODULE] computes the root mean square deviation of atom distances,",
634 "which has the advantage that no fit is needed like in standard RMS",
635 "deviation as computed by [gmx-rms].",
636 "The reference structure is taken from the structure file.",
637 "The RMSD at time t is calculated as the RMS",
638 "of the differences in distance between atom-pairs in the reference",
639 "structure and the structure at time t.[PAR]",
640 "[THISMODULE] can also produce matrices of the rms distances, rms distances",
641 "scaled with the mean distance and the mean distances and matrices with",
642 "NMR averaged distances (1/r^3 and 1/r^6 averaging). Finally, lists",
643 "of atom pairs with 1/r^3 and 1/r^6 averaged distance below the",
644 "maximum distance ([TT]-max[tt], which will default to 0.6 in this case)",
645 "can be generated, by default averaging over equivalent hydrogens",
646 "(all triplets of hydrogens named *[123]). Additionally a list of",
647 "equivalent atoms can be supplied ([TT]-equiv[tt]), each line containing",
648 "a set of equivalent atoms specified as residue number and name and",
649 "atom name; e.g.:[PAR]",
650 "[TT]3 SER HB1 3 SER HB2[tt][PAR]",
651 "Residue and atom names must exactly match those in the structure",
652 "file, including case. Specifying non-sequential atoms is undefined."
656 int natom, i, j, teller, gi, gj;
668 atom_id *index, *noe_index;
670 real **d_r, **d, **dtot, **dtot2, **mean, **rms, **rmsc, *resnr;
671 real **dtot1_3 = NULL, **dtot1_6 = NULL;
672 real rmsnow, meanmax, rmsmax, rmscmax;
674 t_noe_gr *noe_gr = NULL;
678 gmx_bool bRMS, bScale, bMean, bNOE, bNMR3, bNMR6, bNMR;
680 static int nlevels = 40;
681 static real scalemax = -1.0;
682 static gmx_bool bSumH = TRUE;
683 static gmx_bool bPBC = TRUE;
687 { "-nlevels", FALSE, etINT, {&nlevels},
688 "Discretize RMS in this number of levels" },
689 { "-max", FALSE, etREAL, {&scalemax},
690 "Maximum level in matrices" },
691 { "-sumh", FALSE, etBOOL, {&bSumH},
692 "Average distance over equivalent hydrogens" },
693 { "-pbc", FALSE, etBOOL, {&bPBC},
694 "Use periodic boundary conditions when computing distances" }
697 { efTRX, "-f", NULL, ffREAD },
698 { efTPS, NULL, NULL, ffREAD },
699 { efNDX, NULL, NULL, ffOPTRD },
700 { efDAT, "-equiv", "equiv", ffOPTRD },
701 { efXVG, NULL, "distrmsd", ffWRITE },
702 { efXPM, "-rms", "rmsdist", ffOPTWR },
703 { efXPM, "-scl", "rmsscale", ffOPTWR },
704 { efXPM, "-mean", "rmsmean", ffOPTWR },
705 { efXPM, "-nmr3", "nmr3", ffOPTWR },
706 { efXPM, "-nmr6", "nmr6", ffOPTWR },
707 { efDAT, "-noe", "noe", ffOPTWR },
709 #define NFILE asize(fnm)
711 if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
712 NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
717 bRMS = opt2bSet("-rms", NFILE, fnm);
718 bScale = opt2bSet("-scl", NFILE, fnm);
719 bMean = opt2bSet("-mean", NFILE, fnm);
720 bNOE = opt2bSet("-noe", NFILE, fnm);
721 bNMR3 = opt2bSet("-nmr3", NFILE, fnm);
722 bNMR6 = opt2bSet("-nmr6", NFILE, fnm);
723 bNMR = bNMR3 || bNMR6 || bNOE;
729 if (bNOE && scalemax < 0)
732 fprintf(stderr, "WARNING: using -noe without -max "
733 "makes no sense, setting -max to %g\n\n", scalemax);
736 /* get topology and index */
737 read_tps_conf(ftp2fn(efTPS, NFILE, fnm), buf, &top, &ePBC, &x, NULL, box, FALSE);
743 atoms = &(top.atoms);
745 get_index(atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &isize, &index, &grpname);
747 /* initialize arrays */
753 snew(dtot1_3, isize);
754 snew(dtot1_6, isize);
761 for (i = 0; (i < isize); i++)
764 snew(dtot[i], isize);
765 snew(dtot2[i], isize);
768 snew(dtot1_3[i], isize);
769 snew(dtot1_6[i], isize);
771 snew(mean[i], isize);
773 snew(rmsc[i], isize);
779 calc_dist(isize, index, x, ePBC, box, d_r);
782 /*open output files*/
783 fp = xvgropen(ftp2fn(efXVG, NFILE, fnm), "RMS Deviation", "Time (ps)", "RMSD (nm)",
785 if (output_env_get_print_xvgr_codes(oenv))
787 fprintf(fp, "@ subtitle \"of distances between %s atoms\"\n", grpname);
791 natom = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
795 calc_dist_tot(isize, index, x, ePBC, box, d, dtot, dtot2, bNMR, dtot1_3, dtot1_6);
797 rmsnow = rms_diff(isize, d, d_r);
798 fprintf(fp, "%g %g\n", t, rmsnow);
800 while (read_next_x(oenv, status, &t, x, box));
801 fprintf(stderr, "\n");
805 teller = nframes_read(status);
809 calc_rms(isize, teller, dtot, dtot2, mean, &meanmax, rms, &rmsmax, rmsc, &rmscmax);
810 fprintf(stderr, "rmsmax = %g, rmscmax = %g\n", rmsmax, rmscmax);
814 calc_nmr(isize, teller, dtot1_3, dtot1_6, &max1_3, &max1_6);
828 /* make list of noe atom groups */
829 snew(noe_index, isize+1);
831 gnr = analyze_noe_equivalent(opt2fn_null("-equiv", NFILE, fnm),
832 atoms, isize, index, bSumH, noe_index, noe_gr);
833 fprintf(stdout, "Found %d non-equivalent atom-groups in %d atoms\n",
835 /* make half matrix of of noe-group distances from atom distances */
837 for (i = 0; i < gnr; i++)
841 calc_noe(isize, noe_index, dtot1_3, dtot1_6, gnr, noe);
844 rlo.r = 1.0, rlo.g = 1.0, rlo.b = 1.0;
845 rhi.r = 0.0, rhi.g = 0.0, rhi.b = 0.0;
849 write_xpm(opt2FILE("-rms", NFILE, fnm, "w"), 0,
850 "RMS of distance", "RMS (nm)", "Atom Index", "Atom Index",
851 isize, isize, resnr, resnr, rms, 0.0, rmsmax, rlo, rhi, &nlevels);
856 write_xpm(opt2FILE("-scl", NFILE, fnm, "w"), 0,
857 "Relative RMS", "RMS", "Atom Index", "Atom Index",
858 isize, isize, resnr, resnr, rmsc, 0.0, rmscmax, rlo, rhi, &nlevels);
863 write_xpm(opt2FILE("-mean", NFILE, fnm, "w"), 0,
864 "Mean Distance", "Distance (nm)", "Atom Index", "Atom Index",
865 isize, isize, resnr, resnr, mean, 0.0, meanmax, rlo, rhi, &nlevels);
870 write_xpm(opt2FILE("-nmr3", NFILE, fnm, "w"), 0, "1/r^3 averaged distances",
871 "Distance (nm)", "Atom Index", "Atom Index",
872 isize, isize, resnr, resnr, dtot1_3, 0.0, max1_3, rlo, rhi, &nlevels);
876 write_xpm(opt2FILE("-nmr6", NFILE, fnm, "w"), 0, "1/r^6 averaged distances",
877 "Distance (nm)", "Atom Index", "Atom Index",
878 isize, isize, resnr, resnr, dtot1_6, 0.0, max1_6, rlo, rhi, &nlevels);
883 write_noe(opt2FILE("-noe", NFILE, fnm, "w"), gnr, noe, noe_gr, scalemax);
886 do_view(oenv, ftp2fn(efXVG, NFILE, fnm), NULL);