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42 #include "gromacs/utility/smalloc.h"
43 #include "gromacs/legacyheaders/macros.h"
44 #include "gromacs/legacyheaders/typedefs.h"
45 #include "gromacs/fileio/xvgr.h"
46 #include "gromacs/legacyheaders/copyrite.h"
47 #include "gromacs/commandline/pargs.h"
48 #include "gromacs/math/vec.h"
49 #include "gromacs/topology/index.h"
50 #include "gromacs/utility/fatalerror.h"
51 #include "gromacs/utility/futil.h"
53 #include "gromacs/pbcutil/rmpbc.h"
54 #include "gromacs/fileio/matio.h"
55 #include "gromacs/fileio/tpxio.h"
56 #include "gromacs/fileio/trxio.h"
58 #include "gromacs/legacyheaders/viewit.h"
61 #include "gromacs/math/do_fit.h"
63 static void norm_princ(t_atoms *atoms, int isize, atom_id *index, int natoms,
69 /* equalize principal components: */
70 /* orient principal axes, get principal components */
71 orient_princ(atoms, isize, index, natoms, x, NULL, princ);
73 /* calc our own principal components */
75 for (m = 0; m < DIM; m++)
77 for (i = 0; i < isize; i++)
79 vec[m] += sqr(x[index[i]][m]);
81 vec[m] = sqrt(vec[m] / isize);
82 /* calculate scaling constants */
83 vec[m] = 1 / (sqrt(3) * vec[m]);
86 /* scale coordinates */
87 for (i = 0; i < natoms; i++)
89 for (m = 0; m < DIM; m++)
96 int gmx_rms(int argc, char *argv[])
100 "[THISMODULE] compares two structures by computing the root mean square",
101 "deviation (RMSD), the size-independent [GRK]rho[grk] similarity parameter",
102 "([TT]rho[tt]) or the scaled [GRK]rho[grk] ([TT]rhosc[tt]), ",
103 "see Maiorov & Crippen, Proteins [BB]22[bb], 273 (1995).",
104 "This is selected by [TT]-what[tt].[PAR]"
106 "Each structure from a trajectory ([TT]-f[tt]) is compared to a",
107 "reference structure. The reference structure",
108 "is taken from the structure file ([TT]-s[tt]).[PAR]",
110 "With option [TT]-mir[tt] also a comparison with the mirror image of",
111 "the reference structure is calculated.",
112 "This is useful as a reference for 'significant' values, see",
113 "Maiorov & Crippen, Proteins [BB]22[bb], 273 (1995).[PAR]",
115 "Option [TT]-prev[tt] produces the comparison with a previous frame",
116 "the specified number of frames ago.[PAR]",
118 "Option [TT]-m[tt] produces a matrix in [TT].xpm[tt] format of",
119 "comparison values of each structure in the trajectory with respect to",
120 "each other structure. This file can be visualized with for instance",
121 "[TT]xv[tt] and can be converted to postscript with [gmx-xpm2ps].[PAR]",
123 "Option [TT]-fit[tt] controls the least-squares fitting of",
124 "the structures on top of each other: complete fit (rotation and",
125 "translation), translation only, or no fitting at all.[PAR]",
127 "Option [TT]-mw[tt] controls whether mass weighting is done or not.",
128 "If you select the option (default) and ",
129 "supply a valid [TT].tpr[tt] file masses will be taken from there, ",
130 "otherwise the masses will be deduced from the [TT]atommass.dat[tt] file in",
131 "[TT]GMXLIB[tt]. This is fine for proteins, but not",
132 "necessarily for other molecules. A default mass of 12.011 amu (carbon)",
133 "is assigned to unknown atoms. You can check whether this happend by",
134 "turning on the [TT]-debug[tt] flag and inspecting the log file.[PAR]",
136 "With [TT]-f2[tt], the 'other structures' are taken from a second",
137 "trajectory, this generates a comparison matrix of one trajectory",
138 "versus the other.[PAR]",
140 "Option [TT]-bin[tt] does a binary dump of the comparison matrix.[PAR]",
142 "Option [TT]-bm[tt] produces a matrix of average bond angle deviations",
143 "analogously to the [TT]-m[tt] option. Only bonds between atoms in the",
144 "comparison group are considered."
146 static gmx_bool bPBC = TRUE, bFitAll = TRUE, bSplit = FALSE;
147 static gmx_bool bDeltaLog = FALSE;
148 static int prev = 0, freq = 1, freq2 = 1, nlevels = 80, avl = 0;
149 static real rmsd_user_max = -1, rmsd_user_min = -1, bond_user_max = -1,
150 bond_user_min = -1, delta_maxy = 0.0;
151 /* strings and things for selecting difference method */
154 ewSel, ewRMSD, ewRho, ewRhoSc, ewNR
157 const char *what[ewNR + 1] =
158 { NULL, "rmsd", "rho", "rhosc", NULL };
159 const char *whatname[ewNR] =
160 { NULL, "RMSD", "Rho", "Rho sc" };
161 const char *whatlabel[ewNR] =
162 { NULL, "RMSD (nm)", "Rho", "Rho sc" };
163 const char *whatxvgname[ewNR] =
164 { NULL, "RMSD", "\\8r\\4", "\\8r\\4\\ssc\\N" };
165 const char *whatxvglabel[ewNR] =
166 { NULL, "RMSD (nm)", "\\8r\\4", "\\8r\\4\\ssc\\N" };
167 /* strings and things for fitting methods */
170 efSel, efFit, efReset, efNone, efNR
173 const char *fit[efNR + 1] =
174 { NULL, "rot+trans", "translation", "none", NULL };
175 const char *fitgraphlabel[efNR + 1] =
176 { NULL, "lsq fit", "translational fit", "no fit" };
178 static gmx_bool bMassWeighted = TRUE;
181 { "-what", FALSE, etENUM,
182 { what }, "Structural difference measure" },
183 { "-pbc", FALSE, etBOOL,
184 { &bPBC }, "PBC check" },
185 { "-fit", FALSE, etENUM,
186 { fit }, "Fit to reference structure" },
187 { "-prev", FALSE, etINT,
188 { &prev }, "Compare with previous frame" },
189 { "-split", FALSE, etBOOL,
190 { &bSplit }, "Split graph where time is zero" },
191 { "-fitall", FALSE, etBOOL,
192 { &bFitAll }, "HIDDENFit all pairs of structures in matrix" },
193 { "-skip", FALSE, etINT,
194 { &freq }, "Only write every nr-th frame to matrix" },
195 { "-skip2", FALSE, etINT,
196 { &freq2 }, "Only write every nr-th frame to matrix" },
197 { "-max", FALSE, etREAL,
198 { &rmsd_user_max }, "Maximum level in comparison matrix" },
199 { "-min", FALSE, etREAL,
200 { &rmsd_user_min }, "Minimum level in comparison matrix" },
201 { "-bmax", FALSE, etREAL,
202 { &bond_user_max }, "Maximum level in bond angle matrix" },
203 { "-bmin", FALSE, etREAL,
204 { &bond_user_min }, "Minimum level in bond angle matrix" },
205 { "-mw", FALSE, etBOOL,
206 { &bMassWeighted }, "Use mass weighting for superposition" },
207 { "-nlevels", FALSE, etINT,
208 { &nlevels }, "Number of levels in the matrices" },
209 { "-ng", FALSE, etINT,
210 { &nrms }, "Number of groups to compute RMS between" },
211 { "-dlog", FALSE, etBOOL,
213 "HIDDENUse a log x-axis in the delta t matrix" },
214 { "-dmax", FALSE, etREAL,
215 { &delta_maxy }, "HIDDENMaximum level in delta matrix" },
216 { "-aver", FALSE, etINT,
218 "HIDDENAverage over this distance in the RMSD matrix" }
220 int natoms_trx, natoms_trx2, natoms;
221 int i, j, k, m, teller, teller2, tel_mat, tel_mat2;
223 int maxframe = NFRAME, maxframe2 = NFRAME;
224 real t, *w_rls, *w_rms, *w_rls_m = NULL, *w_rms_m = NULL;
225 gmx_bool bNorm, bAv, bFreq2, bFile2, bMat, bBond, bDelta, bMirror, bMass;
226 gmx_bool bFit, bReset;
229 t_iatom *iatom = NULL;
232 rvec *x, *xp, *xm = NULL, **mat_x = NULL, **mat_x2, *mat_x2_j = NULL, vec1,
235 char buf[256], buf2[256];
238 real rlstot = 0, **rls, **rlsm = NULL, *time, *time2, *rlsnorm = NULL,
239 **rmsd_mat = NULL, **bond_mat = NULL, *axis, *axis2, *del_xaxis,
240 *del_yaxis, rmsd_max, rmsd_min, rmsd_avg, bond_max, bond_min, ang;
241 real **rmsdav_mat = NULL, av_tot, weight, weight_tot;
242 real **delta = NULL, delta_max, delta_scalex = 0, delta_scaley = 0,
244 int delta_xsize = 0, del_lev = 100, mx, my, abs_my;
245 gmx_bool bA1, bA2, bPrev, bTop, *bInMat = NULL;
246 int ifit, *irms, ibond = 0, *ind_bond1 = NULL, *ind_bond2 = NULL, n_ind_m =
248 atom_id *ind_fit, **ind_rms, *ind_m = NULL, *rev_ind_m = NULL, *ind_rms_m =
250 char *gn_fit, **gn_rms;
253 gmx_rmpbc_t gpbc = NULL;
257 { efTPS, NULL, NULL, ffREAD },
258 { efTRX, "-f", NULL, ffREAD },
259 { efTRX, "-f2", NULL, ffOPTRD },
260 { efNDX, NULL, NULL, ffOPTRD },
261 { efXVG, NULL, "rmsd", ffWRITE },
262 { efXVG, "-mir", "rmsdmir", ffOPTWR },
263 { efXVG, "-a", "avgrp", ffOPTWR },
264 { efXVG, "-dist", "rmsd-dist", ffOPTWR },
265 { efXPM, "-m", "rmsd", ffOPTWR },
266 { efDAT, "-bin", "rmsd", ffOPTWR },
267 { efXPM, "-bm", "bond", ffOPTWR }
269 #define NFILE asize(fnm)
271 if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW,
272 NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL,
277 /* parse enumerated options: */
279 if (ewhat == ewRho || ewhat == ewRhoSc)
281 please_cite(stdout, "Maiorov95");
284 bFit = efit == efFit;
285 bReset = efit == efReset;
288 bReset = TRUE; /* for fit, reset *must* be set */
295 /* mark active cmdline options */
296 bMirror = opt2bSet("-mir", NFILE, fnm); /* calc RMSD vs mirror of ref. */
297 bFile2 = opt2bSet("-f2", NFILE, fnm);
298 bMat = opt2bSet("-m", NFILE, fnm);
299 bBond = opt2bSet("-bm", NFILE, fnm);
300 bDelta = (delta_maxy > 0); /* calculate rmsd vs delta t matrix from *
301 * your RMSD matrix (hidden option */
302 bNorm = opt2bSet("-a", NFILE, fnm);
303 bFreq2 = opt2parg_bSet("-skip2", asize(pa), pa);
306 fprintf(stderr, "The number of frames to skip is <= 0. "
307 "Writing out all frames.\n\n");
314 else if (bFile2 && freq2 <= 0)
317 "The number of frames to skip in second trajectory is <= 0.\n"
318 " Writing out all frames.\n\n");
325 fprintf(stderr, "WARNING: using option -prev with large trajectories will\n"
326 " require a lot of memory and could lead to crashes\n");
330 fprintf(stderr, "WARNING: option -skip also applies to -prev\n");
334 if (bFile2 && !bMat && !bBond)
338 "WARNING: second trajectory (-f2) useless when not calculating matrix (-m/-bm),\n"
339 " will not read from %s\n", opt2fn("-f2", NFILE,
350 "WARNING: second trajectory (-f2) useless when making delta matrix,\n"
351 " will not read from %s\n", opt2fn("-f2",
357 bTop = read_tps_conf(ftp2fn(efTPS, NFILE, fnm), buf, &top, &ePBC, &xp,
359 snew(w_rls, top.atoms.nr);
360 snew(w_rms, top.atoms.nr);
365 "WARNING: Need a run input file for bond angle matrix,\n"
366 " will not calculate bond angle matrix.\n");
372 fprintf(stderr, "Select group for %s fit\n", bFit ? "least squares"
374 get_index(&(top.atoms), ftp2fn_null(efNDX, NFILE, fnm), 1, &ifit,
384 if (bFit && ifit < 3)
386 gmx_fatal(FARGS, "Need >= 3 points to fit!\n" );
390 for (i = 0; i < ifit; i++)
394 w_rls[ind_fit[i]] = top.atoms.atom[ind_fit[i]].m;
398 w_rls[ind_fit[i]] = 1;
400 bMass = bMass || (top.atoms.atom[ind_fit[i]].m != 0);
404 fprintf(stderr, "All masses in the fit group are 0, using masses of 1\n");
405 for (i = 0; i < ifit; i++)
407 w_rls[ind_fit[i]] = 1;
421 fprintf(stderr, "Select group%s for %s calculation\n",
422 (nrms > 1) ? "s" : "", whatname[ewhat]);
423 get_index(&(top.atoms), ftp2fn_null(efNDX, NFILE, fnm),
424 nrms, irms, ind_rms, gn_rms);
428 snew(rlsnorm, irms[0]);
431 for (j = 0; j < nrms; j++)
433 snew(rls[j], maxframe);
438 for (j = 0; j < nrms; j++)
440 snew(rlsm[j], maxframe);
443 snew(time, maxframe);
444 for (j = 0; j < nrms; j++)
447 for (i = 0; i < irms[j]; i++)
451 w_rms[ind_rms[j][i]] = top.atoms.atom[ind_rms[j][i]].m;
455 w_rms[ind_rms[j][i]] = 1.0;
457 bMass = bMass || (top.atoms.atom[ind_rms[j][i]].m != 0);
461 fprintf(stderr, "All masses in group %d are 0, using masses of 1\n", j);
462 for (i = 0; i < irms[j]; i++)
464 w_rms[ind_rms[j][i]] = 1;
468 /* Prepare reference frame */
471 gpbc = gmx_rmpbc_init(&top.idef, ePBC, top.atoms.nr);
472 gmx_rmpbc(gpbc, top.atoms.nr, box, xp);
476 reset_x(ifit, ind_fit, top.atoms.nr, NULL, xp, w_rls);
480 /* generate reference structure mirror image: */
481 snew(xm, top.atoms.nr);
482 for (i = 0; i < top.atoms.nr; i++)
484 copy_rvec(xp[i], xm[i]);
485 xm[i][XX] = -xm[i][XX];
488 if (ewhat == ewRhoSc)
490 norm_princ(&top.atoms, ifit, ind_fit, top.atoms.nr, xp);
493 /* read first frame */
494 natoms_trx = read_first_x(oenv, &status, opt2fn("-f", NFILE, fnm), &t, &x, box);
495 if (natoms_trx != top.atoms.nr)
498 "\nWARNING: topology has %d atoms, whereas trajectory has %d\n",
499 top.atoms.nr, natoms_trx);
501 natoms = min(top.atoms.nr, natoms_trx);
502 if (bMat || bBond || bPrev)
508 /* With -prev we use all atoms for simplicity */
513 /* Check which atoms we need (fit/rms) */
514 snew(bInMat, natoms);
515 for (i = 0; i < ifit; i++)
517 bInMat[ind_fit[i]] = TRUE;
520 for (i = 0; i < irms[0]; i++)
522 if (!bInMat[ind_rms[0][i]])
524 bInMat[ind_rms[0][i]] = TRUE;
529 /* Make an index of needed atoms */
530 snew(ind_m, n_ind_m);
531 snew(rev_ind_m, natoms);
533 for (i = 0; i < natoms; i++)
535 if (bPrev || bInMat[i])
542 snew(w_rls_m, n_ind_m);
543 snew(ind_rms_m, irms[0]);
544 snew(w_rms_m, n_ind_m);
545 for (i = 0; i < ifit; i++)
547 w_rls_m[rev_ind_m[ind_fit[i]]] = w_rls[ind_fit[i]];
549 for (i = 0; i < irms[0]; i++)
551 ind_rms_m[i] = rev_ind_m[ind_rms[0][i]];
552 w_rms_m[ind_rms_m[i]] = w_rms[ind_rms[0][i]];
560 for (k = 0; k < F_NRE; k++)
564 iatom = top.idef.il[k].iatoms;
565 ncons += top.idef.il[k].nr/3;
568 fprintf(stderr, "Found %d bonds in topology\n", ncons);
569 snew(ind_bond1, ncons);
570 snew(ind_bond2, ncons);
572 for (k = 0; k < F_NRE; k++)
576 iatom = top.idef.il[k].iatoms;
577 ncons = top.idef.il[k].nr/3;
578 for (i = 0; i < ncons; i++)
582 for (j = 0; j < irms[0]; j++)
584 if (iatom[3*i+1] == ind_rms[0][j])
588 if (iatom[3*i+2] == ind_rms[0][j])
595 ind_bond1[ibond] = rev_ind_m[iatom[3*i+1]];
596 ind_bond2[ibond] = rev_ind_m[iatom[3*i+2]];
602 fprintf(stderr, "Using %d bonds for bond angle matrix\n", ibond);
605 gmx_fatal(FARGS, "0 bonds found");
609 /* start looping over frames: */
616 gmx_rmpbc(gpbc, natoms, box, x);
621 reset_x(ifit, ind_fit, natoms, NULL, x, w_rls);
623 if (ewhat == ewRhoSc)
625 norm_princ(&top.atoms, ifit, ind_fit, natoms, x);
630 /*do the least squares fit to original structure*/
631 do_fit(natoms, w_rls, xp, x);
634 if (teller % freq == 0)
636 /* keep frame for matrix calculation */
637 if (bMat || bBond || bPrev)
639 if (tel_mat >= NFRAME)
641 srenew(mat_x, tel_mat+1);
643 snew(mat_x[tel_mat], n_ind_m);
644 for (i = 0; i < n_ind_m; i++)
646 copy_rvec(x[ind_m[i]], mat_x[tel_mat][i]);
652 /*calculate energy of root_least_squares*/
660 for (i = 0; i < n_ind_m; i++)
662 copy_rvec(mat_x[j][i], xp[ind_m[i]]);
666 reset_x(ifit, ind_fit, natoms, NULL, xp, w_rls);
670 do_fit(natoms, w_rls, x, xp);
673 for (j = 0; (j < nrms); j++)
676 calc_similar_ind(ewhat != ewRMSD, irms[j], ind_rms[j], w_rms, x, xp);
680 for (j = 0; (j < irms[0]); j++)
683 calc_similar_ind(ewhat != ewRMSD, 1, &(ind_rms[0][j]), w_rms, x, xp);
691 /*do the least squares fit to mirror of original structure*/
692 do_fit(natoms, w_rls, xm, x);
695 for (j = 0; j < nrms; j++)
698 calc_similar_ind(ewhat != ewRMSD, irms[j], ind_rms[j], w_rms, x, xm);
701 time[teller] = output_env_conv_time(oenv, t);
704 if (teller >= maxframe)
707 srenew(time, maxframe);
708 for (j = 0; (j < nrms); j++)
710 srenew(rls[j], maxframe);
714 for (j = 0; (j < nrms); j++)
716 srenew(rlsm[j], maxframe);
721 while (read_next_x(oenv, status, &t, x, box));
726 snew(time2, maxframe2);
728 fprintf(stderr, "\nWill read second trajectory file\n");
729 snew(mat_x2, NFRAME);
731 read_first_x(oenv, &status, opt2fn("-f2", NFILE, fnm), &t, &x, box);
732 if (natoms_trx2 != natoms_trx)
735 "Second trajectory (%d atoms) does not match the first one"
736 " (%d atoms)", natoms_trx2, natoms_trx);
744 gmx_rmpbc(gpbc, natoms, box, x);
749 reset_x(ifit, ind_fit, natoms, NULL, x, w_rls);
751 if (ewhat == ewRhoSc)
753 norm_princ(&top.atoms, ifit, ind_fit, natoms, x);
758 /*do the least squares fit to original structure*/
759 do_fit(natoms, w_rls, xp, x);
762 if (teller2 % freq2 == 0)
764 /* keep frame for matrix calculation */
767 if (tel_mat2 >= NFRAME)
769 srenew(mat_x2, tel_mat2+1);
771 snew(mat_x2[tel_mat2], n_ind_m);
772 for (i = 0; i < n_ind_m; i++)
774 copy_rvec(x[ind_m[i]], mat_x2[tel_mat2][i]);
780 time2[teller2] = output_env_conv_time(oenv, t);
783 if (teller2 >= maxframe2)
786 srenew(time2, maxframe2);
789 while (read_next_x(oenv, status, &t, x, box));
799 gmx_rmpbc_done(gpbc);
803 /* calculate RMS matrix */
804 fprintf(stderr, "\n");
807 fprintf(stderr, "Building %s matrix, %dx%d elements\n",
808 whatname[ewhat], tel_mat, tel_mat2);
809 snew(rmsd_mat, tel_mat);
813 fprintf(stderr, "Building bond angle matrix, %dx%d elements\n",
815 snew(bond_mat, tel_mat);
818 snew(axis2, tel_mat2);
831 for (j = 0; j < tel_mat2; j++)
833 axis2[j] = time2[freq2*j];
839 delta_scalex = 8.0/log(2.0);
840 delta_xsize = (int)(log(tel_mat/2)*delta_scalex+0.5)+1;
844 delta_xsize = tel_mat/2;
846 delta_scaley = 1.0/delta_maxy;
847 snew(delta, delta_xsize);
848 for (j = 0; j < delta_xsize; j++)
850 snew(delta[j], del_lev+1);
854 snew(rmsdav_mat, tel_mat);
855 for (j = 0; j < tel_mat; j++)
857 snew(rmsdav_mat[j], tel_mat);
864 snew(mat_x2_j, natoms);
866 for (i = 0; i < tel_mat; i++)
868 axis[i] = time[freq*i];
869 fprintf(stderr, "\r element %5d; time %5.2f ", i, axis[i]);
872 snew(rmsd_mat[i], tel_mat2);
876 snew(bond_mat[i], tel_mat2);
878 for (j = 0; j < tel_mat2; j++)
882 for (k = 0; k < n_ind_m; k++)
884 copy_rvec(mat_x2[j][k], mat_x2_j[k]);
886 do_fit(n_ind_m, w_rls_m, mat_x[i], mat_x2_j);
890 mat_x2_j = mat_x2[j];
894 if (bFile2 || (i < j))
897 calc_similar_ind(ewhat != ewRMSD, irms[0], ind_rms_m,
898 w_rms_m, mat_x[i], mat_x2_j);
899 if (rmsd_mat[i][j] > rmsd_max)
901 rmsd_max = rmsd_mat[i][j];
903 if (rmsd_mat[i][j] < rmsd_min)
905 rmsd_min = rmsd_mat[i][j];
907 rmsd_avg += rmsd_mat[i][j];
911 rmsd_mat[i][j] = rmsd_mat[j][i];
916 if (bFile2 || (i <= j))
919 for (m = 0; m < ibond; m++)
921 rvec_sub(mat_x[i][ind_bond1[m]], mat_x[i][ind_bond2[m]], vec1);
922 rvec_sub(mat_x2_j[ind_bond1[m]], mat_x2_j[ind_bond2[m]], vec2);
923 ang += acos(cos_angle(vec1, vec2));
925 bond_mat[i][j] = ang*180.0/(M_PI*ibond);
926 if (bond_mat[i][j] > bond_max)
928 bond_max = bond_mat[i][j];
930 if (bond_mat[i][j] < bond_min)
932 bond_min = bond_mat[i][j];
937 bond_mat[i][j] = bond_mat[j][i];
944 rmsd_avg /= tel_mat*tel_mat2;
948 rmsd_avg /= tel_mat*(tel_mat - 1)/2;
950 if (bMat && (avl > 0))
955 for (j = 0; j < tel_mat-1; j++)
957 for (i = j+1; i < tel_mat; i++)
961 for (my = -avl; my <= avl; my++)
963 if ((j+my >= 0) && (j+my < tel_mat))
966 for (mx = -avl; mx <= avl; mx++)
968 if ((i+mx >= 0) && (i+mx < tel_mat))
970 weight = (real)(avl+1-max(abs(mx), abs_my));
971 av_tot += weight*rmsd_mat[i+mx][j+my];
972 weight_tot += weight;
977 rmsdav_mat[i][j] = av_tot/weight_tot;
978 rmsdav_mat[j][i] = rmsdav_mat[i][j];
979 if (rmsdav_mat[i][j] > rmsd_max)
981 rmsd_max = rmsdav_mat[i][j];
985 rmsd_mat = rmsdav_mat;
990 fprintf(stderr, "\n%s: Min %f, Max %f, Avg %f\n",
991 whatname[ewhat], rmsd_min, rmsd_max, rmsd_avg);
992 rlo.r = 1; rlo.g = 1; rlo.b = 1;
993 rhi.r = 0; rhi.g = 0; rhi.b = 0;
994 if (rmsd_user_max != -1)
996 rmsd_max = rmsd_user_max;
998 if (rmsd_user_min != -1)
1000 rmsd_min = rmsd_user_min;
1002 if ((rmsd_user_max != -1) || (rmsd_user_min != -1))
1004 fprintf(stderr, "Min and Max value set to resp. %f and %f\n",
1005 rmsd_min, rmsd_max);
1007 sprintf(buf, "%s %s matrix", gn_rms[0], whatname[ewhat]);
1008 write_xpm(opt2FILE("-m", NFILE, fnm, "w"), 0, buf, whatlabel[ewhat],
1009 output_env_get_time_label(oenv), output_env_get_time_label(oenv), tel_mat, tel_mat2,
1010 axis, axis2, rmsd_mat, rmsd_min, rmsd_max, rlo, rhi, &nlevels);
1011 /* Print the distribution of RMSD values */
1012 if (opt2bSet("-dist", NFILE, fnm))
1014 low_rmsd_dist(opt2fn("-dist", NFILE, fnm), rmsd_max, tel_mat, rmsd_mat, oenv);
1019 snew(delta_tot, delta_xsize);
1020 for (j = 0; j < tel_mat-1; j++)
1022 for (i = j+1; i < tel_mat; i++)
1029 mx = (int)(log(mx)*delta_scalex+0.5);
1031 my = (int)(rmsd_mat[i][j]*delta_scaley*del_lev+0.5);
1032 delta_tot[mx] += 1.0;
1033 if ((rmsd_mat[i][j] >= 0) && (rmsd_mat[i][j] <= delta_maxy))
1035 delta[mx][my] += 1.0;
1041 for (i = 0; i < delta_xsize; i++)
1043 if (delta_tot[i] > 0.0)
1045 delta_tot[i] = 1.0/delta_tot[i];
1046 for (j = 0; j <= del_lev; j++)
1048 delta[i][j] *= delta_tot[i];
1049 if (delta[i][j] > delta_max)
1051 delta_max = delta[i][j];
1056 fprintf(stderr, "Maximum in delta matrix: %f\n", delta_max);
1057 snew(del_xaxis, delta_xsize);
1058 snew(del_yaxis, del_lev+1);
1059 for (i = 0; i < delta_xsize; i++)
1061 del_xaxis[i] = axis[i]-axis[0];
1063 for (i = 0; i < del_lev+1; i++)
1065 del_yaxis[i] = delta_maxy*i/del_lev;
1067 sprintf(buf, "%s %s vs. delta t", gn_rms[0], whatname[ewhat]);
1068 fp = gmx_ffopen("delta.xpm", "w");
1069 write_xpm(fp, 0, buf, "density", output_env_get_time_label(oenv), whatlabel[ewhat],
1070 delta_xsize, del_lev+1, del_xaxis, del_yaxis,
1071 delta, 0.0, delta_max, rlo, rhi, &nlevels);
1074 if (opt2bSet("-bin", NFILE, fnm))
1076 /* NB: File must be binary if we use fwrite */
1077 fp = ftp2FILE(efDAT, NFILE, fnm, "wb");
1078 for (i = 0; i < tel_mat; i++)
1080 if (fwrite(rmsd_mat[i], sizeof(**rmsd_mat), tel_mat2, fp) != tel_mat2)
1082 gmx_fatal(FARGS, "Error writing to output file");
1090 fprintf(stderr, "\nMin. angle: %f, Max. angle: %f\n", bond_min, bond_max);
1091 if (bond_user_max != -1)
1093 bond_max = bond_user_max;
1095 if (bond_user_min != -1)
1097 bond_min = bond_user_min;
1099 if ((bond_user_max != -1) || (bond_user_min != -1))
1101 fprintf(stderr, "Bond angle Min and Max set to:\n"
1102 "Min. angle: %f, Max. angle: %f\n", bond_min, bond_max);
1104 rlo.r = 1; rlo.g = 1; rlo.b = 1;
1105 rhi.r = 0; rhi.g = 0; rhi.b = 0;
1106 sprintf(buf, "%s av. bond angle deviation", gn_rms[0]);
1107 write_xpm(opt2FILE("-bm", NFILE, fnm, "w"), 0, buf, "degrees",
1108 output_env_get_time_label(oenv), output_env_get_time_label(oenv), tel_mat, tel_mat2,
1109 axis, axis2, bond_mat, bond_min, bond_max, rlo, rhi, &nlevels);
1113 bAv = opt2bSet("-a", NFILE, fnm);
1115 /* Write the RMSD's to file */
1118 sprintf(buf, "%s", whatxvgname[ewhat]);
1122 sprintf(buf, "%s with frame %g %s ago", whatxvgname[ewhat],
1123 time[prev*freq]-time[0], output_env_get_time_label(oenv));
1125 fp = xvgropen(opt2fn("-o", NFILE, fnm), buf, output_env_get_xvgr_tlabel(oenv),
1126 whatxvglabel[ewhat], oenv);
1127 if (output_env_get_print_xvgr_codes(oenv))
1129 fprintf(fp, "@ subtitle \"%s%s after %s%s%s\"\n",
1130 (nrms == 1) ? "" : "of ", gn_rms[0], fitgraphlabel[efit],
1131 bFit ? " to " : "", bFit ? gn_fit : "");
1135 xvgr_legend(fp, nrms, (const char**)gn_rms, oenv);
1137 for (i = 0; (i < teller); i++)
1139 if (bSplit && i > 0 &&
1140 fabs(time[bPrev ? freq*i : i]/output_env_get_time_factor(oenv)) < 1e-5)
1142 fprintf(fp, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
1144 fprintf(fp, "%12.7f", time[bPrev ? freq*i : i]);
1145 for (j = 0; (j < nrms); j++)
1147 fprintf(fp, " %12.7f", rls[j][i]);
1150 rlstot += rls[j][i];
1159 /* Write the mirror RMSD's to file */
1160 sprintf(buf, "%s with Mirror", whatxvgname[ewhat]);
1161 sprintf(buf2, "Mirror %s", whatxvglabel[ewhat]);
1162 fp = xvgropen(opt2fn("-mir", NFILE, fnm), buf, output_env_get_xvgr_tlabel(oenv),
1166 if (output_env_get_print_xvgr_codes(oenv))
1168 fprintf(fp, "@ subtitle \"of %s after lsq fit to mirror of %s\"\n",
1174 if (output_env_get_print_xvgr_codes(oenv))
1176 fprintf(fp, "@ subtitle \"after lsq fit to mirror %s\"\n", gn_fit);
1178 xvgr_legend(fp, nrms, (const char**)gn_rms, oenv);
1180 for (i = 0; (i < teller); i++)
1182 if (bSplit && i > 0 && fabs(time[i]) < 1e-5)
1184 fprintf(fp, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
1186 fprintf(fp, "%12.7f", time[i]);
1187 for (j = 0; (j < nrms); j++)
1189 fprintf(fp, " %12.7f", rlsm[j][i]);
1198 sprintf(buf, "Average %s", whatxvgname[ewhat]);
1199 sprintf(buf2, "Average %s", whatxvglabel[ewhat]);
1200 fp = xvgropen(opt2fn("-a", NFILE, fnm), buf, "Residue", buf2, oenv);
1201 for (j = 0; (j < nrms); j++)
1203 fprintf(fp, "%10d %10g\n", j, rlstot/teller);
1210 fp = xvgropen("aver.xvg", gn_rms[0], "Residue", whatxvglabel[ewhat], oenv);
1211 for (j = 0; (j < irms[0]); j++)
1213 fprintf(fp, "%10d %10g\n", j, rlsnorm[j]/teller);
1217 do_view(oenv, opt2fn_null("-a", NFILE, fnm), "-graphtype bar");
1218 do_view(oenv, opt2fn("-o", NFILE, fnm), NULL);
1219 do_view(oenv, opt2fn_null("-mir", NFILE, fnm), NULL);
1220 do_view(oenv, opt2fn_null("-m", NFILE, fnm), NULL);
1221 do_view(oenv, opt2fn_null("-bm", NFILE, fnm), NULL);
1222 do_view(oenv, opt2fn_null("-dist", NFILE, fnm), NULL);