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42 #include "gromacs/commandline/pargs.h"
45 #include "gromacs/utility/smalloc.h"
47 #include "gmx_fatal.h"
50 #include "gromacs/fileio/futil.h"
52 #include "gromacs/fileio/pdbio.h"
53 #include "gromacs/fileio/confio.h"
54 #include "gromacs/fileio/tpxio.h"
55 #include "gromacs/fileio/trxio.h"
56 #include "gromacs/fileio/matio.h"
65 #include "gromacs/math/do_fit.h"
67 static void calc_entropy_qh(FILE *fp, int n, real eigval[], real temp, int nskip)
70 double hwkT, w, dS, S = 0;
73 hbar = PLANCK1/(2*M_PI);
74 for (i = 0; (i < n-nskip); i++)
78 lambda = eigval[i]*AMU;
79 w = sqrt(BOLTZMANN*temp/lambda)/NANO;
80 hwkT = (hbar*w)/(BOLTZMANN*temp);
81 dS = (hwkT/(exp(hwkT) - 1) - log(1-exp(-hwkT)));
85 fprintf(debug, "i = %5d w = %10g lam = %10g hwkT = %10g dS = %10g\n",
86 i, w, lambda, hwkT, dS);
91 fprintf(stderr, "eigval[%d] = %g\n", i, eigval[i]);
95 fprintf(fp, "The Entropy due to the Quasi Harmonic approximation is %g J/mol K\n",
99 static void calc_entropy_schlitter(FILE *fp, int n, int nskip,
100 real *eigval, real temp)
106 double hbar, kt, kteh, S;
108 hbar = PLANCK1/(2*M_PI);
110 kteh = kt*exp(2.0)/(hbar*hbar)*AMU*(NANO*NANO);
113 fprintf(debug, "n = %d, nskip = %d kteh = %g\n", n, nskip, kteh);
117 for (i = 0; (i < n-nskip); i++)
119 dd = 1+kteh*eigval[i];
124 fprintf(fp, "The Entropy due to the Schlitter formula is %g J/mol K\n", S);
127 const char *proj_unit;
129 static real tick_spacing(real range, int minticks)
138 sp = 0.2*exp(log(10)*ceil(log(range)/log(10)));
139 while (range/sp < minticks-1)
147 static void write_xvgr_graphs(const char *file, int ngraphs, int nsetspergraph,
148 const char *title, const char *subtitle,
149 const char *xlabel, const char **ylabel,
150 int n, real *x, real **y, real ***sy,
151 real scale_x, gmx_bool bZero, gmx_bool bSplit,
152 const output_env_t oenv)
156 real min, max, xsp, ysp;
158 out = gmx_ffopen(file, "w");
159 if (output_env_get_xvg_format(oenv) == exvgXMGRACE)
161 fprintf(out, "@ autoscale onread none\n");
163 for (g = 0; g < ngraphs; g++)
169 for (i = 0; i < n; i++)
185 for (s = 0; s < nsetspergraph; s++)
187 for (i = 0; i < n; i++)
189 if (sy[g][s][i] < min)
193 if (sy[g][s][i] > max)
206 min = min-0.1*(max-min);
208 max = max+0.1*(max-min);
209 xsp = tick_spacing((x[n-1]-x[0])*scale_x, 4);
210 ysp = tick_spacing(max-min, 3);
211 if (output_env_get_print_xvgr_codes(oenv))
213 fprintf(out, "@ with g%d\n@ g%d on\n", g, g);
216 fprintf(out, "@ title \"%s\"\n", title);
219 fprintf(out, "@ subtitle \"%s\"\n", subtitle);
224 fprintf(out, "@ xaxis label \"%s\"\n", xlabel);
228 fprintf(out, "@ xaxis ticklabel off\n");
232 fprintf(out, "@ world xmin %g\n", x[0]*scale_x);
233 fprintf(out, "@ world xmax %g\n", x[n-1]*scale_x);
234 fprintf(out, "@ world ymin %g\n", min);
235 fprintf(out, "@ world ymax %g\n", max);
237 fprintf(out, "@ view xmin 0.15\n");
238 fprintf(out, "@ view xmax 0.85\n");
239 fprintf(out, "@ view ymin %g\n", 0.15+(ngraphs-1-g)*0.7/ngraphs);
240 fprintf(out, "@ view ymax %g\n", 0.15+(ngraphs-g)*0.7/ngraphs);
241 fprintf(out, "@ yaxis label \"%s\"\n", ylabel[g]);
242 fprintf(out, "@ xaxis tick major %g\n", xsp);
243 fprintf(out, "@ xaxis tick minor %g\n", xsp/2);
244 fprintf(out, "@ xaxis ticklabel start type spec\n");
245 fprintf(out, "@ xaxis ticklabel start %g\n", ceil(min/xsp)*xsp);
246 fprintf(out, "@ yaxis tick major %g\n", ysp);
247 fprintf(out, "@ yaxis tick minor %g\n", ysp/2);
248 fprintf(out, "@ yaxis ticklabel start type spec\n");
249 fprintf(out, "@ yaxis ticklabel start %g\n", ceil(min/ysp)*ysp);
250 if ((min < 0) && (max > 0))
252 fprintf(out, "@ zeroxaxis bar on\n");
253 fprintf(out, "@ zeroxaxis bar linestyle 3\n");
256 for (s = 0; s < nsetspergraph; s++)
258 for (i = 0; i < n; i++)
260 if (bSplit && i > 0 && fabs(x[i]) < 1e-5)
262 if (output_env_get_print_xvgr_codes(oenv))
267 fprintf(out, "%10.4f %10.5f\n",
268 x[i]*scale_x, y ? y[g][i] : sy[g][s][i]);
270 if (output_env_get_print_xvgr_codes(oenv))
280 compare(int natoms, int n1, rvec **eigvec1, int n2, rvec **eigvec2,
281 real *eigval1, int neig1, real *eigval2, int neig2)
285 double sum1, sum2, trace1, trace2, sab, samsb2, tmp, ip;
289 n = min(n, min(neig1, neig2));
290 fprintf(stdout, "Will compare the covariance matrices using %d dimensions\n", n);
293 for (i = 0; i < n; i++)
300 eigval1[i] = sqrt(eigval1[i]);
303 for (i = n; i < neig1; i++)
305 trace1 += eigval1[i];
308 for (i = 0; i < n; i++)
315 eigval2[i] = sqrt(eigval2[i]);
318 for (i = n; i < neig2; i++)
320 trace2 += eigval2[i];
323 fprintf(stdout, "Trace of the two matrices: %g and %g\n", sum1, sum2);
324 if (neig1 != n || neig2 != n)
326 fprintf(stdout, "this is %d%% and %d%% of the total trace\n",
327 (int)(100*sum1/trace1+0.5), (int)(100*sum2/trace2+0.5));
329 fprintf(stdout, "Square root of the traces: %g and %g\n",
330 sqrt(sum1), sqrt(sum2));
333 for (i = 0; i < n; i++)
336 for (j = 0; j < n; j++)
339 for (k = 0; k < natoms; k++)
341 ip += iprod(eigvec1[i][k], eigvec2[j][k]);
343 tmp += eigval2[j]*ip*ip;
345 sab += eigval1[i]*tmp;
348 samsb2 = sum1+sum2-2*sab;
354 fprintf(stdout, "The overlap of the covariance matrices:\n");
355 fprintf(stdout, " normalized: %.3f\n", 1-sqrt(samsb2/(sum1+sum2)));
356 tmp = 1-sab/sqrt(sum1*sum2);
361 fprintf(stdout, " shape: %.3f\n", 1-sqrt(tmp));
365 static void inprod_matrix(const char *matfile, int natoms,
366 int nvec1, int *eignr1, rvec **eigvec1,
367 int nvec2, int *eignr2, rvec **eigvec2,
368 gmx_bool bSelect, int noutvec, int *outvec)
372 int i, x1, y1, x, y, nlevels;
374 real inp, *t_x, *t_y, max;
382 for (y1 = 0; y1 < nx; y1++)
384 if (outvec[y1] < nvec2)
386 t_y[ny] = eignr2[outvec[y1]]+1;
395 for (y = 0; y < ny; y++)
397 t_y[y] = eignr2[y]+1;
401 fprintf(stderr, "Calculating inner-product matrix of %dx%d eigenvectors\n",
407 for (x1 = 0; x1 < nx; x1++)
418 t_x[x1] = eignr1[x]+1;
419 fprintf(stderr, " %d", eignr1[x]+1);
420 for (y1 = 0; y1 < ny; y1++)
425 while (outvec[y1] >= nvec2)
435 for (i = 0; i < natoms; i++)
437 inp += iprod(eigvec1[x][i], eigvec2[y][i]);
439 mat[x1][y1] = fabs(inp);
440 if (mat[x1][y1] > max)
446 fprintf(stderr, "\n");
447 rlo.r = 1; rlo.g = 1; rlo.b = 1;
448 rhi.r = 0; rhi.g = 0; rhi.b = 0;
450 out = gmx_ffopen(matfile, "w");
451 write_xpm(out, 0, "Eigenvector inner-products", "in.prod.", "run 1", "run 2",
452 nx, ny, t_x, t_y, mat, 0.0, max, rlo, rhi, &nlevels);
456 static void overlap(const char *outfile, int natoms,
458 int nvec2, int *eignr2, rvec **eigvec2,
459 int noutvec, int *outvec,
460 const output_env_t oenv)
466 fprintf(stderr, "Calculating overlap between eigenvectors of set 2 with eigenvectors\n");
467 for (i = 0; i < noutvec; i++)
469 fprintf(stderr, "%d ", outvec[i]+1);
471 fprintf(stderr, "\n");
473 out = xvgropen(outfile, "Subspace overlap",
474 "Eigenvectors of trajectory 2", "Overlap", oenv);
475 fprintf(out, "@ subtitle \"using %d eigenvectors of trajectory 1\"\n",
478 for (x = 0; x < nvec2; x++)
480 for (v = 0; v < noutvec; v++)
484 for (i = 0; i < natoms; i++)
486 inp += iprod(eigvec1[vec][i], eigvec2[x][i]);
490 fprintf(out, "%5d %5.3f\n", eignr2[x]+1, overlap/noutvec);
496 static void project(const char *trajfile, t_topology *top, int ePBC, matrix topbox,
497 const char *projfile, const char *twodplotfile,
498 const char *threedplotfile, const char *filterfile, int skip,
499 const char *extremefile, gmx_bool bExtrAll, real extreme,
500 int nextr, t_atoms *atoms, int natoms, atom_id *index,
501 gmx_bool bFit, rvec *xref, int nfit, atom_id *ifit, real *w_rls,
502 real *sqrtm, rvec *xav,
503 int *eignr, rvec **eigvec,
504 int noutvec, int *outvec, gmx_bool bSplit,
505 const output_env_t oenv)
507 FILE *xvgrout = NULL;
508 int nat, i, j, d, v, vec, nfr, nframes = 0, snew_size, frame;
509 t_trxstatus *out = NULL;
511 int noutvec_extr, imin, imax;
516 real t, inp, **inprod = NULL, min = 0, max = 0;
517 char str[STRLEN], str2[STRLEN], **ylabel, *c;
519 gmx_rmpbc_t gpbc = NULL;
525 noutvec_extr = noutvec;
535 snew(inprod, noutvec+1);
539 fprintf(stderr, "Writing a filtered trajectory to %s using eigenvectors\n",
541 for (i = 0; i < noutvec; i++)
543 fprintf(stderr, "%d ", outvec[i]+1);
545 fprintf(stderr, "\n");
546 out = open_trx(filterfile, "w");
551 nat = read_first_x(oenv, &status, trajfile, &t, &xread, box);
554 gmx_fatal(FARGS, "the number of atoms in your trajectory (%d) is larger than the number of atoms in your structure file (%d)", nat, atoms->nr);
560 gpbc = gmx_rmpbc_init(&top->idef, ePBC, nat);
563 for (i = 0; i < nat; i++)
573 gmx_rmpbc(gpbc, nat, box, xread);
575 if (nframes >= snew_size)
578 for (i = 0; i < noutvec+1; i++)
580 srenew(inprod[i], snew_size);
583 inprod[noutvec][nframes] = t;
584 /* calculate x: a fitted struture of the selected atoms */
587 reset_x(nfit, ifit, nat, NULL, xread, w_rls);
588 do_fit(nat, w_rls, xref, xread);
590 for (i = 0; i < natoms; i++)
592 copy_rvec(xread[index[i]], x[i]);
595 for (v = 0; v < noutvec; v++)
598 /* calculate (mass-weighted) projection */
600 for (i = 0; i < natoms; i++)
602 inp += (eigvec[vec][i][0]*(x[i][0]-xav[i][0])+
603 eigvec[vec][i][1]*(x[i][1]-xav[i][1])+
604 eigvec[vec][i][2]*(x[i][2]-xav[i][2]))*sqrtm[i];
606 inprod[v][nframes] = inp;
610 for (i = 0; i < natoms; i++)
612 for (d = 0; d < DIM; d++)
614 /* misuse xread for output */
615 xread[index[i]][d] = xav[i][d];
616 for (v = 0; v < noutvec; v++)
618 xread[index[i]][d] +=
619 inprod[v][nframes]*eigvec[outvec[v]][i][d]/sqrtm[i];
623 write_trx(out, natoms, index, atoms, 0, t, box, xread, NULL, NULL);
629 while (read_next_x(oenv, status, &t, xread, box));
639 snew(xread, atoms->nr);
644 gmx_rmpbc_done(gpbc);
650 snew(ylabel, noutvec);
651 for (v = 0; v < noutvec; v++)
653 sprintf(str, "vec %d", eignr[outvec[v]]+1);
654 ylabel[v] = strdup(str);
656 sprintf(str, "projection on eigenvectors (%s)", proj_unit);
657 write_xvgr_graphs(projfile, noutvec, 1, str, NULL, output_env_get_xvgr_tlabel(oenv),
658 (const char **)ylabel,
659 nframes, inprod[noutvec], inprod, NULL,
660 output_env_get_time_factor(oenv), FALSE, bSplit, oenv);
665 sprintf(str, "projection on eigenvector %d (%s)",
666 eignr[outvec[0]]+1, proj_unit);
667 sprintf(str2, "projection on eigenvector %d (%s)",
668 eignr[outvec[noutvec-1]]+1, proj_unit);
669 xvgrout = xvgropen(twodplotfile, "2D projection of trajectory", str, str2,
671 for (i = 0; i < nframes; i++)
673 if (bSplit && i > 0 && fabs(inprod[noutvec][i]) < 1e-5)
675 fprintf(xvgrout, "&\n");
677 fprintf(xvgrout, "%10.5f %10.5f\n", inprod[0][i], inprod[noutvec-1][i]);
679 gmx_ffclose(xvgrout);
694 gmx_fatal(FARGS, "You have selected less than 3 eigenvectors");
698 bPDB = fn2ftp(threedplotfile) == efPDB;
700 box[XX][XX] = box[YY][YY] = box[ZZ][ZZ] = 1;
702 b4D = bPDB && (noutvec >= 4);
705 fprintf(stderr, "You have selected four or more eigenvectors:\n"
706 "fourth eigenvector will be plotted "
707 "in bfactor field of pdb file\n");
708 sprintf(str, "4D proj. of traj. on eigenv. %d, %d, %d and %d",
709 eignr[outvec[0]]+1, eignr[outvec[1]]+1,
710 eignr[outvec[2]]+1, eignr[outvec[3]]+1);
714 sprintf(str, "3D proj. of traj. on eigenv. %d, %d and %d",
715 eignr[outvec[0]]+1, eignr[outvec[1]]+1, eignr[outvec[2]]+1);
717 init_t_atoms(&atoms, nframes, FALSE);
721 resnm = strdup("PRJ");
725 fact = 10000.0/nframes;
732 for (i = 0; i < nframes; i++)
734 atoms.atomname[i] = &atnm;
735 atoms.atom[i].resind = i;
736 atoms.resinfo[i].name = &resnm;
737 atoms.resinfo[i].nr = ceil(i*fact);
738 atoms.resinfo[i].ic = ' ';
739 x[i][XX] = inprod[0][i];
740 x[i][YY] = inprod[1][i];
741 x[i][ZZ] = inprod[2][i];
747 if ( ( b4D || bSplit ) && bPDB)
749 out = gmx_ffopen(threedplotfile, "w");
750 fprintf(out, "HEADER %s\n", str);
753 fprintf(out, "REMARK %s\n", "fourth dimension plotted as B-factor");
756 for (i = 0; i < atoms.nr; i++)
758 if (j > 0 && bSplit && fabs(inprod[noutvec][i]) < 1e-5)
760 fprintf(out, "TER\n");
763 gmx_fprintf_pdb_atomline(out, epdbATOM, i+1, "C", ' ', "PRJ", ' ', j+1, ' ',
764 10*x[i][XX], 10*x[i][YY], 10*x[i][ZZ], 1.0, 10*b[i], "");
767 fprintf(out, "CONECT%5d%5d\n", i, i+1);
771 fprintf(out, "TER\n");
776 write_sto_conf(threedplotfile, str, &atoms, x, NULL, ePBC, box);
778 free_t_atoms(&atoms, FALSE);
783 snew(pmin, noutvec_extr);
784 snew(pmax, noutvec_extr);
787 fprintf(stderr, "%11s %17s %17s\n", "eigenvector", "Minimum", "Maximum");
789 "%11s %10s %10s %10s %10s\n", "", "value", "frame", "value", "frame");
792 for (v = 0; v < noutvec_extr; v++)
794 for (i = 0; i < nframes; i++)
796 if (inprod[v][i] < inprod[v][imin])
800 if (inprod[v][i] > inprod[v][imax])
805 pmin[v] = inprod[v][imin];
806 pmax[v] = inprod[v][imax];
807 fprintf(stderr, "%7d %10.6f %10d %10.6f %10d\n",
809 pmin[v], imin, pmax[v], imax);
817 /* build format string for filename: */
818 strcpy(str, extremefile); /* copy filename */
819 c = strrchr(str, '.'); /* find where extention begins */
820 strcpy(str2, c); /* get extention */
821 sprintf(c, "%%d%s", str2); /* append '%s' and extention to filename */
822 for (v = 0; v < noutvec_extr; v++)
824 /* make filename using format string */
825 if (noutvec_extr == 1)
827 strcpy(str2, extremefile);
831 sprintf(str2, str, eignr[outvec[v]]+1);
833 fprintf(stderr, "Writing %d frames along eigenvector %d to %s\n",
834 nextr, outvec[v]+1, str2);
835 out = open_trx(str2, "w");
836 for (frame = 0; frame < nextr; frame++)
838 if ((extreme == 0) && (nextr <= 3))
840 for (i = 0; i < natoms; i++)
842 atoms->resinfo[atoms->atom[index[i]].resind].chainid = 'A' + frame;
845 for (i = 0; i < natoms; i++)
847 for (d = 0; d < DIM; d++)
850 (xav[i][d] + (pmin[v]*(nextr-frame-1)+pmax[v]*frame)/(nextr-1)
851 *eigvec[outvec[v]][i][d]/sqrtm[i]);
854 write_trx(out, natoms, index, atoms, 0, frame, topbox, xread, NULL, NULL);
861 fprintf(stderr, "\n");
864 static void components(const char *outfile, int natoms,
865 int *eignr, rvec **eigvec,
866 int noutvec, int *outvec,
867 const output_env_t oenv)
871 char str[STRLEN], **ylabel;
873 fprintf(stderr, "Writing eigenvector components to %s\n", outfile);
875 snew(ylabel, noutvec);
878 for (i = 0; i < natoms; i++)
882 for (g = 0; g < noutvec; g++)
885 sprintf(str, "vec %d", eignr[v]+1);
886 ylabel[g] = strdup(str);
888 for (s = 0; s < 4; s++)
890 snew(y[g][s], natoms);
892 for (i = 0; i < natoms; i++)
894 y[g][0][i] = norm(eigvec[v][i]);
895 for (s = 0; s < 3; s++)
897 y[g][s+1][i] = eigvec[v][i][s];
901 write_xvgr_graphs(outfile, noutvec, 4, "Eigenvector components",
902 "black: total, red: x, green: y, blue: z",
903 "Atom number", (const char **)ylabel,
904 natoms, x, NULL, y, 1, FALSE, FALSE, oenv);
905 fprintf(stderr, "\n");
908 static void rmsf(const char *outfile, int natoms, real *sqrtm,
909 int *eignr, rvec **eigvec,
910 int noutvec, int *outvec,
911 real *eigval, int neig,
912 const output_env_t oenv)
916 char str[STRLEN], **ylabel;
918 for (i = 0; i < neig; i++)
926 fprintf(stderr, "Writing rmsf to %s\n", outfile);
928 snew(ylabel, noutvec);
931 for (i = 0; i < natoms; i++)
935 for (g = 0; g < noutvec; g++)
938 if (eignr[v] >= neig)
940 gmx_fatal(FARGS, "Selected vector %d is larger than the number of eigenvalues (%d)", eignr[v]+1, neig);
942 sprintf(str, "vec %d", eignr[v]+1);
943 ylabel[g] = strdup(str);
945 for (i = 0; i < natoms; i++)
947 y[g][i] = sqrt(eigval[eignr[v]]*norm2(eigvec[v][i]))/sqrtm[i];
950 write_xvgr_graphs(outfile, noutvec, 1, "RMS fluctuation (nm) ", NULL,
951 "Atom number", (const char **)ylabel,
952 natoms, x, y, NULL, 1, TRUE, FALSE, oenv);
953 fprintf(stderr, "\n");
956 int gmx_anaeig(int argc, char *argv[])
958 static const char *desc[] = {
959 "[THISMODULE] analyzes eigenvectors. The eigenvectors can be of a",
960 "covariance matrix ([gmx-covar]) or of a Normal Modes analysis",
961 "([gmx-nmeig]).[PAR]",
963 "When a trajectory is projected on eigenvectors, all structures are",
964 "fitted to the structure in the eigenvector file, if present, otherwise",
965 "to the structure in the structure file. When no run input file is",
966 "supplied, periodicity will not be taken into account. Most analyses",
967 "are performed on eigenvectors [TT]-first[tt] to [TT]-last[tt], but when",
968 "[TT]-first[tt] is set to -1 you will be prompted for a selection.[PAR]",
970 "[TT]-comp[tt]: plot the vector components per atom of eigenvectors",
971 "[TT]-first[tt] to [TT]-last[tt].[PAR]",
973 "[TT]-rmsf[tt]: plot the RMS fluctuation per atom of eigenvectors",
974 "[TT]-first[tt] to [TT]-last[tt] (requires [TT]-eig[tt]).[PAR]",
976 "[TT]-proj[tt]: calculate projections of a trajectory on eigenvectors",
977 "[TT]-first[tt] to [TT]-last[tt].",
978 "The projections of a trajectory on the eigenvectors of its",
979 "covariance matrix are called principal components (pc's).",
980 "It is often useful to check the cosine content of the pc's,",
981 "since the pc's of random diffusion are cosines with the number",
982 "of periods equal to half the pc index.",
983 "The cosine content of the pc's can be calculated with the program",
984 "[gmx-analyze].[PAR]",
986 "[TT]-2d[tt]: calculate a 2d projection of a trajectory on eigenvectors",
987 "[TT]-first[tt] and [TT]-last[tt].[PAR]",
989 "[TT]-3d[tt]: calculate a 3d projection of a trajectory on the first",
990 "three selected eigenvectors.[PAR]",
992 "[TT]-filt[tt]: filter the trajectory to show only the motion along",
993 "eigenvectors [TT]-first[tt] to [TT]-last[tt].[PAR]",
995 "[TT]-extr[tt]: calculate the two extreme projections along a trajectory",
996 "on the average structure and interpolate [TT]-nframes[tt] frames",
997 "between them, or set your own extremes with [TT]-max[tt]. The",
998 "eigenvector [TT]-first[tt] will be written unless [TT]-first[tt] and",
999 "[TT]-last[tt] have been set explicitly, in which case all eigenvectors",
1000 "will be written to separate files. Chain identifiers will be added",
1001 "when writing a [TT].pdb[tt] file with two or three structures (you",
1002 "can use [TT]rasmol -nmrpdb[tt] to view such a [TT].pdb[tt] file).[PAR]",
1004 " Overlap calculations between covariance analysis:[BR]",
1005 " [BB]Note:[bb] the analysis should use the same fitting structure[PAR]",
1007 "[TT]-over[tt]: calculate the subspace overlap of the eigenvectors in",
1008 "file [TT]-v2[tt] with eigenvectors [TT]-first[tt] to [TT]-last[tt]",
1009 "in file [TT]-v[tt].[PAR]",
1011 "[TT]-inpr[tt]: calculate a matrix of inner-products between",
1012 "eigenvectors in files [TT]-v[tt] and [TT]-v2[tt]. All eigenvectors",
1013 "of both files will be used unless [TT]-first[tt] and [TT]-last[tt]",
1014 "have been set explicitly.[PAR]",
1016 "When [TT]-v[tt], [TT]-eig[tt], [TT]-v2[tt] and [TT]-eig2[tt] are given,",
1017 "a single number for the overlap between the covariance matrices is",
1018 "generated. The formulas are:[BR]",
1019 " difference = sqrt(tr((sqrt(M1) - sqrt(M2))^2))[BR]",
1020 "normalized overlap = 1 - difference/sqrt(tr(M1) + tr(M2))[BR]",
1021 " shape overlap = 1 - sqrt(tr((sqrt(M1/tr(M1)) - sqrt(M2/tr(M2)))^2))[BR]",
1022 "where M1 and M2 are the two covariance matrices and tr is the trace",
1023 "of a matrix. The numbers are proportional to the overlap of the square",
1024 "root of the fluctuations. The normalized overlap is the most useful",
1025 "number, it is 1 for identical matrices and 0 when the sampled",
1026 "subspaces are orthogonal.[PAR]",
1027 "When the [TT]-entropy[tt] flag is given an entropy estimate will be",
1028 "computed based on the Quasiharmonic approach and based on",
1029 "Schlitter's formula."
1031 static int first = 1, last = -1, skip = 1, nextr = 2, nskip = 6;
1032 static real max = 0.0, temp = 298.15;
1033 static gmx_bool bSplit = FALSE, bEntropy = FALSE;
1035 { "-first", FALSE, etINT, {&first},
1036 "First eigenvector for analysis (-1 is select)" },
1037 { "-last", FALSE, etINT, {&last},
1038 "Last eigenvector for analysis (-1 is till the last)" },
1039 { "-skip", FALSE, etINT, {&skip},
1040 "Only analyse every nr-th frame" },
1041 { "-max", FALSE, etREAL, {&max},
1042 "Maximum for projection of the eigenvector on the average structure, "
1043 "max=0 gives the extremes" },
1044 { "-nframes", FALSE, etINT, {&nextr},
1045 "Number of frames for the extremes output" },
1046 { "-split", FALSE, etBOOL, {&bSplit},
1047 "Split eigenvector projections where time is zero" },
1048 { "-entropy", FALSE, etBOOL, {&bEntropy},
1049 "Compute entropy according to the Quasiharmonic formula or Schlitter's method." },
1050 { "-temp", FALSE, etREAL, {&temp},
1051 "Temperature for entropy calculations" },
1052 { "-nevskip", FALSE, etINT, {&nskip},
1053 "Number of eigenvalues to skip when computing the entropy due to the quasi harmonic approximation. When you do a rotational and/or translational fit prior to the covariance analysis, you get 3 or 6 eigenvalues that are very close to zero, and which should not be taken into account when computing the entropy." }
1055 #define NPA asize(pa)
1061 t_atoms *atoms = NULL;
1062 rvec *xtop, *xref1, *xref2, *xrefp = NULL;
1063 gmx_bool bDMR1, bDMA1, bDMR2, bDMA2;
1064 int nvec1, nvec2, *eignr1 = NULL, *eignr2 = NULL;
1065 rvec *x, *xread, *xav1, *xav2, **eigvec1 = NULL, **eigvec2 = NULL;
1067 real xid, totmass, *sqrtm, *w_rls, t, lambda;
1070 const char *indexfile;
1073 int nout, *iout, noutvec, *outvec, nfit;
1074 atom_id *index, *ifit;
1075 const char *VecFile, *Vec2File, *topfile;
1076 const char *EigFile, *Eig2File;
1077 const char *CompFile, *RmsfFile, *ProjOnVecFile;
1078 const char *TwoDPlotFile, *ThreeDPlotFile;
1079 const char *FilterFile, *ExtremeFile;
1080 const char *OverlapFile, *InpMatFile;
1081 gmx_bool bFit1, bFit2, bM, bIndex, bTPS, bTop, bVec2, bProj;
1082 gmx_bool bFirstToLast, bFirstLastSet, bTraj, bCompare, bPDB3D;
1083 real *eigval1 = NULL, *eigval2 = NULL;
1090 { efTRN, "-v", "eigenvec", ffREAD },
1091 { efTRN, "-v2", "eigenvec2", ffOPTRD },
1092 { efTRX, "-f", NULL, ffOPTRD },
1093 { efTPS, NULL, NULL, ffOPTRD },
1094 { efNDX, NULL, NULL, ffOPTRD },
1095 { efXVG, "-eig", "eigenval", ffOPTRD },
1096 { efXVG, "-eig2", "eigenval2", ffOPTRD },
1097 { efXVG, "-comp", "eigcomp", ffOPTWR },
1098 { efXVG, "-rmsf", "eigrmsf", ffOPTWR },
1099 { efXVG, "-proj", "proj", ffOPTWR },
1100 { efXVG, "-2d", "2dproj", ffOPTWR },
1101 { efSTO, "-3d", "3dproj.pdb", ffOPTWR },
1102 { efTRX, "-filt", "filtered", ffOPTWR },
1103 { efTRX, "-extr", "extreme.pdb", ffOPTWR },
1104 { efXVG, "-over", "overlap", ffOPTWR },
1105 { efXPM, "-inpr", "inprod", ffOPTWR }
1107 #define NFILE asize(fnm)
1109 if (!parse_common_args(&argc, argv,
1110 PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW | PCA_BE_NICE,
1111 NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
1116 indexfile = ftp2fn_null(efNDX, NFILE, fnm);
1118 VecFile = opt2fn("-v", NFILE, fnm);
1119 Vec2File = opt2fn_null("-v2", NFILE, fnm);
1120 topfile = ftp2fn(efTPS, NFILE, fnm);
1121 EigFile = opt2fn_null("-eig", NFILE, fnm);
1122 Eig2File = opt2fn_null("-eig2", NFILE, fnm);
1123 CompFile = opt2fn_null("-comp", NFILE, fnm);
1124 RmsfFile = opt2fn_null("-rmsf", NFILE, fnm);
1125 ProjOnVecFile = opt2fn_null("-proj", NFILE, fnm);
1126 TwoDPlotFile = opt2fn_null("-2d", NFILE, fnm);
1127 ThreeDPlotFile = opt2fn_null("-3d", NFILE, fnm);
1128 FilterFile = opt2fn_null("-filt", NFILE, fnm);
1129 ExtremeFile = opt2fn_null("-extr", NFILE, fnm);
1130 OverlapFile = opt2fn_null("-over", NFILE, fnm);
1131 InpMatFile = ftp2fn_null(efXPM, NFILE, fnm);
1133 bTop = fn2bTPX(topfile);
1134 bProj = ProjOnVecFile || TwoDPlotFile || ThreeDPlotFile
1135 || FilterFile || ExtremeFile;
1137 opt2parg_bSet("-first", NPA, pa) && opt2parg_bSet("-last", NPA, pa);
1138 bFirstToLast = CompFile || RmsfFile || ProjOnVecFile || FilterFile ||
1139 OverlapFile || ((ExtremeFile || InpMatFile) && bFirstLastSet);
1140 bVec2 = Vec2File || OverlapFile || InpMatFile;
1141 bM = RmsfFile || bProj;
1142 bTraj = ProjOnVecFile || FilterFile || (ExtremeFile && (max == 0))
1143 || TwoDPlotFile || ThreeDPlotFile;
1144 bIndex = bM || bProj;
1145 bTPS = ftp2bSet(efTPS, NFILE, fnm) || bM || bTraj ||
1146 FilterFile || (bIndex && indexfile);
1147 bCompare = Vec2File || Eig2File;
1148 bPDB3D = fn2ftp(ThreeDPlotFile) == efPDB;
1150 read_eigenvectors(VecFile, &natoms, &bFit1,
1151 &xref1, &bDMR1, &xav1, &bDMA1,
1152 &nvec1, &eignr1, &eigvec1, &eigval1);
1155 /* Overwrite eigenvalues from separate files if the user provides them */
1156 if (EigFile != NULL)
1158 int neig_tmp = read_xvg(EigFile, &xvgdata, &i);
1159 if (neig_tmp != neig1)
1161 fprintf(stderr, "Warning: number of eigenvalues in xvg file (%d) does not mtch trr file (%d)\n", neig1, natoms);
1164 srenew(eigval1, neig1);
1165 for (j = 0; j < neig1; j++)
1167 real tmp = eigval1[j];
1168 eigval1[j] = xvgdata[1][j];
1169 if (debug && (eigval1[j] != tmp))
1171 fprintf(debug, "Replacing eigenvalue %d. From trr: %10g, from xvg: %10g\n",
1172 j, tmp, eigval1[j]);
1175 for (j = 0; j < i; j++)
1180 fprintf(stderr, "Read %d eigenvalues from %s\n", neig1, EigFile);
1187 gmx_fatal(FARGS, "Can not calculate entropies from mass-weighted eigenvalues, redo the analysis without mass-weighting");
1189 calc_entropy_qh(stdout, neig1, eigval1, temp, nskip);
1190 calc_entropy_schlitter(stdout, neig1, nskip, eigval1, temp);
1197 gmx_fatal(FARGS, "Need a second eigenvector file to do this analysis.");
1199 read_eigenvectors(Vec2File, &neig2, &bFit2,
1200 &xref2, &bDMR2, &xav2, &bDMA2, &nvec2, &eignr2, &eigvec2, &eigval2);
1205 gmx_fatal(FARGS, "Dimensions in the eigenvector files don't match");
1209 if (Eig2File != NULL)
1211 neig2 = read_xvg(Eig2File, &xvgdata, &i);
1212 srenew(eigval2, neig2);
1213 for (j = 0; j < neig2; j++)
1215 eigval2[j] = xvgdata[1][j];
1217 for (j = 0; j < i; j++)
1222 fprintf(stderr, "Read %d eigenvalues from %s\n", neig2, Eig2File);
1226 if ((!bFit1 || xref1) && !bDMR1 && !bDMA1)
1230 if ((xref1 == NULL) && (bM || bTraj))
1246 bTop = read_tps_conf(ftp2fn(efTPS, NFILE, fnm),
1247 title, &top, &ePBC, &xtop, NULL, topbox, bM);
1249 gpbc = gmx_rmpbc_init(&top.idef, ePBC, atoms->nr);
1250 gmx_rmpbc(gpbc, atoms->nr, topbox, xtop);
1251 /* Fitting is only required for the projection */
1256 printf("\nNote: the structure in %s should be the same\n"
1257 " as the one used for the fit in g_covar\n", topfile);
1259 printf("\nSelect the index group that was used for the least squares fit in g_covar\n");
1260 get_index(atoms, indexfile, 1, &nfit, &ifit, &grpname);
1262 snew(w_rls, atoms->nr);
1263 for (i = 0; (i < nfit); i++)
1267 w_rls[ifit[i]] = atoms->atom[ifit[i]].m;
1271 w_rls[ifit[i]] = 1.0;
1275 snew(xrefp, atoms->nr);
1278 /* Safety check between selected fit-group and reference structure read from the eigenvector file */
1281 gmx_fatal(FARGS, "you selected a group with %d elements instead of %d, your selection does not fit the reference structure in the eigenvector file.", nfit, natoms);
1283 for (i = 0; (i < nfit); i++)
1285 copy_rvec(xref1[i], xrefp[ifit[i]]);
1290 /* The top coordinates are the fitting reference */
1291 for (i = 0; (i < nfit); i++)
1293 copy_rvec(xtop[ifit[i]], xrefp[ifit[i]]);
1295 reset_x(nfit, ifit, atoms->nr, NULL, xrefp, w_rls);
1298 gmx_rmpbc_done(gpbc);
1303 printf("\nSelect an index group of %d elements that corresponds to the eigenvectors\n", natoms);
1304 get_index(atoms, indexfile, 1, &i, &index, &grpname);
1307 gmx_fatal(FARGS, "you selected a group with %d elements instead of %d", i, natoms);
1312 snew(sqrtm, natoms);
1315 proj_unit = "u\\S1/2\\Nnm";
1316 for (i = 0; (i < natoms); i++)
1318 sqrtm[i] = sqrt(atoms->atom[index[i]].m);
1324 for (i = 0; (i < natoms); i++)
1334 for (i = 0; (i < natoms); i++)
1336 for (d = 0; (d < DIM); d++)
1338 t += sqr((xav1[i][d]-xav2[i][d])*sqrtm[i]);
1339 totmass += sqr(sqrtm[i]);
1342 fprintf(stdout, "RMSD (without fit) between the two average structures:"
1343 " %.3f (nm)\n\n", sqrt(t/totmass));
1354 /* make an index from first to last */
1355 nout = last-first+1;
1357 for (i = 0; i < nout; i++)
1359 iout[i] = first-1+i;
1362 else if (ThreeDPlotFile)
1364 /* make an index of first+(0,1,2) and last */
1365 nout = bPDB3D ? 4 : 3;
1366 nout = min(last-first+1, nout);
1374 iout[nout-1] = last-1;
1378 /* make an index of first and last */
1387 printf("Select eigenvectors for output, end your selection with 0\n");
1394 srenew(iout, nout+1);
1395 if (1 != scanf("%d", &iout[nout]))
1397 gmx_fatal(FARGS, "Error reading user input");
1401 while (iout[nout] >= 0);
1405 /* make an index of the eigenvectors which are present */
1408 for (i = 0; i < nout; i++)
1411 while ((j < nvec1) && (eignr1[j] != iout[i]))
1415 if ((j < nvec1) && (eignr1[j] == iout[i]))
1417 outvec[noutvec] = j;
1421 fprintf(stderr, "%d eigenvectors selected for output", noutvec);
1424 fprintf(stderr, ":");
1425 for (j = 0; j < noutvec; j++)
1427 fprintf(stderr, " %d", eignr1[outvec[j]]+1);
1430 fprintf(stderr, "\n");
1434 components(CompFile, natoms, eignr1, eigvec1, noutvec, outvec, oenv);
1439 rmsf(RmsfFile, natoms, sqrtm, eignr1, eigvec1, noutvec, outvec, eigval1,
1445 project(bTraj ? opt2fn("-f", NFILE, fnm) : NULL,
1446 bTop ? &top : NULL, ePBC, topbox,
1447 ProjOnVecFile, TwoDPlotFile, ThreeDPlotFile, FilterFile, skip,
1448 ExtremeFile, bFirstLastSet, max, nextr, atoms, natoms, index,
1449 bFit1, xrefp, nfit, ifit, w_rls,
1450 sqrtm, xav1, eignr1, eigvec1, noutvec, outvec, bSplit,
1456 overlap(OverlapFile, natoms,
1457 eigvec1, nvec2, eignr2, eigvec2, noutvec, outvec, oenv);
1462 inprod_matrix(InpMatFile, natoms,
1463 nvec1, eignr1, eigvec1, nvec2, eignr2, eigvec2,
1464 bFirstLastSet, noutvec, outvec);
1469 compare(natoms, nvec1, eigvec1, nvec2, eigvec2, eigval1, neig1, eigval2, neig2);
1473 if (!CompFile && !bProj && !OverlapFile && !InpMatFile &&
1474 !bCompare && !bEntropy)
1476 fprintf(stderr, "\nIf you want some output,"
1477 " set one (or two or ...) of the output file options\n");
1481 view_all(oenv, NFILE, fnm);