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43 #include "gromacs/commandline/pargs.h"
44 #include "gromacs/fileio/confio.h"
45 #include "gromacs/fileio/matio.h"
46 #include "gromacs/fileio/pdbio.h"
47 #include "gromacs/fileio/tpxio.h"
48 #include "gromacs/fileio/trxio.h"
49 #include "gromacs/fileio/xvgr.h"
50 #include "gromacs/gmxana/eigio.h"
51 #include "gromacs/gmxana/gmx_ana.h"
52 #include "gromacs/legacyheaders/macros.h"
53 #include "gromacs/legacyheaders/txtdump.h"
54 #include "gromacs/legacyheaders/typedefs.h"
55 #include "gromacs/legacyheaders/viewit.h"
56 #include "gromacs/math/do_fit.h"
57 #include "gromacs/math/units.h"
58 #include "gromacs/math/vec.h"
59 #include "gromacs/pbcutil/rmpbc.h"
60 #include "gromacs/topology/index.h"
61 #include "gromacs/utility/fatalerror.h"
62 #include "gromacs/utility/futil.h"
63 #include "gromacs/utility/smalloc.h"
65 static void calc_entropy_qh(FILE *fp, int n, real eigval[], real temp, int nskip)
68 double hwkT, w, dS, S = 0;
71 hbar = PLANCK1/(2*M_PI);
72 for (i = 0; (i < n-nskip); i++)
76 lambda = eigval[i]*AMU;
77 w = sqrt(BOLTZMANN*temp/lambda)/NANO;
78 hwkT = (hbar*w)/(BOLTZMANN*temp);
79 dS = (hwkT/gmx_expm1(hwkT) - gmx_log1p(-exp(-hwkT)));
83 fprintf(debug, "i = %5d w = %10g lam = %10g hwkT = %10g dS = %10g\n",
84 i, w, lambda, hwkT, dS);
89 fprintf(stderr, "eigval[%d] = %g\n", i, eigval[i]);
93 fprintf(fp, "The Entropy due to the Quasi Harmonic approximation is %g J/mol K\n",
97 static void calc_entropy_schlitter(FILE *fp, int n, int nskip,
98 real *eigval, real temp)
104 double hbar, kt, kteh, S;
106 hbar = PLANCK1/(2*M_PI);
108 kteh = kt*exp(2.0)/(hbar*hbar)*AMU*(NANO*NANO);
111 fprintf(debug, "n = %d, nskip = %d kteh = %g\n", n, nskip, kteh);
115 for (i = 0; (i < n-nskip); i++)
117 dd = 1+kteh*eigval[i];
122 fprintf(fp, "The Entropy due to the Schlitter formula is %g J/mol K\n", S);
125 const char *proj_unit;
127 static real tick_spacing(real range, int minticks)
136 sp = 0.2*exp(log(10)*ceil(log(range)/log(10)));
137 while (range/sp < minticks-1)
145 static void write_xvgr_graphs(const char *file, int ngraphs, int nsetspergraph,
146 const char *title, const char *subtitle,
147 const char *xlabel, const char **ylabel,
148 int n, real *x, real **y, real ***sy,
149 real scale_x, gmx_bool bZero, gmx_bool bSplit,
150 const output_env_t oenv)
154 real min, max, xsp, ysp;
156 out = gmx_ffopen(file, "w");
157 if (output_env_get_xvg_format(oenv) == exvgXMGRACE)
159 fprintf(out, "@ autoscale onread none\n");
161 for (g = 0; g < ngraphs; g++)
167 for (i = 0; i < n; i++)
183 for (s = 0; s < nsetspergraph; s++)
185 for (i = 0; i < n; i++)
187 if (sy[g][s][i] < min)
191 if (sy[g][s][i] > max)
204 min = min-0.1*(max-min);
206 max = max+0.1*(max-min);
207 xsp = tick_spacing((x[n-1]-x[0])*scale_x, 4);
208 ysp = tick_spacing(max-min, 3);
209 if (output_env_get_print_xvgr_codes(oenv))
211 fprintf(out, "@ with g%d\n@ g%d on\n", g, g);
214 fprintf(out, "@ title \"%s\"\n", title);
217 fprintf(out, "@ subtitle \"%s\"\n", subtitle);
222 fprintf(out, "@ xaxis label \"%s\"\n", xlabel);
226 fprintf(out, "@ xaxis ticklabel off\n");
230 fprintf(out, "@ world xmin %g\n", x[0]*scale_x);
231 fprintf(out, "@ world xmax %g\n", x[n-1]*scale_x);
232 fprintf(out, "@ world ymin %g\n", min);
233 fprintf(out, "@ world ymax %g\n", max);
235 fprintf(out, "@ view xmin 0.15\n");
236 fprintf(out, "@ view xmax 0.85\n");
237 fprintf(out, "@ view ymin %g\n", 0.15+(ngraphs-1-g)*0.7/ngraphs);
238 fprintf(out, "@ view ymax %g\n", 0.15+(ngraphs-g)*0.7/ngraphs);
239 fprintf(out, "@ yaxis label \"%s\"\n", ylabel[g]);
240 fprintf(out, "@ xaxis tick major %g\n", xsp);
241 fprintf(out, "@ xaxis tick minor %g\n", xsp/2);
242 fprintf(out, "@ xaxis ticklabel start type spec\n");
243 fprintf(out, "@ xaxis ticklabel start %g\n", ceil(min/xsp)*xsp);
244 fprintf(out, "@ yaxis tick major %g\n", ysp);
245 fprintf(out, "@ yaxis tick minor %g\n", ysp/2);
246 fprintf(out, "@ yaxis ticklabel start type spec\n");
247 fprintf(out, "@ yaxis ticklabel start %g\n", ceil(min/ysp)*ysp);
248 if ((min < 0) && (max > 0))
250 fprintf(out, "@ zeroxaxis bar on\n");
251 fprintf(out, "@ zeroxaxis bar linestyle 3\n");
254 for (s = 0; s < nsetspergraph; s++)
256 for (i = 0; i < n; i++)
258 if (bSplit && i > 0 && fabs(x[i]) < 1e-5)
260 fprintf(out, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
262 fprintf(out, "%10.4f %10.5f\n",
263 x[i]*scale_x, y ? y[g][i] : sy[g][s][i]);
265 fprintf(out, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
272 compare(int natoms, int n1, rvec **eigvec1, int n2, rvec **eigvec2,
273 real *eigval1, int neig1, real *eigval2, int neig2)
277 double sum1, sum2, trace1, trace2, sab, samsb2, tmp, ip;
281 n = min(n, min(neig1, neig2));
282 fprintf(stdout, "Will compare the covariance matrices using %d dimensions\n", n);
285 for (i = 0; i < n; i++)
292 eigval1[i] = sqrt(eigval1[i]);
295 for (i = n; i < neig1; i++)
297 trace1 += eigval1[i];
300 for (i = 0; i < n; i++)
307 eigval2[i] = sqrt(eigval2[i]);
310 for (i = n; i < neig2; i++)
312 trace2 += eigval2[i];
315 fprintf(stdout, "Trace of the two matrices: %g and %g\n", sum1, sum2);
316 if (neig1 != n || neig2 != n)
318 fprintf(stdout, "this is %d%% and %d%% of the total trace\n",
319 (int)(100*sum1/trace1+0.5), (int)(100*sum2/trace2+0.5));
321 fprintf(stdout, "Square root of the traces: %g and %g\n",
322 sqrt(sum1), sqrt(sum2));
325 for (i = 0; i < n; i++)
328 for (j = 0; j < n; j++)
331 for (k = 0; k < natoms; k++)
333 ip += iprod(eigvec1[i][k], eigvec2[j][k]);
335 tmp += eigval2[j]*ip*ip;
337 sab += eigval1[i]*tmp;
340 samsb2 = sum1+sum2-2*sab;
346 fprintf(stdout, "The overlap of the covariance matrices:\n");
347 fprintf(stdout, " normalized: %.3f\n", 1-sqrt(samsb2/(sum1+sum2)));
348 tmp = 1-sab/sqrt(sum1*sum2);
353 fprintf(stdout, " shape: %.3f\n", 1-sqrt(tmp));
357 static void inprod_matrix(const char *matfile, int natoms,
358 int nvec1, int *eignr1, rvec **eigvec1,
359 int nvec2, int *eignr2, rvec **eigvec2,
360 gmx_bool bSelect, int noutvec, int *outvec)
364 int i, x1, y1, x, y, nlevels;
366 real inp, *t_x, *t_y, max;
374 for (y1 = 0; y1 < nx; y1++)
376 if (outvec[y1] < nvec2)
378 t_y[ny] = eignr2[outvec[y1]]+1;
387 for (y = 0; y < ny; y++)
389 t_y[y] = eignr2[y]+1;
393 fprintf(stderr, "Calculating inner-product matrix of %dx%d eigenvectors\n",
399 for (x1 = 0; x1 < nx; x1++)
410 t_x[x1] = eignr1[x]+1;
411 fprintf(stderr, " %d", eignr1[x]+1);
412 for (y1 = 0; y1 < ny; y1++)
417 while (outvec[y1] >= nvec2)
427 for (i = 0; i < natoms; i++)
429 inp += iprod(eigvec1[x][i], eigvec2[y][i]);
431 mat[x1][y1] = fabs(inp);
432 if (mat[x1][y1] > max)
438 fprintf(stderr, "\n");
439 rlo.r = 1; rlo.g = 1; rlo.b = 1;
440 rhi.r = 0; rhi.g = 0; rhi.b = 0;
442 out = gmx_ffopen(matfile, "w");
443 write_xpm(out, 0, "Eigenvector inner-products", "in.prod.", "run 1", "run 2",
444 nx, ny, t_x, t_y, mat, 0.0, max, rlo, rhi, &nlevels);
448 static void overlap(const char *outfile, int natoms,
450 int nvec2, int *eignr2, rvec **eigvec2,
451 int noutvec, int *outvec,
452 const output_env_t oenv)
458 fprintf(stderr, "Calculating overlap between eigenvectors of set 2 with eigenvectors\n");
459 for (i = 0; i < noutvec; i++)
461 fprintf(stderr, "%d ", outvec[i]+1);
463 fprintf(stderr, "\n");
465 out = xvgropen(outfile, "Subspace overlap",
466 "Eigenvectors of trajectory 2", "Overlap", oenv);
467 if (output_env_get_print_xvgr_codes(oenv))
469 fprintf(out, "@ subtitle \"using %d eigenvectors of trajectory 1\"\n", noutvec);
472 for (x = 0; x < nvec2; x++)
474 for (v = 0; v < noutvec; v++)
478 for (i = 0; i < natoms; i++)
480 inp += iprod(eigvec1[vec][i], eigvec2[x][i]);
484 fprintf(out, "%5d %5.3f\n", eignr2[x]+1, overlap/noutvec);
490 static void project(const char *trajfile, t_topology *top, int ePBC, matrix topbox,
491 const char *projfile, const char *twodplotfile,
492 const char *threedplotfile, const char *filterfile, int skip,
493 const char *extremefile, gmx_bool bExtrAll, real extreme,
494 int nextr, t_atoms *atoms, int natoms, atom_id *index,
495 gmx_bool bFit, rvec *xref, int nfit, atom_id *ifit, real *w_rls,
496 real *sqrtm, rvec *xav,
497 int *eignr, rvec **eigvec,
498 int noutvec, int *outvec, gmx_bool bSplit,
499 const output_env_t oenv)
501 FILE *xvgrout = NULL;
502 int nat, i, j, d, v, vec, nfr, nframes = 0, snew_size, frame;
503 t_trxstatus *out = NULL;
505 int noutvec_extr, imin, imax;
510 real t, inp, **inprod = NULL, min = 0, max = 0;
511 char str[STRLEN], str2[STRLEN], **ylabel, *c;
513 gmx_rmpbc_t gpbc = NULL;
519 noutvec_extr = noutvec;
529 snew(inprod, noutvec+1);
533 fprintf(stderr, "Writing a filtered trajectory to %s using eigenvectors\n",
535 for (i = 0; i < noutvec; i++)
537 fprintf(stderr, "%d ", outvec[i]+1);
539 fprintf(stderr, "\n");
540 out = open_trx(filterfile, "w");
545 nat = read_first_x(oenv, &status, trajfile, &t, &xread, box);
548 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);
554 gpbc = gmx_rmpbc_init(&top->idef, ePBC, nat);
557 for (i = 0; i < nat; i++)
567 gmx_rmpbc(gpbc, nat, box, xread);
569 if (nframes >= snew_size)
572 for (i = 0; i < noutvec+1; i++)
574 srenew(inprod[i], snew_size);
577 inprod[noutvec][nframes] = t;
578 /* calculate x: a fitted struture of the selected atoms */
581 reset_x(nfit, ifit, nat, NULL, xread, w_rls);
582 do_fit(nat, w_rls, xref, xread);
584 for (i = 0; i < natoms; i++)
586 copy_rvec(xread[index[i]], x[i]);
589 for (v = 0; v < noutvec; v++)
592 /* calculate (mass-weighted) projection */
594 for (i = 0; i < natoms; i++)
596 inp += (eigvec[vec][i][0]*(x[i][0]-xav[i][0])+
597 eigvec[vec][i][1]*(x[i][1]-xav[i][1])+
598 eigvec[vec][i][2]*(x[i][2]-xav[i][2]))*sqrtm[i];
600 inprod[v][nframes] = inp;
604 for (i = 0; i < natoms; i++)
606 for (d = 0; d < DIM; d++)
608 /* misuse xread for output */
609 xread[index[i]][d] = xav[i][d];
610 for (v = 0; v < noutvec; v++)
612 xread[index[i]][d] +=
613 inprod[v][nframes]*eigvec[outvec[v]][i][d]/sqrtm[i];
617 write_trx(out, natoms, index, atoms, 0, t, box, xread, NULL, NULL);
623 while (read_next_x(oenv, status, &t, xread, box));
633 snew(xread, atoms->nr);
638 gmx_rmpbc_done(gpbc);
644 snew(ylabel, noutvec);
645 for (v = 0; v < noutvec; v++)
647 sprintf(str, "vec %d", eignr[outvec[v]]+1);
648 ylabel[v] = gmx_strdup(str);
650 sprintf(str, "projection on eigenvectors (%s)", proj_unit);
651 write_xvgr_graphs(projfile, noutvec, 1, str, NULL, output_env_get_xvgr_tlabel(oenv),
652 (const char **)ylabel,
653 nframes, inprod[noutvec], inprod, NULL,
654 output_env_get_time_factor(oenv), FALSE, bSplit, oenv);
659 sprintf(str, "projection on eigenvector %d (%s)",
660 eignr[outvec[0]]+1, proj_unit);
661 sprintf(str2, "projection on eigenvector %d (%s)",
662 eignr[outvec[noutvec-1]]+1, proj_unit);
663 xvgrout = xvgropen(twodplotfile, "2D projection of trajectory", str, str2,
665 for (i = 0; i < nframes; i++)
667 if (bSplit && i > 0 && fabs(inprod[noutvec][i]) < 1e-5)
669 fprintf(xvgrout, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
671 fprintf(xvgrout, "%10.5f %10.5f\n", inprod[0][i], inprod[noutvec-1][i]);
688 gmx_fatal(FARGS, "You have selected less than 3 eigenvectors");
692 bPDB = fn2ftp(threedplotfile) == efPDB;
694 box[XX][XX] = box[YY][YY] = box[ZZ][ZZ] = 1;
696 b4D = bPDB && (noutvec >= 4);
699 fprintf(stderr, "You have selected four or more eigenvectors:\n"
700 "fourth eigenvector will be plotted "
701 "in bfactor field of pdb file\n");
702 sprintf(str, "4D proj. of traj. on eigenv. %d, %d, %d and %d",
703 eignr[outvec[0]]+1, eignr[outvec[1]]+1,
704 eignr[outvec[2]]+1, eignr[outvec[3]]+1);
708 sprintf(str, "3D proj. of traj. on eigenv. %d, %d and %d",
709 eignr[outvec[0]]+1, eignr[outvec[1]]+1, eignr[outvec[2]]+1);
711 init_t_atoms(&atoms, nframes, FALSE);
714 atnm = gmx_strdup("C");
715 resnm = gmx_strdup("PRJ");
719 fact = 10000.0/nframes;
726 for (i = 0; i < nframes; i++)
728 atoms.atomname[i] = &atnm;
729 atoms.atom[i].resind = i;
730 atoms.resinfo[i].name = &resnm;
731 atoms.resinfo[i].nr = ceil(i*fact);
732 atoms.resinfo[i].ic = ' ';
733 x[i][XX] = inprod[0][i];
734 x[i][YY] = inprod[1][i];
735 x[i][ZZ] = inprod[2][i];
741 if ( ( b4D || bSplit ) && bPDB)
743 out = gmx_ffopen(threedplotfile, "w");
744 fprintf(out, "HEADER %s\n", str);
747 fprintf(out, "REMARK %s\n", "fourth dimension plotted as B-factor");
750 for (i = 0; i < atoms.nr; i++)
752 if (j > 0 && bSplit && fabs(inprod[noutvec][i]) < 1e-5)
754 fprintf(out, "TER\n");
757 gmx_fprintf_pdb_atomline(out, epdbATOM, i+1, "C", ' ', "PRJ", ' ', j+1, ' ',
758 10*x[i][XX], 10*x[i][YY], 10*x[i][ZZ], 1.0, 10*b[i], "");
761 fprintf(out, "CONECT%5d%5d\n", i, i+1);
765 fprintf(out, "TER\n");
770 write_sto_conf(threedplotfile, str, &atoms, x, NULL, ePBC, box);
772 free_t_atoms(&atoms, FALSE);
777 snew(pmin, noutvec_extr);
778 snew(pmax, noutvec_extr);
781 fprintf(stderr, "%11s %17s %17s\n", "eigenvector", "Minimum", "Maximum");
783 "%11s %10s %10s %10s %10s\n", "", "value", "frame", "value", "frame");
786 for (v = 0; v < noutvec_extr; v++)
788 for (i = 0; i < nframes; i++)
790 if (inprod[v][i] < inprod[v][imin])
794 if (inprod[v][i] > inprod[v][imax])
799 pmin[v] = inprod[v][imin];
800 pmax[v] = inprod[v][imax];
801 fprintf(stderr, "%7d %10.6f %10d %10.6f %10d\n",
803 pmin[v], imin, pmax[v], imax);
811 /* build format string for filename: */
812 strcpy(str, extremefile); /* copy filename */
813 c = strrchr(str, '.'); /* find where extention begins */
814 strcpy(str2, c); /* get extention */
815 sprintf(c, "%%d%s", str2); /* append '%s' and extention to filename */
816 for (v = 0; v < noutvec_extr; v++)
818 /* make filename using format string */
819 if (noutvec_extr == 1)
821 strcpy(str2, extremefile);
825 sprintf(str2, str, eignr[outvec[v]]+1);
827 fprintf(stderr, "Writing %d frames along eigenvector %d to %s\n",
828 nextr, outvec[v]+1, str2);
829 out = open_trx(str2, "w");
830 for (frame = 0; frame < nextr; frame++)
832 if ((extreme == 0) && (nextr <= 3))
834 for (i = 0; i < natoms; i++)
836 atoms->resinfo[atoms->atom[index[i]].resind].chainid = 'A' + frame;
839 for (i = 0; i < natoms; i++)
841 for (d = 0; d < DIM; d++)
844 (xav[i][d] + (pmin[v]*(nextr-frame-1)+pmax[v]*frame)/(nextr-1)
845 *eigvec[outvec[v]][i][d]/sqrtm[i]);
848 write_trx(out, natoms, index, atoms, 0, frame, topbox, xread, NULL, NULL);
855 fprintf(stderr, "\n");
858 static void components(const char *outfile, int natoms,
859 int *eignr, rvec **eigvec,
860 int noutvec, int *outvec,
861 const output_env_t oenv)
865 char str[STRLEN], **ylabel;
867 fprintf(stderr, "Writing eigenvector components to %s\n", outfile);
869 snew(ylabel, noutvec);
872 for (i = 0; i < natoms; i++)
876 for (g = 0; g < noutvec; g++)
879 sprintf(str, "vec %d", eignr[v]+1);
880 ylabel[g] = gmx_strdup(str);
882 for (s = 0; s < 4; s++)
884 snew(y[g][s], natoms);
886 for (i = 0; i < natoms; i++)
888 y[g][0][i] = norm(eigvec[v][i]);
889 for (s = 0; s < 3; s++)
891 y[g][s+1][i] = eigvec[v][i][s];
895 write_xvgr_graphs(outfile, noutvec, 4, "Eigenvector components",
896 "black: total, red: x, green: y, blue: z",
897 "Atom number", (const char **)ylabel,
898 natoms, x, NULL, y, 1, FALSE, FALSE, oenv);
899 fprintf(stderr, "\n");
902 static void rmsf(const char *outfile, int natoms, real *sqrtm,
903 int *eignr, rvec **eigvec,
904 int noutvec, int *outvec,
905 real *eigval, int neig,
906 const output_env_t oenv)
910 char str[STRLEN], **ylabel;
912 for (i = 0; i < neig; i++)
920 fprintf(stderr, "Writing rmsf to %s\n", outfile);
922 snew(ylabel, noutvec);
925 for (i = 0; i < natoms; i++)
929 for (g = 0; g < noutvec; g++)
932 if (eignr[v] >= neig)
934 gmx_fatal(FARGS, "Selected vector %d is larger than the number of eigenvalues (%d)", eignr[v]+1, neig);
936 sprintf(str, "vec %d", eignr[v]+1);
937 ylabel[g] = gmx_strdup(str);
939 for (i = 0; i < natoms; i++)
941 y[g][i] = sqrt(eigval[eignr[v]]*norm2(eigvec[v][i]))/sqrtm[i];
944 write_xvgr_graphs(outfile, noutvec, 1, "RMS fluctuation (nm) ", NULL,
945 "Atom number", (const char **)ylabel,
946 natoms, x, y, NULL, 1, TRUE, FALSE, oenv);
947 fprintf(stderr, "\n");
950 int gmx_anaeig(int argc, char *argv[])
952 static const char *desc[] = {
953 "[THISMODULE] analyzes eigenvectors. The eigenvectors can be of a",
954 "covariance matrix ([gmx-covar]) or of a Normal Modes analysis",
955 "([gmx-nmeig]).[PAR]",
957 "When a trajectory is projected on eigenvectors, all structures are",
958 "fitted to the structure in the eigenvector file, if present, otherwise",
959 "to the structure in the structure file. When no run input file is",
960 "supplied, periodicity will not be taken into account. Most analyses",
961 "are performed on eigenvectors [TT]-first[tt] to [TT]-last[tt], but when",
962 "[TT]-first[tt] is set to -1 you will be prompted for a selection.[PAR]",
964 "[TT]-comp[tt]: plot the vector components per atom of eigenvectors",
965 "[TT]-first[tt] to [TT]-last[tt].[PAR]",
967 "[TT]-rmsf[tt]: plot the RMS fluctuation per atom of eigenvectors",
968 "[TT]-first[tt] to [TT]-last[tt] (requires [TT]-eig[tt]).[PAR]",
970 "[TT]-proj[tt]: calculate projections of a trajectory on eigenvectors",
971 "[TT]-first[tt] to [TT]-last[tt].",
972 "The projections of a trajectory on the eigenvectors of its",
973 "covariance matrix are called principal components (pc's).",
974 "It is often useful to check the cosine content of the pc's,",
975 "since the pc's of random diffusion are cosines with the number",
976 "of periods equal to half the pc index.",
977 "The cosine content of the pc's can be calculated with the program",
978 "[gmx-analyze].[PAR]",
980 "[TT]-2d[tt]: calculate a 2d projection of a trajectory on eigenvectors",
981 "[TT]-first[tt] and [TT]-last[tt].[PAR]",
983 "[TT]-3d[tt]: calculate a 3d projection of a trajectory on the first",
984 "three selected eigenvectors.[PAR]",
986 "[TT]-filt[tt]: filter the trajectory to show only the motion along",
987 "eigenvectors [TT]-first[tt] to [TT]-last[tt].[PAR]",
989 "[TT]-extr[tt]: calculate the two extreme projections along a trajectory",
990 "on the average structure and interpolate [TT]-nframes[tt] frames",
991 "between them, or set your own extremes with [TT]-max[tt]. The",
992 "eigenvector [TT]-first[tt] will be written unless [TT]-first[tt] and",
993 "[TT]-last[tt] have been set explicitly, in which case all eigenvectors",
994 "will be written to separate files. Chain identifiers will be added",
995 "when writing a [REF].pdb[ref] file with two or three structures (you",
996 "can use [TT]rasmol -nmrpdb[tt] to view such a [REF].pdb[ref] file).[PAR]",
998 "Overlap calculations between covariance analysis",
999 "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^",
1001 "[BB]Note:[bb] the analysis should use the same fitting structure",
1003 "[TT]-over[tt]: calculate the subspace overlap of the eigenvectors in",
1004 "file [TT]-v2[tt] with eigenvectors [TT]-first[tt] to [TT]-last[tt]",
1005 "in file [TT]-v[tt].[PAR]",
1007 "[TT]-inpr[tt]: calculate a matrix of inner-products between",
1008 "eigenvectors in files [TT]-v[tt] and [TT]-v2[tt]. All eigenvectors",
1009 "of both files will be used unless [TT]-first[tt] and [TT]-last[tt]",
1010 "have been set explicitly.[PAR]",
1012 "When [TT]-v[tt], [TT]-eig[tt], [TT]-v2[tt] and [TT]-eig2[tt] are given,",
1013 "a single number for the overlap between the covariance matrices is",
1014 "generated. The formulas are::",
1016 " difference = sqrt(tr((sqrt(M1) - sqrt(M2))^2))",
1017 " normalized overlap = 1 - difference/sqrt(tr(M1) + tr(M2))",
1018 " shape overlap = 1 - sqrt(tr((sqrt(M1/tr(M1)) - sqrt(M2/tr(M2)))^2))",
1020 "where M1 and M2 are the two covariance matrices and tr is the trace",
1021 "of a matrix. The numbers are proportional to the overlap of the square",
1022 "root of the fluctuations. The normalized overlap is the most useful",
1023 "number, it is 1 for identical matrices and 0 when the sampled",
1024 "subspaces are orthogonal.[PAR]",
1025 "When the [TT]-entropy[tt] flag is given an entropy estimate will be",
1026 "computed based on the Quasiharmonic approach and based on",
1027 "Schlitter's formula."
1029 static int first = 1, last = -1, skip = 1, nextr = 2, nskip = 6;
1030 static real max = 0.0, temp = 298.15;
1031 static gmx_bool bSplit = FALSE, bEntropy = FALSE;
1033 { "-first", FALSE, etINT, {&first},
1034 "First eigenvector for analysis (-1 is select)" },
1035 { "-last", FALSE, etINT, {&last},
1036 "Last eigenvector for analysis (-1 is till the last)" },
1037 { "-skip", FALSE, etINT, {&skip},
1038 "Only analyse every nr-th frame" },
1039 { "-max", FALSE, etREAL, {&max},
1040 "Maximum for projection of the eigenvector on the average structure, "
1041 "max=0 gives the extremes" },
1042 { "-nframes", FALSE, etINT, {&nextr},
1043 "Number of frames for the extremes output" },
1044 { "-split", FALSE, etBOOL, {&bSplit},
1045 "Split eigenvector projections where time is zero" },
1046 { "-entropy", FALSE, etBOOL, {&bEntropy},
1047 "Compute entropy according to the Quasiharmonic formula or Schlitter's method." },
1048 { "-temp", FALSE, etREAL, {&temp},
1049 "Temperature for entropy calculations" },
1050 { "-nevskip", FALSE, etINT, {&nskip},
1051 "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." }
1053 #define NPA asize(pa)
1059 t_atoms *atoms = NULL;
1060 rvec *xtop, *xref1, *xref2, *xrefp = NULL;
1061 gmx_bool bDMR1, bDMA1, bDMR2, bDMA2;
1062 int nvec1, nvec2, *eignr1 = NULL, *eignr2 = NULL;
1063 rvec *x, *xread, *xav1, *xav2, **eigvec1 = NULL, **eigvec2 = NULL;
1065 real xid, totmass, *sqrtm, *w_rls, t, lambda;
1068 const char *indexfile;
1071 int nout, *iout, noutvec, *outvec, nfit;
1072 atom_id *index, *ifit;
1073 const char *VecFile, *Vec2File, *topfile;
1074 const char *EigFile, *Eig2File;
1075 const char *CompFile, *RmsfFile, *ProjOnVecFile;
1076 const char *TwoDPlotFile, *ThreeDPlotFile;
1077 const char *FilterFile, *ExtremeFile;
1078 const char *OverlapFile, *InpMatFile;
1079 gmx_bool bFit1, bFit2, bM, bIndex, bTPS, bTop, bVec2, bProj;
1080 gmx_bool bFirstToLast, bFirstLastSet, bTraj, bCompare, bPDB3D;
1081 real *eigval1 = NULL, *eigval2 = NULL;
1088 { efTRN, "-v", "eigenvec", ffREAD },
1089 { efTRN, "-v2", "eigenvec2", ffOPTRD },
1090 { efTRX, "-f", NULL, ffOPTRD },
1091 { efTPS, NULL, NULL, ffOPTRD },
1092 { efNDX, NULL, NULL, ffOPTRD },
1093 { efXVG, "-eig", "eigenval", ffOPTRD },
1094 { efXVG, "-eig2", "eigenval2", ffOPTRD },
1095 { efXVG, "-comp", "eigcomp", ffOPTWR },
1096 { efXVG, "-rmsf", "eigrmsf", ffOPTWR },
1097 { efXVG, "-proj", "proj", ffOPTWR },
1098 { efXVG, "-2d", "2dproj", ffOPTWR },
1099 { efSTO, "-3d", "3dproj.pdb", ffOPTWR },
1100 { efTRX, "-filt", "filtered", ffOPTWR },
1101 { efTRX, "-extr", "extreme.pdb", ffOPTWR },
1102 { efXVG, "-over", "overlap", ffOPTWR },
1103 { efXPM, "-inpr", "inprod", ffOPTWR }
1105 #define NFILE asize(fnm)
1107 if (!parse_common_args(&argc, argv,
1108 PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW,
1109 NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
1114 indexfile = ftp2fn_null(efNDX, NFILE, fnm);
1116 VecFile = opt2fn("-v", NFILE, fnm);
1117 Vec2File = opt2fn_null("-v2", NFILE, fnm);
1118 topfile = ftp2fn(efTPS, NFILE, fnm);
1119 EigFile = opt2fn_null("-eig", NFILE, fnm);
1120 Eig2File = opt2fn_null("-eig2", NFILE, fnm);
1121 CompFile = opt2fn_null("-comp", NFILE, fnm);
1122 RmsfFile = opt2fn_null("-rmsf", NFILE, fnm);
1123 ProjOnVecFile = opt2fn_null("-proj", NFILE, fnm);
1124 TwoDPlotFile = opt2fn_null("-2d", NFILE, fnm);
1125 ThreeDPlotFile = opt2fn_null("-3d", NFILE, fnm);
1126 FilterFile = opt2fn_null("-filt", NFILE, fnm);
1127 ExtremeFile = opt2fn_null("-extr", NFILE, fnm);
1128 OverlapFile = opt2fn_null("-over", NFILE, fnm);
1129 InpMatFile = ftp2fn_null(efXPM, NFILE, fnm);
1131 bTop = fn2bTPX(topfile);
1132 bProj = ProjOnVecFile || TwoDPlotFile || ThreeDPlotFile
1133 || FilterFile || ExtremeFile;
1135 opt2parg_bSet("-first", NPA, pa) && opt2parg_bSet("-last", NPA, pa);
1136 bFirstToLast = CompFile || RmsfFile || ProjOnVecFile || FilterFile ||
1137 OverlapFile || ((ExtremeFile || InpMatFile) && bFirstLastSet);
1138 bVec2 = Vec2File || OverlapFile || InpMatFile;
1139 bM = RmsfFile || bProj;
1140 bTraj = ProjOnVecFile || FilterFile || (ExtremeFile && (max == 0))
1141 || TwoDPlotFile || ThreeDPlotFile;
1142 bIndex = bM || bProj;
1143 bTPS = ftp2bSet(efTPS, NFILE, fnm) || bM || bTraj ||
1144 FilterFile || (bIndex && indexfile);
1145 bCompare = Vec2File || Eig2File;
1146 bPDB3D = fn2ftp(ThreeDPlotFile) == efPDB;
1148 read_eigenvectors(VecFile, &natoms, &bFit1,
1149 &xref1, &bDMR1, &xav1, &bDMA1,
1150 &nvec1, &eignr1, &eigvec1, &eigval1);
1153 /* Overwrite eigenvalues from separate files if the user provides them */
1154 if (EigFile != NULL)
1156 int neig_tmp = read_xvg(EigFile, &xvgdata, &i);
1157 if (neig_tmp != neig1)
1159 fprintf(stderr, "Warning: number of eigenvalues in xvg file (%d) does not mtch trr file (%d)\n", neig1, natoms);
1162 srenew(eigval1, neig1);
1163 for (j = 0; j < neig1; j++)
1165 real tmp = eigval1[j];
1166 eigval1[j] = xvgdata[1][j];
1167 if (debug && (eigval1[j] != tmp))
1169 fprintf(debug, "Replacing eigenvalue %d. From trr: %10g, from xvg: %10g\n",
1170 j, tmp, eigval1[j]);
1173 for (j = 0; j < i; j++)
1178 fprintf(stderr, "Read %d eigenvalues from %s\n", neig1, EigFile);
1185 gmx_fatal(FARGS, "Can not calculate entropies from mass-weighted eigenvalues, redo the analysis without mass-weighting");
1187 calc_entropy_qh(stdout, neig1, eigval1, temp, nskip);
1188 calc_entropy_schlitter(stdout, neig1, nskip, eigval1, temp);
1195 gmx_fatal(FARGS, "Need a second eigenvector file to do this analysis.");
1197 read_eigenvectors(Vec2File, &neig2, &bFit2,
1198 &xref2, &bDMR2, &xav2, &bDMA2, &nvec2, &eignr2, &eigvec2, &eigval2);
1203 gmx_fatal(FARGS, "Dimensions in the eigenvector files don't match");
1207 if (Eig2File != NULL)
1209 neig2 = read_xvg(Eig2File, &xvgdata, &i);
1210 srenew(eigval2, neig2);
1211 for (j = 0; j < neig2; j++)
1213 eigval2[j] = xvgdata[1][j];
1215 for (j = 0; j < i; j++)
1220 fprintf(stderr, "Read %d eigenvalues from %s\n", neig2, Eig2File);
1224 if ((!bFit1 || xref1) && !bDMR1 && !bDMA1)
1228 if ((xref1 == NULL) && (bM || bTraj))
1244 bTop = read_tps_conf(ftp2fn(efTPS, NFILE, fnm),
1245 title, &top, &ePBC, &xtop, NULL, topbox, bM);
1247 gpbc = gmx_rmpbc_init(&top.idef, ePBC, atoms->nr);
1248 gmx_rmpbc(gpbc, atoms->nr, topbox, xtop);
1249 /* Fitting is only required for the projection */
1254 printf("\nNote: the structure in %s should be the same\n"
1255 " as the one used for the fit in g_covar\n", topfile);
1257 printf("\nSelect the index group that was used for the least squares fit in g_covar\n");
1258 get_index(atoms, indexfile, 1, &nfit, &ifit, &grpname);
1260 snew(w_rls, atoms->nr);
1261 for (i = 0; (i < nfit); i++)
1265 w_rls[ifit[i]] = atoms->atom[ifit[i]].m;
1269 w_rls[ifit[i]] = 1.0;
1273 snew(xrefp, atoms->nr);
1276 /* Safety check between selected fit-group and reference structure read from the eigenvector file */
1279 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);
1281 for (i = 0; (i < nfit); i++)
1283 copy_rvec(xref1[i], xrefp[ifit[i]]);
1288 /* The top coordinates are the fitting reference */
1289 for (i = 0; (i < nfit); i++)
1291 copy_rvec(xtop[ifit[i]], xrefp[ifit[i]]);
1293 reset_x(nfit, ifit, atoms->nr, NULL, xrefp, w_rls);
1296 gmx_rmpbc_done(gpbc);
1301 printf("\nSelect an index group of %d elements that corresponds to the eigenvectors\n", natoms);
1302 get_index(atoms, indexfile, 1, &i, &index, &grpname);
1305 gmx_fatal(FARGS, "you selected a group with %d elements instead of %d", i, natoms);
1310 snew(sqrtm, natoms);
1313 proj_unit = "u\\S1/2\\Nnm";
1314 for (i = 0; (i < natoms); i++)
1316 sqrtm[i] = sqrt(atoms->atom[index[i]].m);
1322 for (i = 0; (i < natoms); i++)
1332 for (i = 0; (i < natoms); i++)
1334 for (d = 0; (d < DIM); d++)
1336 t += sqr((xav1[i][d]-xav2[i][d])*sqrtm[i]);
1337 totmass += sqr(sqrtm[i]);
1340 fprintf(stdout, "RMSD (without fit) between the two average structures:"
1341 " %.3f (nm)\n\n", sqrt(t/totmass));
1352 /* make an index from first to last */
1353 nout = last-first+1;
1355 for (i = 0; i < nout; i++)
1357 iout[i] = first-1+i;
1360 else if (ThreeDPlotFile)
1362 /* make an index of first+(0,1,2) and last */
1363 nout = bPDB3D ? 4 : 3;
1364 nout = min(last-first+1, nout);
1372 iout[nout-1] = last-1;
1376 /* make an index of first and last */
1385 printf("Select eigenvectors for output, end your selection with 0\n");
1392 srenew(iout, nout+1);
1393 if (1 != scanf("%d", &iout[nout]))
1395 gmx_fatal(FARGS, "Error reading user input");
1399 while (iout[nout] >= 0);
1403 /* make an index of the eigenvectors which are present */
1406 for (i = 0; i < nout; i++)
1409 while ((j < nvec1) && (eignr1[j] != iout[i]))
1413 if ((j < nvec1) && (eignr1[j] == iout[i]))
1415 outvec[noutvec] = j;
1419 fprintf(stderr, "%d eigenvectors selected for output", noutvec);
1422 fprintf(stderr, ":");
1423 for (j = 0; j < noutvec; j++)
1425 fprintf(stderr, " %d", eignr1[outvec[j]]+1);
1428 fprintf(stderr, "\n");
1432 components(CompFile, natoms, eignr1, eigvec1, noutvec, outvec, oenv);
1437 rmsf(RmsfFile, natoms, sqrtm, eignr1, eigvec1, noutvec, outvec, eigval1,
1443 project(bTraj ? opt2fn("-f", NFILE, fnm) : NULL,
1444 bTop ? &top : NULL, ePBC, topbox,
1445 ProjOnVecFile, TwoDPlotFile, ThreeDPlotFile, FilterFile, skip,
1446 ExtremeFile, bFirstLastSet, max, nextr, atoms, natoms, index,
1447 bFit1, xrefp, nfit, ifit, w_rls,
1448 sqrtm, xav1, eignr1, eigvec1, noutvec, outvec, bSplit,
1454 overlap(OverlapFile, natoms,
1455 eigvec1, nvec2, eignr2, eigvec2, noutvec, outvec, oenv);
1460 inprod_matrix(InpMatFile, natoms,
1461 nvec1, eignr1, eigvec1, nvec2, eignr2, eigvec2,
1462 bFirstLastSet, noutvec, outvec);
1467 compare(natoms, nvec1, eigvec1, nvec2, eigvec2, eigval1, neig1, eigval2, neig2);
1471 if (!CompFile && !bProj && !OverlapFile && !InpMatFile &&
1472 !bCompare && !bEntropy)
1474 fprintf(stderr, "\nIf you want some output,"
1475 " set one (or two or ...) of the output file options\n");
1479 view_all(oenv, NFILE, fnm);