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42 #include "gromacs/commandline/pargs.h"
43 #include "gromacs/fileio/confio.h"
44 #include "gromacs/fileio/pdbio.h"
45 #include "gromacs/fileio/strdb.h"
46 #include "gromacs/fileio/tpxio.h"
47 #include "gromacs/fileio/trxio.h"
48 #include "gromacs/gmxana/gmx_ana.h"
49 #include "gromacs/gmxana/princ.h"
50 #include "gromacs/gmxlib/conformation-utilities.h"
51 #include "gromacs/legacyheaders/macros.h"
52 #include "gromacs/legacyheaders/txtdump.h"
53 #include "gromacs/legacyheaders/typedefs.h"
54 #include "gromacs/legacyheaders/viewit.h"
55 #include "gromacs/math/units.h"
56 #include "gromacs/math/vec.h"
57 #include "gromacs/pbcutil/pbc.h"
58 #include "gromacs/pbcutil/rmpbc.h"
59 #include "gromacs/topology/atomprop.h"
60 #include "gromacs/topology/index.h"
61 #include "gromacs/utility/fatalerror.h"
62 #include "gromacs/utility/smalloc.h"
80 real calc_mass(t_atoms *atoms, gmx_bool bGetMass, gmx_atomprop_t aps)
86 for (i = 0; (i < atoms->nr); i++)
90 gmx_atomprop_query(aps, epropMass,
91 *atoms->resinfo[atoms->atom[i].resind].name,
92 *atoms->atomname[i], &(atoms->atom[i].m));
94 tmass += atoms->atom[i].m;
100 real calc_geom(int isize, atom_id *index, rvec *x, rvec geom_center, rvec min,
101 rvec max, gmx_bool bDiam)
107 clear_rvec(geom_center);
124 for (j = 0; j < DIM; j++)
126 min[j] = max[j] = x[ii][j];
128 for (i = 0; i < isize; i++)
138 rvec_inc(geom_center, x[ii]);
139 for (j = 0; j < DIM; j++)
141 if (x[ii][j] < min[j])
145 if (x[ii][j] > max[j])
154 for (j = i + 1; j < isize; j++)
156 d = distance2(x[ii], x[index[j]]);
157 diam2 = max(d, diam2);
162 for (j = i + 1; j < isize; j++)
164 d = distance2(x[i], x[j]);
165 diam2 = max(d, diam2);
170 svmul(1.0 / isize, geom_center, geom_center);
176 void center_conf(int natom, rvec *x, rvec center, rvec geom_cent)
181 rvec_sub(center, geom_cent, shift);
183 printf(" shift :%7.3f%7.3f%7.3f (nm)\n", shift[XX], shift[YY],
186 for (i = 0; (i < natom); i++)
188 rvec_inc(x[i], shift);
192 void scale_conf(int natom, rvec x[], matrix box, rvec scale)
196 for (i = 0; i < natom; i++)
198 for (j = 0; j < DIM; j++)
203 for (i = 0; i < DIM; i++)
205 for (j = 0; j < DIM; j++)
207 box[i][j] *= scale[j];
212 void read_bfac(const char *fn, int *n_bfac, double **bfac_val, int **bfac_nr)
217 *n_bfac = get_lines(fn, &bfac_lines);
218 snew(*bfac_val, *n_bfac);
219 snew(*bfac_nr, *n_bfac);
220 fprintf(stderr, "Reading %d B-factors from %s\n", *n_bfac, fn);
221 for (i = 0; (i < *n_bfac); i++)
223 /*fprintf(stderr, "Line %d: %s",i,bfac_lines[i]);*/
224 sscanf(bfac_lines[i], "%d %lf", &(*bfac_nr)[i], &(*bfac_val)[i]);
225 /*fprintf(stderr," nr %d val %g\n",(*bfac_nr)[i],(*bfac_val)[i]);*/
230 void set_pdb_conf_bfac(int natoms, int nres, t_atoms *atoms, int n_bfac,
231 double *bfac, int *bfac_nr, gmx_bool peratom)
234 real bfac_min, bfac_max;
240 for (i = 0; (i < n_bfac); i++)
242 if (bfac_nr[i] - 1 >= atoms->nres)
246 /* if ((bfac_nr[i]-1<0) || (bfac_nr[i]-1>=atoms->nr))
247 gmx_fatal(FARGS,"Index of B-Factor %d is out of range: %d (%g)",
248 i+1,bfac_nr[i],bfac[i]); */
249 if (bfac[i] > bfac_max)
253 if (bfac[i] < bfac_min)
258 while ((bfac_max > 99.99) || (bfac_min < -99.99))
261 "Range of values for B-factors too large (min %g, max %g) "
262 "will scale down a factor 10\n", bfac_min, bfac_max);
263 for (i = 0; (i < n_bfac); i++)
270 while ((fabs(bfac_max) < 0.5) && (fabs(bfac_min) < 0.5))
273 "Range of values for B-factors too small (min %g, max %g) "
274 "will scale up a factor 10\n", bfac_min, bfac_max);
275 for (i = 0; (i < n_bfac); i++)
283 for (i = 0; (i < natoms); i++)
285 atoms->pdbinfo[i].bfac = 0;
290 fprintf(stderr, "Will attach %d B-factors to %d residues\n", n_bfac,
292 for (i = 0; (i < n_bfac); i++)
295 for (n = 0; (n < natoms); n++)
297 if (bfac_nr[i] == atoms->resinfo[atoms->atom[n].resind].nr)
299 atoms->pdbinfo[n].bfac = bfac[i];
305 gmx_warning("Residue nr %d not found\n", bfac_nr[i]);
311 fprintf(stderr, "Will attach %d B-factors to %d atoms\n", n_bfac,
313 for (i = 0; (i < n_bfac); i++)
315 atoms->pdbinfo[bfac_nr[i] - 1].bfac = bfac[i];
320 void pdb_legend(FILE *out, int natoms, int nres, t_atoms *atoms, rvec x[])
322 real bfac_min, bfac_max, xmin, ymin, zmin;
331 for (i = 0; (i < natoms); i++)
333 xmin = min(xmin, x[i][XX]);
334 ymin = min(ymin, x[i][YY]);
335 zmin = min(zmin, x[i][ZZ]);
336 bfac_min = min(bfac_min, atoms->pdbinfo[i].bfac);
337 bfac_max = max(bfac_max, atoms->pdbinfo[i].bfac);
339 fprintf(stderr, "B-factors range from %g to %g\n", bfac_min, bfac_max);
340 for (i = 1; (i < 12); i++)
343 "%-6s%5u %-4.4s%3.3s %c%4d%c %8.3f%8.3f%8.3f%6.2f%6.2f\n",
344 "ATOM ", natoms + 1 + i, "CA", "LEG", space, nres + 1, space,
345 (xmin + (i * 0.12)) * 10, ymin * 10, zmin * 10, 1.0, bfac_min
346 + ((i - 1.0) * (bfac_max - bfac_min) / 10));
350 void visualize_images(const char *fn, int ePBC, matrix box)
358 init_t_atoms(&atoms, nat, FALSE);
361 /* FIXME: Constness should not be cast away */
363 ala = (char *) "ALA";
364 for (i = 0; i < nat; i++)
366 atoms.atomname[i] = &c;
367 atoms.atom[i].resind = i;
368 atoms.resinfo[i].name = &ala;
369 atoms.resinfo[i].nr = i + 1;
370 atoms.resinfo[i].chainid = 'A' + i / NCUCVERT;
372 calc_triclinic_images(box, img + 1);
374 write_sto_conf(fn, "Images", &atoms, img, NULL, ePBC, box);
376 free_t_atoms(&atoms, FALSE);
380 void visualize_box(FILE *out, int a0, int r0, matrix box, rvec gridsize)
384 int nx, ny, nz, nbox, nat;
388 0, 1, 1, 3, 3, 2, 0, 2, 0, 4, 1, 5, 3, 7, 2, 6, 4, 5, 5, 7, 7, 6, 6,
395 nx = (int) (gridsize[XX] + 0.5);
396 ny = (int) (gridsize[YY] + 0.5);
397 nz = (int) (gridsize[ZZ] + 0.5);
401 nat = nbox * NCUCVERT;
403 calc_compact_unitcell_vertices(ecenterDEF, box, vert);
405 for (z = 0; z < nz; z++)
407 for (y = 0; y < ny; y++)
409 for (x = 0; x < nx; x++)
411 for (i = 0; i < DIM; i++)
413 shift[i] = x * box[0][i] + y * box[1][i] + z
416 for (i = 0; i < NCUCVERT; i++)
418 rvec_add(vert[i], shift, vert[j]);
425 for (i = 0; i < nat; i++)
427 gmx_fprintf_pdb_atomline(out, epdbATOM, a0 + i, "C", ' ', "BOX", 'K' + i / NCUCVERT, r0 + i, ' ',
428 10*vert[i][XX], 10*vert[i][YY], 10*vert[i][ZZ], 1.0, 0.0, "");
431 edge = compact_unitcell_edges();
432 for (j = 0; j < nbox; j++)
434 for (i = 0; i < NCUCEDGE; i++)
436 fprintf(out, "CONECT%5d%5d\n", a0 + j * NCUCVERT + edge[2 * i],
437 a0 + j * NCUCVERT + edge[2 * i + 1]);
446 for (z = 0; z <= 1; z++)
448 for (y = 0; y <= 1; y++)
450 for (x = 0; x <= 1; x++)
452 gmx_fprintf_pdb_atomline(out, epdbATOM, a0 + i, "C", ' ', "BOX", 'K' + i/8, r0+i, ' ',
453 x * 10 * box[XX][XX], y * 10 * box[YY][YY], z * 10 * box[ZZ][ZZ], 1.0, 0.0, "");
458 for (i = 0; i < 24; i += 2)
460 fprintf(out, "CONECT%5d%5d\n", a0 + rectedge[i], a0 + rectedge[i
466 void calc_rotmatrix(rvec principal_axis, rvec targetvec, matrix rotmatrix)
469 real ux, uy, uz, costheta, sintheta;
471 costheta = cos_angle(principal_axis, targetvec);
472 sintheta = sqrt(1.0-costheta*costheta); /* sign is always positive since 0<theta<pi */
474 /* Determine rotation from cross product with target vector */
475 cprod(principal_axis, targetvec, rotvec);
476 unitv(rotvec, rotvec);
477 printf("Aligning %g %g %g to %g %g %g : xprod %g %g %g\n",
478 principal_axis[XX], principal_axis[YY], principal_axis[ZZ], targetvec[XX], targetvec[YY], targetvec[ZZ],
479 rotvec[XX], rotvec[YY], rotvec[ZZ]);
484 rotmatrix[0][0] = ux*ux + (1.0-ux*ux)*costheta;
485 rotmatrix[0][1] = ux*uy*(1-costheta)-uz*sintheta;
486 rotmatrix[0][2] = ux*uz*(1-costheta)+uy*sintheta;
487 rotmatrix[1][0] = ux*uy*(1-costheta)+uz*sintheta;
488 rotmatrix[1][1] = uy*uy + (1.0-uy*uy)*costheta;
489 rotmatrix[1][2] = uy*uz*(1-costheta)-ux*sintheta;
490 rotmatrix[2][0] = ux*uz*(1-costheta)-uy*sintheta;
491 rotmatrix[2][1] = uy*uz*(1-costheta)+ux*sintheta;
492 rotmatrix[2][2] = uz*uz + (1.0-uz*uz)*costheta;
494 printf("Rotation matrix: \n%g %g %g\n%g %g %g\n%g %g %g\n",
495 rotmatrix[0][0], rotmatrix[0][1], rotmatrix[0][2],
496 rotmatrix[1][0], rotmatrix[1][1], rotmatrix[1][2],
497 rotmatrix[2][0], rotmatrix[2][1], rotmatrix[2][2]);
500 static void renum_resnr(t_atoms *atoms, int isize, const int *index,
503 int i, resind_prev, resind;
506 for (i = 0; i < isize; i++)
508 resind = atoms->atom[index == NULL ? i : index[i]].resind;
509 if (resind != resind_prev)
511 atoms->resinfo[resind].nr = resnr_start;
514 resind_prev = resind;
518 int gmx_editconf(int argc, char *argv[])
522 "[THISMODULE] converts generic structure format to [TT].gro[tt], [TT].g96[tt]",
525 "The box can be modified with options [TT]-box[tt], [TT]-d[tt] and",
526 "[TT]-angles[tt]. Both [TT]-box[tt] and [TT]-d[tt]",
527 "will center the system in the box, unless [TT]-noc[tt] is used.",
529 "Option [TT]-bt[tt] determines the box type: [TT]triclinic[tt] is a",
530 "triclinic box, [TT]cubic[tt] is a rectangular box with all sides equal",
531 "[TT]dodecahedron[tt] represents a rhombic dodecahedron and",
532 "[TT]octahedron[tt] is a truncated octahedron.",
533 "The last two are special cases of a triclinic box.",
534 "The length of the three box vectors of the truncated octahedron is the",
535 "shortest distance between two opposite hexagons.",
536 "Relative to a cubic box with some periodic image distance, the volume of a ",
537 "dodecahedron with this same periodic distance is 0.71 times that of the cube, ",
538 "and that of a truncated octahedron is 0.77 times.",
540 "Option [TT]-box[tt] requires only",
541 "one value for a cubic, rhombic dodecahedral, or truncated octahedral box.",
543 "With [TT]-d[tt] and a [TT]triclinic[tt] box the size of the system in the [IT]x[it]-, [IT]y[it]-,",
544 "and [IT]z[it]-directions is used. With [TT]-d[tt] and [TT]cubic[tt],",
545 "[TT]dodecahedron[tt] or [TT]octahedron[tt] boxes, the dimensions are set",
546 "to the diameter of the system (largest distance between atoms) plus twice",
547 "the specified distance.",
549 "Option [TT]-angles[tt] is only meaningful with option [TT]-box[tt] and",
550 "a triclinic box and cannot be used with option [TT]-d[tt].",
552 "When [TT]-n[tt] or [TT]-ndef[tt] is set, a group",
553 "can be selected for calculating the size and the geometric center,",
554 "otherwise the whole system is used.",
556 "[TT]-rotate[tt] rotates the coordinates and velocities.",
558 "[TT]-princ[tt] aligns the principal axes of the system along the",
559 "coordinate axes, with the longest axis aligned with the [IT]x[it]-axis. ",
560 "This may allow you to decrease the box volume,",
561 "but beware that molecules can rotate significantly in a nanosecond.",
563 "Scaling is applied before any of the other operations are",
564 "performed. Boxes and coordinates can be scaled to give a certain density (option",
565 "[TT]-density[tt]). Note that this may be inaccurate in case a [TT].gro[tt]",
566 "file is given as input. A special feature of the scaling option is that when the",
567 "factor -1 is given in one dimension, one obtains a mirror image,",
568 "mirrored in one of the planes. When one uses -1 in three dimensions, ",
569 "a point-mirror image is obtained.[PAR]",
570 "Groups are selected after all operations have been applied.[PAR]",
571 "Periodicity can be removed in a crude manner.",
572 "It is important that the box vectors at the bottom of your input file",
573 "are correct when the periodicity is to be removed.",
575 "When writing [TT].pdb[tt] files, B-factors can be",
576 "added with the [TT]-bf[tt] option. B-factors are read",
577 "from a file with with following format: first line states number of",
578 "entries in the file, next lines state an index",
579 "followed by a B-factor. The B-factors will be attached per residue",
580 "unless an index is larger than the number of residues or unless the",
581 "[TT]-atom[tt] option is set. Obviously, any type of numeric data can",
582 "be added instead of B-factors. [TT]-legend[tt] will produce",
583 "a row of CA atoms with B-factors ranging from the minimum to the",
584 "maximum value found, effectively making a legend for viewing.",
586 "With the option [TT]-mead[tt] a special [TT].pdb[tt] ([TT].pqr[tt])",
587 "file for the MEAD electrostatics",
588 "program (Poisson-Boltzmann solver) can be made. A further prerequisite",
589 "is that the input file is a run input file.",
590 "The B-factor field is then filled with the Van der Waals radius",
591 "of the atoms while the occupancy field will hold the charge.",
593 "The option [TT]-grasp[tt] is similar, but it puts the charges in the B-factor",
594 "and the radius in the occupancy.",
596 "Option [TT]-align[tt] allows alignment",
597 "of the principal axis of a specified group against the given vector, ",
598 "with an optional center of rotation specified by [TT]-aligncenter[tt].",
600 "Finally, with option [TT]-label[tt], [TT]editconf[tt] can add a chain identifier",
601 "to a [TT].pdb[tt] file, which can be useful for analysis with e.g. Rasmol.",
603 "To convert a truncated octrahedron file produced by a package which uses",
604 "a cubic box with the corners cut off (such as GROMOS), use:[BR]",
605 "[TT]gmx editconf -f in -rotate 0 45 35.264 -bt o -box veclen -o out[tt][BR]",
606 "where [TT]veclen[tt] is the size of the cubic box times [SQRT]3[sqrt]/2."
610 "For complex molecules, the periodicity removal routine may break down, "
611 "in that case you can use [gmx-trjconv]."
613 static real dist = 0.0, rbox = 0.0, to_diam = 0.0;
614 static gmx_bool bNDEF = FALSE, bRMPBC = FALSE, bCenter = FALSE, bReadVDW =
615 FALSE, bCONECT = FALSE;
616 static gmx_bool peratom = FALSE, bLegend = FALSE, bOrient = FALSE, bMead =
617 FALSE, bGrasp = FALSE, bSig56 = FALSE;
619 { 1, 1, 1 }, newbox =
620 { 0, 0, 0 }, newang =
622 static real rho = 1000.0, rvdw = 0.12;
624 { 0, 0, 0 }, translation =
625 { 0, 0, 0 }, rotangles =
626 { 0, 0, 0 }, aligncenter =
627 { 0, 0, 0 }, targetvec =
629 static const char *btype[] =
630 { NULL, "triclinic", "cubic", "dodecahedron", "octahedron", NULL },
634 static int resnr_start = -1;
638 { "-ndef", FALSE, etBOOL,
639 { &bNDEF }, "Choose output from default index groups" },
640 { "-visbox", FALSE, etRVEC,
642 "HIDDENVisualize a grid of boxes, -1 visualizes the 14 box images" },
643 { "-bt", FALSE, etENUM,
644 { btype }, "Box type for [TT]-box[tt] and [TT]-d[tt]" },
645 { "-box", FALSE, etRVEC,
646 { newbox }, "Box vector lengths (a,b,c)" },
647 { "-angles", FALSE, etRVEC,
648 { newang }, "Angles between the box vectors (bc,ac,ab)" },
649 { "-d", FALSE, etREAL,
650 { &dist }, "Distance between the solute and the box" },
651 { "-c", FALSE, etBOOL,
653 "Center molecule in box (implied by [TT]-box[tt] and [TT]-d[tt])" },
654 { "-center", FALSE, etRVEC,
655 { center }, "Coordinates of geometrical center" },
656 { "-aligncenter", FALSE, etRVEC,
657 { aligncenter }, "Center of rotation for alignment" },
658 { "-align", FALSE, etRVEC,
660 "Align to target vector" },
661 { "-translate", FALSE, etRVEC,
662 { translation }, "Translation" },
663 { "-rotate", FALSE, etRVEC,
665 "Rotation around the X, Y and Z axes in degrees" },
666 { "-princ", FALSE, etBOOL,
668 "Orient molecule(s) along their principal axes" },
669 { "-scale", FALSE, etRVEC,
670 { scale }, "Scaling factor" },
671 { "-density", FALSE, etREAL,
673 "Density (g/L) of the output box achieved by scaling" },
674 { "-pbc", FALSE, etBOOL,
676 "Remove the periodicity (make molecule whole again)" },
677 { "-resnr", FALSE, etINT,
679 " Renumber residues starting from resnr" },
680 { "-grasp", FALSE, etBOOL,
682 "Store the charge of the atom in the B-factor field and the radius of the atom in the occupancy field" },
684 "-rvdw", FALSE, etREAL,
686 "Default Van der Waals radius (in nm) if one can not be found in the database or if no parameters are present in the topology file"
688 { "-sig56", FALSE, etBOOL,
690 "Use rmin/2 (minimum in the Van der Waals potential) rather than [GRK]sigma[grk]/2 " },
692 "-vdwread", FALSE, etBOOL,
694 "Read the Van der Waals radii from the file [TT]vdwradii.dat[tt] rather than computing the radii based on the force field"
696 { "-atom", FALSE, etBOOL,
697 { &peratom }, "Force B-factor attachment per atom" },
698 { "-legend", FALSE, etBOOL,
699 { &bLegend }, "Make B-factor legend" },
700 { "-label", FALSE, etSTR,
701 { &label }, "Add chain label for all residues" },
703 "-conect", FALSE, etBOOL,
705 "Add CONECT records to a [TT].pdb[tt] file when written. Can only be done when a topology is present"
708 #define NPA asize(pa)
711 const char *infile, *outfile;
713 int outftp, inftp, natom, i, j, n_bfac, itype, ntype;
714 double *bfac = NULL, c6, c12;
716 t_topology *top = NULL;
718 char *grpname, *sgrpname, *agrpname;
719 int isize, ssize, tsize, asize;
720 atom_id *index, *sindex, *tindex, *aindex;
721 rvec *x, *v, gc, min, max, size;
723 matrix box, rotmatrix, trans;
725 gmx_bool bIndex, bSetSize, bSetAng, bCubic, bDist, bSetCenter, bAlign;
726 gmx_bool bHaveV, bScale, bRho, bTranslate, bRotate, bCalcGeom, bCalcDiam;
727 real xs, ys, zs, xcent, ycent, zcent, diam = 0, mass = 0, d, vdw;
733 { efSTX, "-f", NULL, ffREAD },
734 { efNDX, "-n", NULL, ffOPTRD },
735 { efSTO, NULL, NULL, ffOPTWR },
736 { efPQR, "-mead", "mead", ffOPTWR },
737 { efDAT, "-bf", "bfact", ffOPTRD }
739 #define NFILE asize(fnm)
741 if (!parse_common_args(&argc, argv, PCA_CAN_VIEW, NFILE, fnm, NPA, pa,
742 asize(desc), desc, asize(bugs), bugs, &oenv))
747 bIndex = opt2bSet("-n", NFILE, fnm) || bNDEF;
748 bMead = opt2bSet("-mead", NFILE, fnm);
749 bSetSize = opt2parg_bSet("-box", NPA, pa);
750 bSetAng = opt2parg_bSet("-angles", NPA, pa);
751 bSetCenter = opt2parg_bSet("-center", NPA, pa);
752 bDist = opt2parg_bSet("-d", NPA, pa);
753 bAlign = opt2parg_bSet("-align", NPA, pa);
754 /* Only automatically turn on centering without -noc */
755 if ((bDist || bSetSize || bSetCenter) && !opt2parg_bSet("-c", NPA, pa))
759 bScale = opt2parg_bSet("-scale", NPA, pa);
760 bRho = opt2parg_bSet("-density", NPA, pa);
761 bTranslate = opt2parg_bSet("-translate", NPA, pa);
762 bRotate = opt2parg_bSet("-rotate", NPA, pa);
765 fprintf(stderr, "WARNING: setting -density overrides -scale\n");
767 bScale = bScale || bRho;
768 bCalcGeom = bCenter || bRotate || bOrient || bScale;
769 bCalcDiam = btype[0][0] == 'c' || btype[0][0] == 'd' || btype[0][0] == 'o';
771 infile = ftp2fn(efSTX, NFILE, fnm);
774 outfile = ftp2fn(efPQR, NFILE, fnm);
778 outfile = ftp2fn(efSTO, NFILE, fnm);
780 outftp = fn2ftp(outfile);
781 inftp = fn2ftp(infile);
783 aps = gmx_atomprop_init();
787 printf("Incompatible options -mead and -grasp. Turning off -grasp\n");
790 if (bGrasp && (outftp != efPDB))
792 gmx_fatal(FARGS, "Output file should be a .pdb file"
793 " when using the -grasp option\n");
795 if ((bMead || bGrasp) && (fn2ftp(infile) != efTPR))
797 gmx_fatal(FARGS, "Input file should be a .tpr file"
798 " when using the -mead option\n");
801 get_stx_coordnum(infile, &natom);
802 init_t_atoms(&atoms, natom, TRUE);
805 read_stx_conf(infile, title, &atoms, x, v, &ePBC, box);
806 if (fn2ftp(infile) == efPDB)
808 get_pdb_atomnumber(&atoms, aps);
810 printf("Read %d atoms\n", atoms.nr);
812 /* Get the element numbers if available in a pdb file */
813 if (fn2ftp(infile) == efPDB)
815 get_pdb_atomnumber(&atoms, aps);
818 if (ePBC != epbcNONE)
821 printf("Volume: %g nm^3, corresponds to roughly %d electrons\n",
822 vol, 100*((int)(vol*4.5)));
825 if (bMead || bGrasp || bCONECT)
827 top = read_top(infile, NULL);
832 if (atoms.nr != top->atoms.nr)
834 gmx_fatal(FARGS, "Atom numbers don't match (%d vs. %d)", atoms.nr, top->atoms.nr);
836 snew(atoms.pdbinfo, top->atoms.nr);
837 ntype = top->idef.atnr;
838 for (i = 0; (i < atoms.nr); i++)
840 /* Determine the Van der Waals radius from the force field */
843 if (!gmx_atomprop_query(aps, epropVDW,
844 *top->atoms.resinfo[top->atoms.atom[i].resind].name,
845 *top->atoms.atomname[i], &vdw))
852 itype = top->atoms.atom[i].type;
853 c12 = top->idef.iparams[itype*ntype+itype].lj.c12;
854 c6 = top->idef.iparams[itype*ntype+itype].lj.c6;
855 if ((c6 != 0) && (c12 != 0))
866 vdw = 0.5*pow(sig6, 1.0/6.0);
873 /* Factor of 10 for nm -> Angstroms */
878 atoms.pdbinfo[i].occup = top->atoms.atom[i].q;
879 atoms.pdbinfo[i].bfac = vdw;
883 atoms.pdbinfo[i].occup = vdw;
884 atoms.pdbinfo[i].bfac = top->atoms.atom[i].q;
889 for (i = 0; (i < natom) && !bHaveV; i++)
891 for (j = 0; (j < DIM) && !bHaveV; j++)
893 bHaveV = bHaveV || (v[i][j] != 0);
896 printf("%selocities found\n", bHaveV ? "V" : "No v");
902 gmx_fatal(FARGS, "Sorry, can not visualize box with index groups");
906 gmx_fatal(FARGS, "Sorry, can only visualize box with a pdb file");
909 else if (visbox[0] == -1)
911 visualize_images("images.pdb", ePBC, box);
917 rm_gropbc(&atoms, x, box);
924 fprintf(stderr, "\nSelect a group for determining the system size:\n");
925 get_index(&atoms, ftp2fn_null(efNDX, NFILE, fnm),
926 1, &ssize, &sindex, &sgrpname);
933 diam = calc_geom(ssize, sindex, x, gc, min, max, bCalcDiam);
934 rvec_sub(max, min, size);
935 printf(" system size :%7.3f%7.3f%7.3f (nm)\n",
936 size[XX], size[YY], size[ZZ]);
939 printf(" diameter :%7.3f (nm)\n", diam);
941 printf(" center :%7.3f%7.3f%7.3f (nm)\n", gc[XX], gc[YY], gc[ZZ]);
942 printf(" box vectors :%7.3f%7.3f%7.3f (nm)\n",
943 norm(box[XX]), norm(box[YY]), norm(box[ZZ]));
944 printf(" box angles :%7.2f%7.2f%7.2f (degrees)\n",
945 norm2(box[ZZ]) == 0 ? 0 :
946 RAD2DEG*acos(cos_angle_no_table(box[YY], box[ZZ])),
947 norm2(box[ZZ]) == 0 ? 0 :
948 RAD2DEG*acos(cos_angle_no_table(box[XX], box[ZZ])),
949 norm2(box[YY]) == 0 ? 0 :
950 RAD2DEG*acos(cos_angle_no_table(box[XX], box[YY])));
951 printf(" box volume :%7.2f (nm^3)\n", det(box));
954 if (bRho || bOrient || bAlign)
956 mass = calc_mass(&atoms, !fn2bTPX(infile), aps);
964 /* Get a group for principal component analysis */
965 fprintf(stderr, "\nSelect group for the determining the orientation\n");
966 get_index(&atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &isize, &index, &grpnames);
968 /* Orient the principal axes along the coordinate axes */
969 orient_princ(&atoms, isize, index, natom, x, bHaveV ? v : NULL, NULL);
976 /* scale coordinates and box */
979 /* Compute scaling constant */
983 dens = (mass*AMU)/(vol*NANO*NANO*NANO);
984 fprintf(stderr, "Volume of input %g (nm^3)\n", vol);
985 fprintf(stderr, "Mass of input %g (a.m.u.)\n", mass);
986 fprintf(stderr, "Density of input %g (g/l)\n", dens);
987 if (vol == 0 || mass == 0)
989 gmx_fatal(FARGS, "Cannot scale density with "
990 "zero mass (%g) or volume (%g)\n", mass, vol);
993 scale[XX] = scale[YY] = scale[ZZ] = pow(dens/rho, 1.0/3.0);
994 fprintf(stderr, "Scaling all box vectors by %g\n", scale[XX]);
996 scale_conf(atoms.nr, x, box, scale);
1003 fprintf(stderr, "\nSelect a group that you want to align:\n");
1004 get_index(&atoms, ftp2fn_null(efNDX, NFILE, fnm),
1005 1, &asize, &aindex, &agrpname);
1010 snew(aindex, asize);
1011 for (i = 0; i < asize; i++)
1016 printf("Aligning %d atoms (out of %d) to %g %g %g, center of rotation %g %g %g\n", asize, natom,
1017 targetvec[XX], targetvec[YY], targetvec[ZZ],
1018 aligncenter[XX], aligncenter[YY], aligncenter[ZZ]);
1019 /*subtract out pivot point*/
1020 for (i = 0; i < asize; i++)
1022 rvec_dec(x[aindex[i]], aligncenter);
1024 /*now determine transform and rotate*/
1026 principal_comp(asize, aindex, atoms.atom, x, trans, princd);
1028 unitv(targetvec, targetvec);
1029 printf("Using %g %g %g as principal axis\n", trans[0][2], trans[1][2], trans[2][2]);
1030 tmpvec[XX] = trans[0][2]; tmpvec[YY] = trans[1][2]; tmpvec[ZZ] = trans[2][2];
1031 calc_rotmatrix(tmpvec, targetvec, rotmatrix);
1032 /* rotmatrix finished */
1034 for (i = 0; i < asize; ++i)
1036 mvmul(rotmatrix, x[aindex[i]], tmpvec);
1037 copy_rvec(tmpvec, x[aindex[i]]);
1040 /*add pivot point back*/
1041 for (i = 0; i < asize; i++)
1043 rvec_inc(x[aindex[i]], aligncenter);
1055 fprintf(stderr, "\nSelect a group that you want to translate:\n");
1056 get_index(&atoms, ftp2fn_null(efNDX, NFILE, fnm),
1057 1, &ssize, &sindex, &sgrpname);
1064 printf("Translating %d atoms (out of %d) by %g %g %g nm\n", ssize, natom,
1065 translation[XX], translation[YY], translation[ZZ]);
1068 for (i = 0; i < ssize; i++)
1070 rvec_inc(x[sindex[i]], translation);
1075 for (i = 0; i < natom; i++)
1077 rvec_inc(x[i], translation);
1084 printf("Rotating %g, %g, %g degrees around the X, Y and Z axis respectively\n", rotangles[XX], rotangles[YY], rotangles[ZZ]);
1085 for (i = 0; i < DIM; i++)
1087 rotangles[i] *= DEG2RAD;
1089 rotate_conf(natom, x, v, rotangles[XX], rotangles[YY], rotangles[ZZ]);
1094 /* recalc geometrical center and max and min coordinates and size */
1095 calc_geom(ssize, sindex, x, gc, min, max, FALSE);
1096 rvec_sub(max, min, size);
1097 if (bScale || bOrient || bRotate)
1099 printf("new system size : %6.3f %6.3f %6.3f\n",
1100 size[XX], size[YY], size[ZZ]);
1104 if (bSetSize || bDist || (btype[0][0] == 't' && bSetAng))
1107 if (!(bSetSize || bDist))
1109 for (i = 0; i < DIM; i++)
1111 newbox[i] = norm(box[i]);
1115 /* calculate new boxsize */
1116 switch (btype[0][0])
1121 for (i = 0; i < DIM; i++)
1123 newbox[i] = size[i]+2*dist;
1128 box[XX][XX] = newbox[XX];
1129 box[YY][YY] = newbox[YY];
1130 box[ZZ][ZZ] = newbox[ZZ];
1134 matrix_convert(box, newbox, newang);
1148 if (btype[0][0] == 'c')
1150 for (i = 0; i < DIM; i++)
1155 else if (btype[0][0] == 'd')
1161 box[ZZ][ZZ] = d*sqrt(2)/2;
1167 box[YY][YY] = d*sqrt(2)*2/3;
1169 box[ZZ][YY] = d*sqrt(2)/3;
1170 box[ZZ][ZZ] = d*sqrt(6)/3;
1176 /* calculate new coords for geometrical center */
1179 calc_box_center(ecenterDEF, box, center);
1182 /* center molecule on 'center' */
1185 center_conf(natom, x, center, gc);
1191 calc_geom(ssize, sindex, x, gc, min, max, FALSE);
1192 printf("new center :%7.3f%7.3f%7.3f (nm)\n", gc[XX], gc[YY], gc[ZZ]);
1194 if (bOrient || bScale || bDist || bSetSize)
1196 printf("new box vectors :%7.3f%7.3f%7.3f (nm)\n",
1197 norm(box[XX]), norm(box[YY]), norm(box[ZZ]));
1198 printf("new box angles :%7.2f%7.2f%7.2f (degrees)\n",
1199 norm2(box[ZZ]) == 0 ? 0 :
1200 RAD2DEG*acos(cos_angle_no_table(box[YY], box[ZZ])),
1201 norm2(box[ZZ]) == 0 ? 0 :
1202 RAD2DEG*acos(cos_angle_no_table(box[XX], box[ZZ])),
1203 norm2(box[YY]) == 0 ? 0 :
1204 RAD2DEG*acos(cos_angle_no_table(box[XX], box[YY])));
1205 printf("new box volume :%7.2f (nm^3)\n", det(box));
1208 if (check_box(epbcXYZ, box))
1210 printf("\nWARNING: %s\n"
1211 "See the GROMACS manual for a description of the requirements that\n"
1212 "must be satisfied by descriptions of simulation cells.\n",
1213 check_box(epbcXYZ, box));
1216 if (bDist && btype[0][0] == 't')
1220 printf("\nWARNING: Your box is triclinic with non-orthogonal axes. In this case, the\n"
1221 "distance from the solute to a box surface along the corresponding normal\n"
1222 "vector might be somewhat smaller than your specified value %f.\n"
1223 "You can check the actual value with g_mindist -pi\n", dist);
1225 else if (!opt2parg_bSet("-bt", NPA, pa))
1227 printf("\nWARNING: No boxtype specified - distance condition applied in each dimension.\n"
1228 "If the molecule rotates the actual distance will be smaller. You might want\n"
1229 "to use a cubic box instead, or why not try a dodecahedron today?\n");
1232 if (bCONECT && (outftp == efPDB) && (inftp == efTPR))
1234 conect = gmx_conect_generate(top);
1243 fprintf(stderr, "\nSelect a group for output:\n");
1244 get_index(&atoms, opt2fn_null("-n", NFILE, fnm),
1245 1, &isize, &index, &grpname);
1247 if (resnr_start >= 0)
1249 renum_resnr(&atoms, isize, index, resnr_start);
1252 if (opt2parg_bSet("-label", NPA, pa))
1254 for (i = 0; (i < atoms.nr); i++)
1256 atoms.resinfo[atoms.atom[i].resind].chainid = label[0];
1260 if (opt2bSet("-bf", NFILE, fnm) || bLegend)
1262 gmx_fatal(FARGS, "Sorry, cannot do bfactors with an index group.");
1265 if (outftp == efPDB)
1267 out = gmx_ffopen(outfile, "w");
1268 write_pdbfile_indexed(out, title, &atoms, x, ePBC, box, ' ', 1, isize, index, conect, TRUE);
1273 write_sto_conf_indexed(outfile, title, &atoms, x, bHaveV ? v : NULL, ePBC, box, isize, index);
1278 if (resnr_start >= 0)
1280 renum_resnr(&atoms, atoms.nr, NULL, resnr_start);
1283 if ((outftp == efPDB) || (outftp == efPQR))
1285 out = gmx_ffopen(outfile, "w");
1288 fprintf(out, "REMARK "
1289 "The B-factors in this file hold atomic radii\n");
1290 fprintf(out, "REMARK "
1291 "The occupancy in this file hold atomic charges\n");
1295 fprintf(out, "GRASP PDB FILE\nFORMAT NUMBER=1\n");
1296 fprintf(out, "REMARK "
1297 "The B-factors in this file hold atomic charges\n");
1298 fprintf(out, "REMARK "
1299 "The occupancy in this file hold atomic radii\n");
1301 else if (opt2bSet("-bf", NFILE, fnm))
1303 read_bfac(opt2fn("-bf", NFILE, fnm), &n_bfac, &bfac, &bfac_nr);
1304 set_pdb_conf_bfac(atoms.nr, atoms.nres, &atoms,
1305 n_bfac, bfac, bfac_nr, peratom);
1307 if (opt2parg_bSet("-label", NPA, pa))
1309 for (i = 0; (i < atoms.nr); i++)
1311 atoms.resinfo[atoms.atom[i].resind].chainid = label[0];
1314 write_pdbfile(out, title, &atoms, x, ePBC, box, ' ', -1, conect, TRUE);
1317 pdb_legend(out, atoms.nr, atoms.nres, &atoms, x);
1321 visualize_box(out, bLegend ? atoms.nr+12 : atoms.nr,
1322 bLegend ? atoms.nres = 12 : atoms.nres, box, visbox);
1328 write_sto_conf(outfile, title, &atoms, x, bHaveV ? v : NULL, ePBC, box);
1331 gmx_atomprop_destroy(aps);
1333 do_view(oenv, outfile, NULL);