#include "confio.h"
-#include <cerrno>
-#include <cmath>
#include <cstdio>
-#include <cstdlib>
#include <cstring>
-#include <algorithm>
-
-#include "gromacs/fileio/filenm.h"
-#include "gromacs/fileio/gmxfio.h"
-#include "gromacs/fileio/pdbio.h"
-#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trx.h"
-#include "gromacs/fileio/trxio.h"
-#include "gromacs/fileio/xdrf.h"
-#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/topology/symtab.h"
-#include "gromacs/topology/topology.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/utility/smalloc.h"
-
-#define CHAR_SHIFT 24
-
-static int read_g96_pos(char line[], t_symtab *symtab,
- FILE *fp, const char *infile,
- t_trxframe *fr)
-{
- t_atoms *atoms;
- gmx_bool bEnd;
- int nwanted, natoms, atnr, resnr = 0, oldres, newres, shift;
- char anm[STRLEN], resnm[STRLEN];
- char c1, c2;
- double db1, db2, db3;
-
- nwanted = fr->natoms;
-
- atoms = fr->atoms;
-
- natoms = 0;
-
- if (fr->bX)
- {
- if (fr->bAtoms)
- {
- shift = CHAR_SHIFT;
- }
- else
- {
- shift = 0;
- }
- newres = -1;
- oldres = -666; /* Unlikely number for the first residue! */
- bEnd = FALSE;
- while (!bEnd && fgets2(line, STRLEN, fp))
- {
- bEnd = (std::strncmp(line, "END", 3) == 0);
- if (!bEnd && (line[0] != '#'))
- {
- if (sscanf(line+shift, "%15lf%15lf%15lf", &db1, &db2, &db3) != 3)
- {
- gmx_fatal(FARGS, "Did not find 3 coordinates for atom %d in %s\n",
- natoms+1, infile);
- }
- if ((nwanted != -1) && (natoms >= nwanted))
- {
- gmx_fatal(FARGS,
- "Found more coordinates (%d) in %s than expected %d\n",
- natoms, infile, nwanted);
- }
- if (atoms)
- {
- if (fr->bAtoms &&
- (sscanf(line, "%5d%c%5s%c%5s%7d", &resnr, &c1, resnm, &c2, anm, &atnr)
- != 6))
- {
- if (oldres >= 0)
- {
- resnr = oldres;
- }
- else
- {
- resnr = 1;
- strncpy(resnm, "???", sizeof(resnm)-1);
- }
- strncpy(anm, "???", sizeof(anm)-1);
- }
- atoms->atomname[natoms] = put_symtab(symtab, anm);
- if (resnr != oldres)
- {
- oldres = resnr;
- newres++;
- if (newres >= atoms->nr)
- {
- gmx_fatal(FARGS, "More residues than atoms in %s (natoms = %d)",
- infile, atoms->nr);
- }
- atoms->atom[natoms].resind = newres;
- if (newres+1 > atoms->nres)
- {
- atoms->nres = newres+1;
- }
- t_atoms_set_resinfo(atoms, natoms, symtab, resnm, resnr, ' ', 0, ' ');
- }
- else
- {
- atoms->atom[natoms].resind = newres;
- }
- }
- if (fr->x)
- {
- fr->x[natoms][0] = db1;
- fr->x[natoms][1] = db2;
- fr->x[natoms][2] = db3;
- }
- natoms++;
- }
- }
- if ((nwanted != -1) && natoms != nwanted)
- {
- fprintf(stderr,
- "Warning: found less coordinates (%d) in %s than expected %d\n",
- natoms, infile, nwanted);
- }
- }
-
- fr->natoms = natoms;
-
- return natoms;
-}
-
-static int read_g96_vel(char line[], FILE *fp, const char *infile,
- t_trxframe *fr)
-{
- gmx_bool bEnd;
- int nwanted, natoms = -1, shift;
- double db1, db2, db3;
-
- nwanted = fr->natoms;
-
- if (fr->v && fr->bV)
- {
- if (strcmp(line, "VELOCITYRED") == 0)
- {
- shift = 0;
- }
- else
- {
- shift = CHAR_SHIFT;
- }
- natoms = 0;
- bEnd = FALSE;
- while (!bEnd && fgets2(line, STRLEN, fp))
- {
- bEnd = (strncmp(line, "END", 3) == 0);
- if (!bEnd && (line[0] != '#'))
- {
- if (sscanf(line+shift, "%15lf%15lf%15lf", &db1, &db2, &db3) != 3)
- {
- gmx_fatal(FARGS, "Did not find 3 velocities for atom %d in %s",
- natoms+1, infile);
- }
- if ((nwanted != -1) && (natoms >= nwanted))
- {
- gmx_fatal(FARGS, "Found more velocities (%d) in %s than expected %d\n",
- natoms, infile, nwanted);
- }
- if (fr->v)
- {
- fr->v[natoms][0] = db1;
- fr->v[natoms][1] = db2;
- fr->v[natoms][2] = db3;
- }
- natoms++;
- }
- }
- if ((nwanted != -1) && (natoms != nwanted))
- {
- fprintf(stderr,
- "Warning: found less velocities (%d) in %s than expected %d\n",
- natoms, infile, nwanted);
- }
- }
-
- return natoms;
-}
-
-int read_g96_conf(FILE *fp, const char *infile, t_trxframe *fr, char *line)
-{
- t_symtab *symtab = NULL;
- gmx_bool bAtStart, bTime, bAtoms, bPos, bVel, bBox, bEnd, bFinished;
- int natoms, nbp;
- double db1, db2, db3, db4, db5, db6, db7, db8, db9;
-
- bAtStart = (ftell(fp) == 0);
-
- clear_trxframe(fr, FALSE);
-
- if (!symtab)
- {
- snew(symtab, 1);
- open_symtab(symtab);
- }
-
- natoms = 0;
-
- if (bAtStart)
- {
- while (!fr->bTitle && fgets2(line, STRLEN, fp))
- {
- fr->bTitle = (std::strcmp(line, "TITLE") == 0);
- }
- if (fr->title == NULL)
- {
- fgets2(line, STRLEN, fp);
- fr->title = gmx_strdup(line);
- }
- bEnd = FALSE;
- while (!bEnd && fgets2(line, STRLEN, fp))
- {
- bEnd = (std::strcmp(line, "END") == 0);
- }
- fgets2(line, STRLEN, fp);
- }
-
- /* Do not get a line if we are not at the start of the file, *
- * because without a parameter file we don't know what is in *
- * the trajectory and we have already read the line in the *
- * previous call (VERY DIRTY). */
- bFinished = FALSE;
- do
- {
- bTime = (std::strcmp(line, "TIMESTEP") == 0);
- bAtoms = (std::strcmp(line, "POSITION") == 0);
- bPos = (bAtoms || (strcmp(line, "POSITIONRED") == 0));
- bVel = (std::strncmp(line, "VELOCITY", 8) == 0);
- bBox = (std::strcmp(line, "BOX") == 0);
- if (bTime)
- {
- if (!fr->bTime && !fr->bX)
- {
- fr->bStep = bTime;
- fr->bTime = bTime;
- do
- {
- bFinished = (fgets2(line, STRLEN, fp) == NULL);
- }
- while (!bFinished && (line[0] == '#'));
- sscanf(line, "%15d%15lf", &(fr->step), &db1);
- fr->time = db1;
- }
- else
- {
- bFinished = TRUE;
- }
- }
- if (bPos)
- {
- if (!fr->bX)
- {
- fr->bAtoms = bAtoms;
- fr->bX = bPos;
- natoms = read_g96_pos(line, symtab, fp, infile, fr);
- }
- else
- {
- bFinished = TRUE;
- }
- }
- if (fr->v && bVel)
- {
- fr->bV = bVel;
- natoms = read_g96_vel(line, fp, infile, fr);
- }
- if (bBox)
- {
- fr->bBox = bBox;
- clear_mat(fr->box);
- bEnd = FALSE;
- while (!bEnd && fgets2(line, STRLEN, fp))
- {
- bEnd = (strncmp(line, "END", 3) == 0);
- if (!bEnd && (line[0] != '#'))
- {
- nbp = sscanf(line, "%15lf%15lf%15lf%15lf%15lf%15lf%15lf%15lf%15lf",
- &db1, &db2, &db3, &db4, &db5, &db6, &db7, &db8, &db9);
- if (nbp < 3)
- {
- gmx_fatal(FARGS, "Found a BOX line, but no box in %s", infile);
- }
- fr->box[XX][XX] = db1;
- fr->box[YY][YY] = db2;
- fr->box[ZZ][ZZ] = db3;
- if (nbp == 9)
- {
- fr->box[XX][YY] = db4;
- fr->box[XX][ZZ] = db5;
- fr->box[YY][XX] = db6;
- fr->box[YY][ZZ] = db7;
- fr->box[ZZ][XX] = db8;
- fr->box[ZZ][YY] = db9;
- }
- }
- }
- bFinished = TRUE;
- }
- }
- while (!bFinished && fgets2(line, STRLEN, fp));
-
- free_symtab(symtab);
-
- fr->natoms = natoms;
-
- return natoms;
-}
-
-void write_g96_conf(FILE *out, t_trxframe *fr,
- int nindex, const atom_id *index)
-{
- t_atoms *atoms;
- int nout, i, a;
-
- atoms = fr->atoms;
-
- if (index)
- {
- nout = nindex;
- }
- else
- {
- nout = fr->natoms;
- }
-
- if (fr->bTitle)
- {
- fprintf(out, "TITLE\n%s\nEND\n", fr->title);
- }
- if (fr->bStep || fr->bTime)
- {
- /* Officially the time format is %15.9, which is not enough for 10 ns */
- fprintf(out, "TIMESTEP\n%15d%15.6f\nEND\n", fr->step, fr->time);
- }
- if (fr->bX)
- {
- if (fr->bAtoms)
- {
- fprintf(out, "POSITION\n");
- for (i = 0; i < nout; i++)
- {
- if (index)
- {
- a = index[i];
- }
- else
- {
- a = i;
- }
- fprintf(out, "%5d %-5s %-5s%7d%15.9f%15.9f%15.9f\n",
- (atoms->resinfo[atoms->atom[a].resind].nr) % 100000,
- *atoms->resinfo[atoms->atom[a].resind].name,
- *atoms->atomname[a], (i+1) % 10000000,
- fr->x[a][XX], fr->x[a][YY], fr->x[a][ZZ]);
- }
- }
- else
- {
- fprintf(out, "POSITIONRED\n");
- for (i = 0; i < nout; i++)
- {
- if (index)
- {
- a = index[i];
- }
- else
- {
- a = i;
- }
- fprintf(out, "%15.9f%15.9f%15.9f\n",
- fr->x[a][XX], fr->x[a][YY], fr->x[a][ZZ]);
- }
- }
- fprintf(out, "END\n");
- }
- if (fr->bV)
- {
- if (fr->bAtoms)
- {
- fprintf(out, "VELOCITY\n");
- for (i = 0; i < nout; i++)
- {
- if (index)
- {
- a = index[i];
- }
- else
- {
- a = i;
- }
- fprintf(out, "%5d %-5s %-5s%7d%15.9f%15.9f%15.9f\n",
- (atoms->resinfo[atoms->atom[a].resind].nr) % 100000,
- *atoms->resinfo[atoms->atom[a].resind].name,
- *atoms->atomname[a], (i+1) % 10000000,
- fr->v[a][XX], fr->v[a][YY], fr->v[a][ZZ]);
- }
- }
- else
- {
- fprintf(out, "VELOCITYRED\n");
- for (i = 0; i < nout; i++)
- {
- if (index)
- {
- a = index[i];
- }
- else
- {
- a = i;
- }
- fprintf(out, "%15.9f%15.9f%15.9f\n",
- fr->v[a][XX], fr->v[a][YY], fr->v[a][ZZ]);
- }
- }
- fprintf(out, "END\n");
- }
- if (fr->bBox)
- {
- fprintf(out, "BOX\n");
- fprintf(out, "%15.9f%15.9f%15.9f",
- fr->box[XX][XX], fr->box[YY][YY], fr->box[ZZ][ZZ]);
- if (fr->box[XX][YY] || fr->box[XX][ZZ] || fr->box[YY][XX] ||
- fr->box[YY][ZZ] || fr->box[ZZ][XX] || fr->box[ZZ][YY])
- {
- fprintf(out, "%15.9f%15.9f%15.9f%15.9f%15.9f%15.9f",
- fr->box[XX][YY], fr->box[XX][ZZ], fr->box[YY][XX],
- fr->box[YY][ZZ], fr->box[ZZ][XX], fr->box[ZZ][YY]);
- }
- fprintf(out, "\n");
- fprintf(out, "END\n");
- }
-}
-
-static int get_espresso_word(FILE *fp, char word[])
-{
- int ret, nc, i;
-
- ret = 0;
- nc = 0;
-
- do
- {
- i = fgetc(fp);
- if (i != EOF)
- {
- if (i == ' ' || i == '\n' || i == '\t')
- {
- if (nc > 0)
- {
- ret = 1;
- }
- }
- else if (i == '{')
- {
- if (nc == 0)
- {
- word[nc++] = '{';
- }
- ret = 2;
- }
- else if (i == '}')
- {
- if (nc == 0)
- {
- word[nc++] = '}';
- }
- ret = 3;
- }
- else
- {
- word[nc++] = (char)i;
- }
- }
- }
- while (i != EOF && ret == 0);
-
- word[nc] = '\0';
-
- /* printf("'%s'\n",word); */
-
- return ret;
-}
-
-static int check_open_parenthesis(FILE *fp, int r,
- const char *infile, const char *keyword)
-{
- int level_inc;
- char word[STRLEN];
-
- level_inc = 0;
- if (r == 2)
- {
- level_inc++;
- }
- else
- {
- r = get_espresso_word(fp, word);
- if (r == 2)
- {
- level_inc++;
- }
- else
- {
- gmx_fatal(FARGS, "Expected '{' after '%s' in file '%s'",
- keyword, infile);
- }
- }
-
- return level_inc;
-}
-
-static int check_close_parenthesis(FILE *fp, int r,
- const char *infile, const char *keyword)
-{
- int level_inc;
- char word[STRLEN];
-
- level_inc = 0;
- if (r == 3)
- {
- level_inc--;
- }
- else
- {
- r = get_espresso_word(fp, word);
- if (r == 3)
- {
- level_inc--;
- }
- else
- {
- gmx_fatal(FARGS, "Expected '}' after section '%s' in file '%s'",
- keyword, infile);
- }
- }
-
- return level_inc;
-}
-
-enum {
- espID, espPOS, espTYPE, espQ, espV, espF, espMOLECULE, espNR
-};
-const char *esp_prop[espNR] = {
- "id", "pos", "type", "q", "v", "f",
- "molecule"
-};
-
-static void read_espresso_conf(const char *infile, char *title,
- t_atoms *atoms, rvec x[], rvec *v, matrix box)
-{
- t_symtab *symtab = NULL;
- FILE *fp;
- char word[STRLEN], buf[STRLEN];
- int level, r, nprop, p, i, m, molnr;
- int prop[32];
- double d;
- gmx_bool bFoundParticles, bFoundProp, bFoundVariable, bMol;
-
- if (!symtab)
- {
- snew(symtab, 1);
- open_symtab(symtab);
- }
- // TODO: The code does not understand titles it writes...
- title[0] = '\0';
-
- clear_mat(box);
-
- fp = gmx_fio_fopen(infile, "r");
-
- bFoundParticles = FALSE;
- bFoundVariable = FALSE;
- bMol = FALSE;
- level = 0;
- while ((r = get_espresso_word(fp, word)))
- {
- if (level == 1 && std::strcmp(word, "particles") == 0 && !bFoundParticles)
- {
- bFoundParticles = TRUE;
- level += check_open_parenthesis(fp, r, infile, "particles");
- nprop = 0;
- while (level == 2 && (r = get_espresso_word(fp, word)))
- {
- bFoundProp = FALSE;
- for (p = 0; p < espNR; p++)
- {
- if (strcmp(word, esp_prop[p]) == 0)
- {
- bFoundProp = TRUE;
- prop[nprop++] = p;
- /* printf(" prop[%d] = %s\n",nprop-1,esp_prop[prop[nprop-1]]); */
- }
- }
- if (!bFoundProp && word[0] != '}')
- {
- gmx_fatal(FARGS, "Can not read Espresso files with particle property '%s'", word);
- }
- if (bFoundProp && p == espMOLECULE)
- {
- bMol = TRUE;
- }
- if (r == 3)
- {
- level--;
- }
- }
-
- i = 0;
- while (level > 0 && (r = get_espresso_word(fp, word)))
- {
- if (r == 2)
- {
- level++;
- }
- else if (r == 3)
- {
- level--;
- }
- if (level == 2)
- {
- for (p = 0; p < nprop; p++)
- {
- switch (prop[p])
- {
- case espID:
- r = get_espresso_word(fp, word);
- /* Not used */
- break;
- case espPOS:
- for (m = 0; m < 3; m++)
- {
- r = get_espresso_word(fp, word);
- sscanf(word, "%lf", &d);
- x[i][m] = d;
- }
- break;
- case espTYPE:
- r = get_espresso_word(fp, word);
- atoms->atom[i].type = std::strtol(word, NULL, 10);
- break;
- case espQ:
- r = get_espresso_word(fp, word);
- sscanf(word, "%lf", &d);
- atoms->atom[i].q = d;
- break;
- case espV:
- for (m = 0; m < 3; m++)
- {
- r = get_espresso_word(fp, word);
- sscanf(word, "%lf", &d);
- v[i][m] = d;
- }
- break;
- case espF:
- for (m = 0; m < 3; m++)
- {
- r = get_espresso_word(fp, word);
- /* not used */
- }
- break;
- case espMOLECULE:
- r = get_espresso_word(fp, word);
- molnr = std::strtol(word, NULL, 10);
- if (i == 0 ||
- atoms->resinfo[atoms->atom[i-1].resind].nr != molnr)
- {
- atoms->atom[i].resind =
- (i == 0 ? 0 : atoms->atom[i-1].resind+1);
- atoms->resinfo[atoms->atom[i].resind].nr = molnr;
- atoms->resinfo[atoms->atom[i].resind].ic = ' ';
- atoms->resinfo[atoms->atom[i].resind].chainid = ' ';
- atoms->resinfo[atoms->atom[i].resind].chainnum = molnr; /* Not sure if this is right? */
- }
- else
- {
- atoms->atom[i].resind = atoms->atom[i-1].resind;
- }
- break;
- }
- }
- /* Generate an atom name from the particle type */
- sprintf(buf, "T%d", atoms->atom[i].type);
- atoms->atomname[i] = put_symtab(symtab, buf);
- if (bMol)
- {
- if (i == 0 || atoms->atom[i].resind != atoms->atom[i-1].resind)
- {
- atoms->resinfo[atoms->atom[i].resind].name =
- put_symtab(symtab, "MOL");
- }
- }
- else
- {
- /* Residue number is the atom number */
- atoms->atom[i].resind = i;
- /* Generate an residue name from the particle type */
- if (atoms->atom[i].type < 26)
- {
- sprintf(buf, "T%c", 'A'+atoms->atom[i].type);
- }
- else
- {
- sprintf(buf, "T%c%c",
- 'A'+atoms->atom[i].type/26, 'A'+atoms->atom[i].type%26);
- }
- t_atoms_set_resinfo(atoms, i, symtab, buf, i, ' ', 0, ' ');
- }
-
- if (r == 3)
- {
- level--;
- }
- i++;
- }
- }
- atoms->nres = atoms->nr;
-
- if (i != atoms->nr)
- {
- gmx_fatal(FARGS, "Internal inconsistency in Espresso routines, read %d atoms, expected %d atoms", i, atoms->nr);
- }
- }
- else if (level == 1 && std::strcmp(word, "variable") == 0 && !bFoundVariable)
- {
- bFoundVariable = TRUE;
- level += check_open_parenthesis(fp, r, infile, "variable");
- while (level == 2 && (r = get_espresso_word(fp, word)))
- {
- if (level == 2 && std::strcmp(word, "box_l") == 0)
- {
- for (m = 0; m < 3; m++)
- {
- r = get_espresso_word(fp, word);
- sscanf(word, "%lf", &d);
- box[m][m] = d;
- }
- level += check_close_parenthesis(fp, r, infile, "box_l");
- }
- }
- }
- else if (r == 2)
- {
- level++;
- }
- else if (r == 3)
- {
- level--;
- }
- }
-
- if (!bFoundParticles)
- {
- fprintf(stderr, "Did not find a particles section in Espresso file '%s'\n",
- infile);
- }
-
- gmx_fio_fclose(fp);
-}
-
-static int get_espresso_coordnum(const char *infile)
-{
- FILE *fp;
- char word[STRLEN];
- int natoms, level, r;
- gmx_bool bFoundParticles;
-
- natoms = 0;
-
- fp = gmx_fio_fopen(infile, "r");
-
- bFoundParticles = FALSE;
- level = 0;
- while ((r = get_espresso_word(fp, word)) && !bFoundParticles)
- {
- if (level == 1 && strcmp(word, "particles") == 0 && !bFoundParticles)
- {
- bFoundParticles = TRUE;
- level += check_open_parenthesis(fp, r, infile, "particles");
- while (level > 0 && (r = get_espresso_word(fp, word)))
- {
- if (r == 2)
- {
- level++;
- if (level == 2)
- {
- natoms++;
- }
- }
- else if (r == 3)
- {
- level--;
- }
- }
- }
- else if (r == 2)
- {
- level++;
- }
- else if (r == 3)
- {
- level--;
- }
- }
- if (!bFoundParticles)
- {
- fprintf(stderr, "Did not find a particles section in Espresso file '%s'\n",
- infile);
- }
-
- gmx_fio_fclose(fp);
-
- return natoms;
-}
-
-static void write_espresso_conf_indexed(FILE *out, const char *title,
- t_atoms *atoms, int nx, atom_id *index,
- rvec *x, rvec *v, matrix box)
-{
- int i, j;
-
- fprintf(out, "# %s\n", title);
- if (TRICLINIC(box))
- {
- gmx_warning("The Espresso format does not support triclinic unit-cells");
- }
- fprintf(out, "{variable {box_l %f %f %f}}\n", box[0][0], box[1][1], box[2][2]);
-
- fprintf(out, "{particles {id pos type q%s}\n", v ? " v" : "");
- for (i = 0; i < nx; i++)
- {
- if (index)
- {
- j = index[i];
- }
- else
- {
- j = i;
- }
- fprintf(out, "\t{%d %f %f %f %d %g",
- j, x[j][XX], x[j][YY], x[j][ZZ],
- atoms->atom[j].type, atoms->atom[j].q);
- if (v)
- {
- fprintf(out, " %f %f %f", v[j][XX], v[j][YY], v[j][ZZ]);
- }
- fprintf(out, "}\n");
- }
- fprintf(out, "}\n");
-}
-
-static void get_coordnum_fp (FILE *in, char *title, int *natoms)
-{
- char line[STRLEN+1];
-
- fgets2 (title, STRLEN, in);
- fgets2 (line, STRLEN, in);
- if (sscanf (line, "%d", natoms) != 1)
- {
- gmx_fatal(FARGS, "gro file does not have the number of atoms on the second line");
- }
-}
-
-static void get_coordnum (const char *infile, int *natoms)
-{
- FILE *in;
- char title[STRLEN];
-
- in = gmx_fio_fopen(infile, "r");
- get_coordnum_fp(in, title, natoms);
- gmx_fio_fclose (in);
-}
-
-static gmx_bool get_w_conf(FILE *in, const char *infile, char *title,
- t_symtab *symtab, t_atoms *atoms, int *ndec,
- rvec x[], rvec *v, matrix box)
-{
- char name[6];
- char resname[6], oldresname[6];
- char line[STRLEN+1], *ptr;
- char buf[256];
- double x1, y1, z1, x2, y2, z2;
- rvec xmin, xmax;
- int natoms, i, m, resnr, newres, oldres, ddist, c;
- gmx_bool bFirst, bVel;
- char *p1, *p2, *p3;
-
- newres = -1;
- oldres = NOTSET; /* Unlikely number for the first residue! */
- ddist = 0;
-
- /* Read the title and number of atoms */
- get_coordnum_fp(in, title, &natoms);
-
- if (natoms > atoms->nr)
- {
- gmx_fatal(FARGS, "gro file contains more atoms (%d) than expected (%d)",
- natoms, atoms->nr);
- }
- else if (natoms < atoms->nr)
- {
- fprintf(stderr, "Warning: gro file contains less atoms (%d) than expected"
- " (%d)\n", natoms, atoms->nr);
- }
-
- bFirst = TRUE;
-
- bVel = FALSE;
-
- resname[0] = '\0';
- oldresname[0] = '\0';
-
- /* just pray the arrays are big enough */
- for (i = 0; (i < natoms); i++)
- {
- if ((fgets2 (line, STRLEN, in)) == NULL)
- {
- gmx_fatal(FARGS, "Unexpected end of file in file %s at line %d",
- infile, i+2);
- }
- if (strlen(line) < 39)
- {
- gmx_fatal(FARGS, "Invalid line in %s for atom %d:\n%s", infile, i+1, line);
- }
-
- /* determine read precision from distance between periods
- (decimal points) */
- if (bFirst)
- {
- bFirst = FALSE;
- p1 = strchr(line, '.');
- if (p1 == NULL)
- {
- gmx_fatal(FARGS, "A coordinate in file %s does not contain a '.'", infile);
- }
- p2 = strchr(&p1[1], '.');
- if (p2 == NULL)
- {
- gmx_fatal(FARGS, "A coordinate in file %s does not contain a '.'", infile);
- }
- ddist = p2 - p1;
- *ndec = ddist - 5;
-
- p3 = strchr(&p2[1], '.');
- if (p3 == NULL)
- {
- gmx_fatal(FARGS, "A coordinate in file %s does not contain a '.'", infile);
- }
-
- if (p3 - p2 != ddist)
- {
- gmx_fatal(FARGS, "The spacing of the decimal points in file %s is not consistent for x, y and z", infile);
- }
- }
-
- /* residue number*/
- memcpy(name, line, 5);
- name[5] = '\0';
- sscanf(name, "%d", &resnr);
- sscanf(line+5, "%5s", resname);
-
- if (resnr != oldres || strncmp(resname, oldresname, sizeof(resname)))
- {
- oldres = resnr;
- newres++;
- if (newres >= natoms)
- {
- gmx_fatal(FARGS, "More residues than atoms in %s (natoms = %d)",
- infile, natoms);
- }
- atoms->atom[i].resind = newres;
- t_atoms_set_resinfo(atoms, i, symtab, resname, resnr, ' ', 0, ' ');
- }
- else
- {
- atoms->atom[i].resind = newres;
- }
-
- /* atomname */
- std::memcpy(name, line+10, 5);
- atoms->atomname[i] = put_symtab(symtab, name);
-
- /* Copy resname to oldresname after we are done with the sanity check above */
- std::strncpy(oldresname, resname, sizeof(oldresname));
-
- /* eventueel controle atomnumber met i+1 */
-
- /* coordinates (start after residue data) */
- ptr = line + 20;
- /* Read fixed format */
- for (m = 0; m < DIM; m++)
- {
- for (c = 0; (c < ddist && ptr[0]); c++)
- {
- buf[c] = ptr[0];
- ptr++;
- }
- buf[c] = '\0';
- if (sscanf (buf, "%lf %lf", &x1, &x2) != 1)
- {
- gmx_fatal(FARGS, "Something is wrong in the coordinate formatting of file %s. Note that gro is fixed format (see the manual)", infile);
- }
- else
- {
- x[i][m] = x1;
- }
- }
-
- /* velocities (start after residues and coordinates) */
- if (v)
- {
- /* Read fixed format */
- for (m = 0; m < DIM; m++)
- {
- for (c = 0; (c < ddist && ptr[0]); c++)
- {
- buf[c] = ptr[0];
- ptr++;
- }
- buf[c] = '\0';
- if (sscanf (buf, "%lf", &x1) != 1)
- {
- v[i][m] = 0;
- }
- else
- {
- v[i][m] = x1;
- bVel = TRUE;
- }
- }
- }
- }
- atoms->nres = newres + 1;
-
- /* box */
- fgets2 (line, STRLEN, in);
- if (sscanf (line, "%lf%lf%lf", &x1, &y1, &z1) != 3)
- {
- gmx_warning("Bad box in file %s", infile);
-
- /* Generate a cubic box */
- for (m = 0; (m < DIM); m++)
- {
- xmin[m] = xmax[m] = x[0][m];
- }
- for (i = 1; (i < atoms->nr); i++)
- {
- for (m = 0; (m < DIM); m++)
- {
- xmin[m] = std::min(xmin[m], x[i][m]);
- xmax[m] = std::max(xmax[m], x[i][m]);
- }
- }
- for (i = 0; i < DIM; i++)
- {
- for (m = 0; m < DIM; m++)
- {
- box[i][m] = 0.0;
- }
- }
- for (m = 0; (m < DIM); m++)
- {
- box[m][m] = (xmax[m]-xmin[m]);
- }
- fprintf(stderr, "Generated a cubic box %8.3f x %8.3f x %8.3f\n",
- box[XX][XX], box[YY][YY], box[ZZ][ZZ]);
- }
- else
- {
- /* We found the first three values, the diagonal elements */
- box[XX][XX] = x1;
- box[YY][YY] = y1;
- box[ZZ][ZZ] = z1;
- if (sscanf (line, "%*f%*f%*f%lf%lf%lf%lf%lf%lf",
- &x1, &y1, &z1, &x2, &y2, &z2) != 6)
- {
- x1 = y1 = z1 = x2 = y2 = z2 = 0.0;
- }
- box[XX][YY] = x1;
- box[XX][ZZ] = y1;
- box[YY][XX] = z1;
- box[YY][ZZ] = x2;
- box[ZZ][XX] = y2;
- box[ZZ][YY] = z2;
- }
-
- return bVel;
-}
-
-static void read_whole_conf(const char *infile, char *title,
- t_atoms *atoms, rvec x[], rvec *v, matrix box)
-{
- FILE *in;
- int ndec;
- t_symtab symtab;
-
- /* open file */
- in = gmx_fio_fopen(infile, "r");
-
- open_symtab(&symtab);
- get_w_conf(in, infile, title, &symtab, atoms, &ndec, x, v, box);
- /* We can't free the symbols, as they are still used in atoms, so
- * the only choice is to leak them. */
- free_symtab(&symtab);
-
- gmx_fio_fclose(in);
-}
-
-static gmx_bool gmx_one_before_eof(FILE *fp)
-{
- char data[4];
- gmx_bool beof;
-
- if ((beof = fread(data, 1, 1, fp)) == 1)
- {
- gmx_fseek(fp, -1, SEEK_CUR);
- }
- return !beof;
-}
-
-gmx_bool gro_next_x_or_v(FILE *status, t_trxframe *fr)
-{
- t_atoms atoms;
- t_symtab symtab;
- char title[STRLEN], *p;
- double tt;
- int ndec = 0, i;
-
- if (gmx_one_before_eof(status))
- {
- return FALSE;
- }
-
- open_symtab(&symtab);
- atoms.nr = fr->natoms;
- snew(atoms.atom, fr->natoms);
- atoms.nres = fr->natoms;
- snew(atoms.resinfo, fr->natoms);
- snew(atoms.atomname, fr->natoms);
-
- fr->bV = get_w_conf(status, title, title, &symtab, &atoms, &ndec, fr->x, fr->v, fr->box);
- fr->bPrec = TRUE;
- fr->prec = 1;
- /* prec = 10^ndec: */
- for (i = 0; i < ndec; i++)
- {
- fr->prec *= 10;
- }
- fr->title = title;
- fr->bTitle = TRUE;
- fr->bX = TRUE;
- fr->bBox = TRUE;
-
- sfree(atoms.atom);
- sfree(atoms.resinfo);
- sfree(atoms.atomname);
- done_symtab(&symtab);
-
- if ((p = strstr(title, "t=")) != NULL)
- {
- p += 2;
- if (sscanf(p, "%lf", &tt) == 1)
- {
- fr->time = tt;
- fr->bTime = TRUE;
- }
- else
- {
- fr->time = 0;
- fr->bTime = FALSE;
- }
- }
-
- if (atoms.nr != fr->natoms)
- {
- gmx_fatal(FARGS, "Number of atoms in gro frame (%d) doesn't match the number in the previous frame (%d)", atoms.nr, fr->natoms);
- }
-
- return TRUE;
-}
-
-int gro_first_x_or_v(FILE *status, t_trxframe *fr)
-{
- char title[STRLEN];
-
- frewind(status);
- fprintf(stderr, "Reading frames from gro file");
- get_coordnum_fp(status, title, &fr->natoms);
- frewind(status);
- fprintf(stderr, " '%s', %d atoms.\n", title, fr->natoms);
- fr->bTitle = TRUE;
- fr->title = title;
- if (fr->natoms == 0)
- {
- gmx_file("No coordinates in gro file");
- }
-
- snew(fr->x, fr->natoms);
- snew(fr->v, fr->natoms);
- gro_next_x_or_v(status, fr);
-
- return fr->natoms;
-}
-
-static void make_hconf_format(int pr, gmx_bool bVel, char format[])
-{
- int l, vpr;
-
- /* build format string for printing,
- something like "%8.3f" for x and "%8.4f" for v */
- if (pr < 0)
- {
- pr = 0;
- }
- if (pr > 30)
- {
- pr = 30;
- }
- l = pr+5;
- vpr = pr+1;
- if (bVel)
- {
- sprintf(format, "%%%d.%df%%%d.%df%%%d.%df%%%d.%df%%%d.%df%%%d.%df\n",
- l, pr, l, pr, l, pr, l, vpr, l, vpr, l, vpr);
- }
- else
- {
- sprintf(format, "%%%d.%df%%%d.%df%%%d.%df\n", l, pr, l, pr, l, pr);
- }
-
-}
-
-static void write_hconf_box(FILE *out, int pr, matrix box)
-{
- char format[100];
- int l;
-
- if (pr < 5)
- {
- pr = 5;
- }
- l = pr+5;
-
- if (box[XX][YY] || box[XX][ZZ] || box[YY][XX] || box[YY][ZZ] ||
- box[ZZ][XX] || box[ZZ][YY])
- {
- sprintf(format, "%%%d.%df%%%d.%df%%%d.%df"
- "%%%d.%df%%%d.%df%%%d.%df%%%d.%df%%%d.%df%%%d.%df\n",
- l, pr, l, pr, l, pr, l, pr, l, pr, l, pr, l, pr, l, pr, l, pr);
- fprintf(out, format,
- box[XX][XX], box[YY][YY], box[ZZ][ZZ],
- box[XX][YY], box[XX][ZZ], box[YY][XX],
- box[YY][ZZ], box[ZZ][XX], box[ZZ][YY]);
- }
- else
- {
- sprintf(format, "%%%d.%df%%%d.%df%%%d.%df\n", l, pr, l, pr, l, pr);
- fprintf(out, format,
- box[XX][XX], box[YY][YY], box[ZZ][ZZ]);
- }
-}
-
-void write_hconf_indexed_p(FILE *out, const char *title, t_atoms *atoms,
- int nx, const atom_id index[], int pr,
- rvec *x, rvec *v, matrix box)
-{
- char resnm[6], nm[6], format[100];
- int ai, i, resind, resnr;
-
- bromacs(format, 99);
- fprintf (out, "%s\n", (title && title[0]) ? title : format);
- fprintf (out, "%5d\n", nx);
-
- make_hconf_format(pr, v != NULL, format);
-
- for (i = 0; (i < nx); i++)
- {
- ai = index[i];
-
- resind = atoms->atom[ai].resind;
- std::strncpy(resnm, " ??? ", sizeof(resnm)-1);
- if (resind < atoms->nres)
- {
- std::strncpy(resnm, *atoms->resinfo[resind].name, sizeof(resnm)-1);
- resnr = atoms->resinfo[resind].nr;
- }
- else
- {
- std::strncpy(resnm, " ??? ", sizeof(resnm)-1);
- resnr = resind + 1;
- }
-
- if (atoms->atom)
- {
- std::strncpy(nm, *atoms->atomname[ai], sizeof(nm)-1);
- }
- else
- {
- std::strncpy(nm, " ??? ", sizeof(nm)-1);
- }
-
- fprintf(out, "%5d%-5.5s%5.5s%5d", resnr%100000, resnm, nm, (ai+1)%100000);
- /* next fprintf uses built format string */
- if (v)
- {
- fprintf(out, format,
- x[ai][XX], x[ai][YY], x[ai][ZZ], v[ai][XX], v[ai][YY], v[ai][ZZ]);
- }
- else
- {
- fprintf(out, format,
- x[ai][XX], x[ai][YY], x[ai][ZZ]);
- }
- }
-
- write_hconf_box(out, pr, box);
-
- fflush(out);
-}
-
-static void write_hconf_mtop(FILE *out, const char *title, gmx_mtop_t *mtop,
- int pr,
- rvec *x, rvec *v, matrix box)
-{
- char format[100];
- int i, resnr;
- gmx_mtop_atomloop_all_t aloop;
- t_atom *atom;
- char *atomname, *resname;
-
- bromacs(format, 99);
- fprintf (out, "%s\n", (title && title[0]) ? title : format);
- fprintf (out, "%5d\n", mtop->natoms);
-
- make_hconf_format(pr, v != NULL, format);
-
- aloop = gmx_mtop_atomloop_all_init(mtop);
- while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
- {
- gmx_mtop_atomloop_all_names(aloop, &atomname, &resnr, &resname);
-
- fprintf(out, "%5d%-5.5s%5.5s%5d",
- resnr%100000, resname, atomname, (i+1)%100000);
- /* next fprintf uses built format string */
- if (v)
- {
- fprintf(out, format,
- x[i][XX], x[i][YY], x[i][ZZ], v[i][XX], v[i][YY], v[i][ZZ]);
- }
- else
- {
- fprintf(out, format,
- x[i][XX], x[i][YY], x[i][ZZ]);
- }
- }
-
- write_hconf_box(out, pr, box);
-
- fflush(out);
-}
-
-void write_hconf_p(FILE *out, const char *title, t_atoms *atoms, int pr,
- rvec *x, rvec *v, matrix box)
-{
- atom_id *aa;
- int i;
-
- snew(aa, atoms->nr);
- for (i = 0; (i < atoms->nr); i++)
- {
- aa[i] = i;
- }
- write_hconf_indexed_p(out, title, atoms, atoms->nr, aa, pr, x, v, box);
- sfree(aa);
-}
-
-void write_conf_p(const char *outfile, const char *title,
- t_atoms *atoms, int pr,
- rvec *x, rvec *v, matrix box)
-{
- FILE *out;
-
- out = gmx_fio_fopen(outfile, "w");
- write_hconf_p(out, title, atoms, pr, x, v, box);
-
- gmx_fio_fclose (out);
-}
-
-static void write_conf(const char *outfile, const char *title, t_atoms *atoms,
- rvec *x, rvec *v, matrix box)
-{
- write_conf_p(outfile, title, atoms, 3, x, v, box);
-}
+#include "gromacs/fileio/espio.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/g96io.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/groio.h"
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trx.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/atomprop.h"
+#include "gromacs/topology/atoms.h"
+#include "gromacs/topology/block.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/topology/symtab.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
void write_sto_conf_indexed(const char *outfile, const char *title,
t_atoms *atoms,
switch (ftp)
{
case efGRO:
- write_conf(outfile, title, atoms, x, v, box);
+ write_conf_p(outfile, title, atoms, 3, x, v, box);
break;
case efG96:
clear_trxframe(&fr, TRUE);
}
}
+static void tpx_make_chain_identifiers(t_atoms *atoms, t_block *mols)
+{
+ int m, a, a0, a1, r;
+ char c, chainid;
+ int chainnum;
+
+ /* We always assign a new chain number, but save the chain id characters
+ * for larger molecules.
+ */
+#define CHAIN_MIN_ATOMS 15
+
+ chainnum = 0;
+ chainid = 'A';
+ for (m = 0; m < mols->nr; m++)
+ {
+ a0 = mols->index[m];
+ a1 = mols->index[m+1];
+ if ((a1-a0 >= CHAIN_MIN_ATOMS) && (chainid <= 'Z'))
+ {
+ c = chainid;
+ chainid++;
+ }
+ else
+ {
+ c = ' ';
+ }
+ for (a = a0; a < a1; a++)
+ {
+ atoms->resinfo[atoms->atom[a].resind].chainnum = chainnum;
+ atoms->resinfo[atoms->atom[a].resind].chainid = c;
+ }
+ chainnum++;
+ }
+
+ /* Blank out the chain id if there was only one chain */
+ if (chainid == 'B')
+ {
+ for (r = 0; r < atoms->nres; r++)
+ {
+ atoms->resinfo[r].chainid = ' ';
+ }
+ }
+}
+
void read_stx_conf(const char *infile, char *title, t_atoms *atoms,
rvec x[], rvec *v, int *ePBC, matrix box)
{
gmx_incons("Not supported in read_stx_conf");
}
}
+
+static void done_gmx_groups_t(gmx_groups_t *g)
+{
+ int i;
+
+ for (i = 0; (i < egcNR); i++)
+ {
+ if (NULL != g->grps[i].nm_ind)
+ {
+ sfree(g->grps[i].nm_ind);
+ g->grps[i].nm_ind = NULL;
+ }
+ if (NULL != g->grpnr[i])
+ {
+ sfree(g->grpnr[i]);
+ g->grpnr[i] = NULL;
+ }
+ }
+ /* The contents of this array is in symtab, don't free it here */
+ sfree(g->grpname);
+}
+
+gmx_bool read_tps_conf(const char *infile, char *title, t_topology *top, int *ePBC,
+ rvec **x, rvec **v, matrix box, gmx_bool bMass)
+{
+ t_tpxheader header;
+ int natoms, i, version, generation;
+ gmx_bool bTop, bXNULL = FALSE;
+ gmx_mtop_t *mtop;
+ gmx_atomprop_t aps;
+
+ bTop = fn2bTPX(infile);
+ *ePBC = -1;
+ if (bTop)
+ {
+ read_tpxheader(infile, &header, TRUE, &version, &generation);
+ if (x)
+ {
+ snew(*x, header.natoms);
+ }
+ if (v)
+ {
+ snew(*v, header.natoms);
+ }
+ snew(mtop, 1);
+ *ePBC = read_tpx(infile, NULL, box, &natoms,
+ (x == NULL) ? NULL : *x, (v == NULL) ? NULL : *v, NULL, mtop);
+ *top = gmx_mtop_t_to_t_topology(mtop);
+ /* In this case we need to throw away the group data too */
+ done_gmx_groups_t(&mtop->groups);
+ sfree(mtop);
+ std::strcpy(title, *top->name);
+ tpx_make_chain_identifiers(&top->atoms, &top->mols);
+ }
+ else
+ {
+ get_stx_coordnum(infile, &natoms);
+ init_t_atoms(&top->atoms, natoms, (fn2ftp(infile) == efPDB));
+ if (x == NULL)
+ {
+ snew(x, 1);
+ bXNULL = TRUE;
+ }
+ snew(*x, natoms);
+ if (v)
+ {
+ snew(*v, natoms);
+ }
+ read_stx_conf(infile, title, &top->atoms, *x, (v == NULL) ? NULL : *v, ePBC, box);
+ if (bXNULL)
+ {
+ sfree(*x);
+ sfree(x);
+ }
+ if (bMass)
+ {
+ aps = gmx_atomprop_init();
+ for (i = 0; (i < natoms); i++)
+ {
+ if (!gmx_atomprop_query(aps, epropMass,
+ *top->atoms.resinfo[top->atoms.atom[i].resind].name,
+ *top->atoms.atomname[i],
+ &(top->atoms.atom[i].m)))
+ {
+ if (debug)
+ {
+ fprintf(debug, "Can not find mass for atom %s %d %s, setting to 1\n",
+ *top->atoms.resinfo[top->atoms.atom[i].resind].name,
+ top->atoms.resinfo[top->atoms.atom[i].resind].nr,
+ *top->atoms.atomname[i]);
+ }
+ }
+ }
+ gmx_atomprop_destroy(aps);
+ }
+ top->idef.ntypes = -1;
+ }
+
+ return bTop;
+}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff