#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/legacyheaders/copyrite.h"
#include "gromacs/math/vec.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/topology/atomprop.h"
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 = -12345; /* 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);
-}
-
void write_sto_conf_indexed(const char *outfile, const char *title,
t_atoms *atoms,
rvec x[], rvec *v, int ePBC, matrix box,
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);
#include <stdio.h>
-#include "gromacs/fileio/trx.h"
#include "gromacs/legacyheaders/types/simple.h"
/* For reading coordinate files it is assumed that enough memory
struct t_atoms;
struct t_topology;
-gmx_bool gro_next_x_or_v(FILE *status, t_trxframe *fr);
-int gro_first_x_or_v(FILE *status, t_trxframe *fr);
-/* read first/next x and/or v frame from gro file */
-
-void write_hconf_indexed_p(FILE *out, const char *title, struct t_atoms *atoms,
- int nx, const atom_id index[], int ndec,
- rvec *x, rvec *v, matrix box);
-
-void write_hconf_p(FILE *out, const char *title, struct t_atoms *atoms, int ndec,
- rvec *x, rvec *v, matrix box);
-/* Write a Gromos file with precision ndec: number of decimal places in x,
- * v has one place more. */
-
void write_sto_conf_indexed(const char *outfile, const char *title,
struct t_atoms *atoms,
rvec x[], rvec *v, int ePBC, matrix box,
}
#endif
-#endif /* GMX_FILEIO_CONFIO_H */
+#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#include "groio.h"
+
+#include <cstdio>
+#include <cstring>
+
+#include <algorithm>
+
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/trx.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/topology/atoms.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"
+
+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");
+ }
+}
+
+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 = -12345; /* 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;
+}
+
+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);
+}
+
+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);
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifndef GMX_FILEIO_GROIO_H
+#define GMX_FILEIO_GROIO_H
+
+#include <stdio.h>
+
+#include "gromacs/legacyheaders/types/simple.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+struct gmx_mtop_t;
+struct t_atoms;
+struct t_topology;
+struct t_trxframe;
+
+void get_coordnum(const char *infile, int *natoms);
+void read_whole_conf(const char *infile, char *title,
+ struct t_atoms *atoms, rvec x[], rvec *v, matrix box);
+
+gmx_bool gro_next_x_or_v(FILE *status, struct t_trxframe *fr);
+int gro_first_x_or_v(FILE *status, struct t_trxframe *fr);
+/* read first/next x and/or v frame from gro file */
+
+void write_hconf_indexed_p(FILE *out, const char *title, struct t_atoms *atoms,
+ int nx, const atom_id index[], int ndec,
+ rvec *x, rvec *v, matrix box);
+
+void write_hconf_mtop(FILE *out, const char *title, struct gmx_mtop_t *mtop, int pr,
+ rvec *x, rvec *v, matrix box);
+
+void write_hconf_p(FILE *out, const char *title, struct t_atoms *atoms, int ndec,
+ rvec *x, rvec *v, matrix box);
+/* Write a Gromos file with precision ndec: number of decimal places in x,
+ * v has one place more. */
+
+void write_conf_p(const char *outfile, const char *title,
+ struct t_atoms *atoms, int pr,
+ rvec *x, rvec *v, matrix box);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
#include "gromacs/fileio/g96io.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/gmxfio-xdr.h"
+#include "gromacs/fileio/groio.h"
#include "gromacs/fileio/pdbio.h"
#include "gromacs/fileio/timecontrol.h"
#include "gromacs/fileio/tngio.h"
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/groio.h"
#include "gromacs/fileio/pdbio.h"
#include "gromacs/gmxana/gmx_ana.h"
#include "gromacs/legacyheaders/macros.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/g96io.h"
#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/groio.h"
#include "gromacs/fileio/pdbio.h"
#include "gromacs/fileio/tngio_for_tools.h"
#include "gromacs/fileio/tpxio.h"
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff