#include <algorithm>
#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/g96io.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/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/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;
char *p1, *p2, *p3;
newres = -1;
- oldres = NOTSET; /* Unlikely number for the first residue! */
+ oldres = -12345; /* Unlikely number for the first residue! */
ddist = 0;
/* Read the title and number of atoms */
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff