#define CHAR_SHIFT 24
-static int read_g96_pos(char line[], t_symtab *symtab,
- FILE *fp, const char *infile,
- t_trxframe *fr)
+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;
+ 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;
if (fr->atoms != nullptr)
{
- GMX_RELEASE_ASSERT(symtab != nullptr, "Reading a conformation from a g96 format with atom data requires a valid symbol table");
+ GMX_RELEASE_ASSERT(symtab != nullptr,
+ "Reading a conformation from a g96 format with atom data requires a "
+ "valid symbol table");
}
atoms = fr->atoms;
if (atoms != nullptr)
{
shift = 0;
}
- newres = -1;
- oldres = -666; /* Unlikely number for the first residue! */
- bEnd = FALSE;
+ 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 (!bEnd && (line[0] != '#'))
{
- if (sscanf(line+shift, "%15lf%15lf%15lf", &db1, &db2, &db3) != 3)
+ 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);
+ 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);
+ 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 (fr->bAtoms
+ && (sscanf(line, "%5d%c%5s%c%5s%7d", &resnr, &c1, resnm, &c2, anm, &atnr) != 6))
{
if (oldres >= 0)
{
}
else
{
- resnr = 1;
- strncpy(resnm, "???", sizeof(resnm)-1);
+ resnr = 1;
+ strncpy(resnm, "???", sizeof(resnm) - 1);
}
- strncpy(anm, "???", sizeof(anm)-1);
+ strncpy(anm, "???", sizeof(anm) - 1);
}
atoms->atomname[natoms] = put_symtab(symtab, anm);
if (resnr != oldres)
newres++;
if (newres >= atoms->nr)
{
- gmx_fatal(FARGS, "More residues than atoms in %s (natoms = %d)",
- infile, 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)
+ if (newres + 1 > atoms->nres)
{
- atoms->nres = newres+1;
+ atoms->nres = newres + 1;
}
t_atoms_set_resinfo(atoms, natoms, symtab, resnm, resnr, ' ', 0, ' ');
}
}
if ((nwanted != -1) && natoms != nwanted)
{
- fprintf(stderr,
- "Warning: found less coordinates (%d) in %s than expected %d\n",
- natoms, infile, nwanted);
+ fprintf(stderr, "Warning: found less coordinates (%d) in %s than expected %d\n", natoms,
+ infile, nwanted);
}
}
return natoms;
}
-static int read_g96_vel(char line[], FILE *fp, const char *infile,
- t_trxframe *fr)
+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;
+ gmx_bool bEnd;
+ int nwanted, natoms = -1, shift;
+ double db1, db2, db3;
nwanted = fr->natoms;
bEnd = (strncmp(line, "END", 3) == 0);
if (!bEnd && (line[0] != '#'))
{
- if (sscanf(line+shift, "%15lf%15lf%15lf", &db1, &db2, &db3) != 3)
+ 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);
+ 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);
+ gmx_fatal(FARGS, "Found more velocities (%d) in %s than expected %d\n", natoms,
+ infile, nwanted);
}
if (fr->v)
{
}
if ((nwanted != -1) && (natoms != nwanted))
{
- fprintf(stderr,
- "Warning: found less velocities (%d) in %s than expected %d\n",
- natoms, infile, 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, char **name, t_trxframe *fr,
- t_symtab *symtab, char *line)
+int read_g96_conf(FILE* fp, const char* infile, char** name, t_trxframe* fr, t_symtab* symtab, char* line)
{
- gmx_bool bAtStart, bTime, bAtoms, bPos, bVel, bBox, bEnd, bFinished;
- int natoms, nbp;
- double db1, db2, db3, db4, db5, db6, db7, db8, db9;
+ 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);
do
{
bFinished = (fgets2(line, STRLEN, fp) == nullptr);
- }
- while (!bFinished && (line[0] == '#'));
+ } while (!bFinished && (line[0] == '#'));
sscanf(line, "%15" SCNd64 "%15lf", &(fr->step), &db1);
fr->time = db1;
}
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);
+ 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);
}
bFinished = TRUE;
}
- }
- while (!bFinished && (fgets2(line, STRLEN, fp) != nullptr));
+ } while (!bFinished && (fgets2(line, STRLEN, fp) != nullptr));
fr->natoms = natoms;
return natoms;
}
-void write_g96_conf(FILE *out, const char *title, const t_trxframe *fr,
- int nindex, const int *index)
+void write_g96_conf(FILE* out, const char* title, const t_trxframe* fr, int nindex, const int* index)
{
- t_atoms *atoms;
+ t_atoms* atoms;
int nout, i, a;
atoms = fr->atoms;
}
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]);
+ *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
{
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, "%15.9f%15.9f%15.9f\n", fr->x[a][XX], fr->x[a][YY], fr->x[a][ZZ]);
}
}
fprintf(out, "END\n");
}
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]);
+ *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
{
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, "%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] != 0.0F) || (fr->box[XX][ZZ] != 0.0F) || (fr->box[YY][XX] != 0.0F) ||
- (fr->box[YY][ZZ] != 0.0F) || (fr->box[ZZ][XX] != 0.0F) || (fr->box[ZZ][YY] != 0.0F))
+ 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] != 0.0F) || (fr->box[XX][ZZ] != 0.0F) || (fr->box[YY][XX] != 0.0F)
+ || (fr->box[YY][ZZ] != 0.0F) || (fr->box[ZZ][XX] != 0.0F) || (fr->box[ZZ][YY] != 0.0F))
{
- 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, "%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");
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff