#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-static void get_coordnum_fp(FILE *in, char *title, int *natoms)
+static void get_coordnum_fp(FILE* in, char* title, int* natoms)
{
- char line[STRLEN+1];
+ char line[STRLEN + 1];
fgets2(title, STRLEN, in);
fgets2(line, STRLEN, in);
}
}
-void get_coordnum(const char *infile, int *natoms)
+void get_coordnum(const char* infile, int* natoms)
{
- FILE *in;
+ FILE* in;
char title[STRLEN];
in = gmx_fio_fopen(infile, "r");
* We have removed writing of variable precision to avoid compatibility
* issues with other software packages.
*/
-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)
+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, oldResFirst;
- char *p1, *p2, *p3;
+ 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, oldResFirst;
+ char * p1, *p2, *p3;
oldres = -1;
newres = -1;
if (natoms > atoms->nr)
{
- gmx_fatal(FARGS, "gro file contains more atoms (%d) than expected (%d)",
- natoms, atoms->nr);
+ gmx_fatal(FARGS, "gro file contains more atoms (%d) than expected (%d)", natoms, atoms->nr);
}
- else if (natoms < atoms->nr)
+ else if (natoms < atoms->nr)
{
- fprintf(stderr, "Warning: gro file contains less atoms (%d) than expected"
- " (%d)\n", natoms, atoms->nr);
+ fprintf(stderr,
+ "Warning: gro file contains less atoms (%d) than expected"
+ " (%d)\n",
+ natoms, atoms->nr);
}
atoms->haveMass = FALSE;
bVel = FALSE;
- resname[0] = '\0';
- oldresname[0] = '\0';
+ resname[0] = '\0';
+ oldresname[0] = '\0';
/* just pray the arrays are big enough */
for (i = 0; (i < natoms); i++)
{
if ((fgets2(line, STRLEN, in)) == nullptr)
{
- gmx_fatal(FARGS, "Unexpected end of file in file %s at line %d",
- infile, i+2);
+ 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);
+ gmx_fatal(FARGS, "Invalid line in %s for atom %d:\n%s", infile, i + 1, line);
}
/* determine read precision from distance between periods
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);
+ gmx_fatal(FARGS,
+ "The spacing of the decimal points in file %s is not consistent for x, y "
+ "and z",
+ infile);
}
}
memcpy(name, line, 5);
name[5] = '\0';
sscanf(name, "%d", &resnr);
- sscanf(line+5, "%5s", resname);
+ sscanf(line + 5, "%5s", resname);
if (!oldResFirst || oldres != resnr || strncmp(resname, oldresname, sizeof(resname)) != 0)
{
newres++;
if (newres >= natoms)
{
- gmx_fatal(FARGS, "More residues than atoms in %s (natoms = %d)",
- infile, 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, ' ');
}
/* atomname */
- std::memcpy(name, line+10, 5);
+ 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 */
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);
+ gmx_fatal(FARGS,
+ "Something is wrong in the coordinate formatting of file %s. Note that "
+ "gro is fixed format (see the manual)",
+ infile);
}
else
{
}
for (m = 0; (m < DIM); m++)
{
- box[m][m] = (xmax[m]-xmin[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]);
+ 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
{
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)
+ 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;
}
return bVel;
}
-void gmx_gro_read_conf(const char *infile,
- t_symtab *symtab, char **name, t_atoms *atoms,
- rvec x[], rvec *v, matrix box)
+void gmx_gro_read_conf(const char* infile, t_symtab* symtab, char** name, t_atoms* atoms, rvec x[], rvec* v, matrix box)
{
- FILE *in = gmx_fio_fopen(infile, "r");
+ FILE* in = gmx_fio_fopen(infile, "r");
int ndec;
char title[STRLEN];
get_w_conf(in, infile, title, symtab, atoms, &ndec, x, v, box);
gmx_fio_fclose(in);
}
-static gmx_bool gmx_one_before_eof(FILE *fp)
+static gmx_bool gmx_one_before_eof(FILE* fp)
{
char data[4];
gmx_bool beof = fread(data, 1, 1, fp) != 1;
return beof;
}
-gmx_bool gro_next_x_or_v(FILE *status, t_trxframe *fr)
+gmx_bool gro_next_x_or_v(FILE* status, t_trxframe* fr)
{
t_atoms atoms;
t_symtab symtab;
{
fr->prec *= 10;
}
- fr->bX = TRUE;
- fr->bBox = TRUE;
+ fr->bX = TRUE;
+ fr->bBox = TRUE;
sfree(atoms.atom);
sfree(atoms.resinfo);
if ((p = std::strstr(title, "step=")) != nullptr)
{
- p += 5;
+ p += 5;
fr->step = 0; // Default value if fr-bStep is false
fr->bStep = (sscanf(p, "%" SCNd64, &fr->step) == 1);
}
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);
+ 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)
+int gro_first_x_or_v(FILE* status, t_trxframe* fr)
{
char title[STRLEN];
return fr->natoms;
}
-static const char *get_hconf_format(bool haveVelocities)
+static const char* get_hconf_format(bool haveVelocities)
{
if (haveVelocities)
{
{
return "%8.3f%8.3f%8.3f\n";
}
-
}
-static void write_hconf_box(FILE *out, const matrix box)
+static void write_hconf_box(FILE* out, const matrix box)
{
- if ((box[XX][YY] != 0.0f) || (box[XX][ZZ] != 0.0f) || (box[YY][XX] != 0.0f) || (box[YY][ZZ] != 0.0f) ||
- (box[ZZ][XX] != 0.0f) || (box[ZZ][YY] != 0.0f))
+ if ((box[XX][YY] != 0.0F) || (box[XX][ZZ] != 0.0F) || (box[YY][XX] != 0.0F)
+ || (box[YY][ZZ] != 0.0F) || (box[ZZ][XX] != 0.0F) || (box[ZZ][YY] != 0.0F))
{
- fprintf(out, "%10.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f\n",
- 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]);
+ fprintf(out, "%10.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f\n", 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
{
- fprintf(out, "%10.5f %9.5f %9.5f\n",
- box[XX][XX], box[YY][YY], box[ZZ][ZZ]);
+ fprintf(out, "%10.5f %9.5f %9.5f\n", box[XX][XX], box[YY][YY], box[ZZ][ZZ]);
}
}
-void write_hconf_indexed_p(FILE *out, const char *title, const t_atoms *atoms,
- int nx, const int index[],
- const rvec *x, const rvec *v, const matrix box)
+void write_hconf_indexed_p(FILE* out,
+ const char* title,
+ const t_atoms* atoms,
+ int nx,
+ const int index[],
+ const rvec* x,
+ const rvec* v,
+ const matrix box)
{
- int ai, i, resind, resnr;
+ int ai, i, resind, resnr;
fprintf(out, "%s\n", (title && title[0]) ? title : gmx::bromacs().c_str());
fprintf(out, "%5d\n", nx);
- const char *format = get_hconf_format(v != nullptr);
+ const char* format = get_hconf_format(v != nullptr);
for (i = 0; (i < nx); i++)
{
nm = " ??? ";
}
- fprintf(out, "%5d%-5.5s%5.5s%5d", resnr%100000, resnm.c_str(), nm.c_str(), (ai+1)%100000);
+ fprintf(out, "%5d%-5.5s%5.5s%5d", resnr % 100000, resnm.c_str(), nm.c_str(), (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]);
+ 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]);
+ fprintf(out, format, x[ai][XX], x[ai][YY], x[ai][ZZ]);
}
}
fflush(out);
}
-void write_hconf_mtop(FILE *out, const char *title, gmx_mtop_t *mtop,
- const rvec *x, const rvec *v, const matrix box)
+void write_hconf_mtop(FILE* out, const char* title, const gmx_mtop_t* mtop, const rvec* x, const rvec* v, const matrix box)
{
- int i, resnr;
- gmx_mtop_atomloop_all_t aloop;
- const t_atom *atom;
- char *atomname, *resname;
-
fprintf(out, "%s\n", (title && title[0]) ? title : gmx::bromacs().c_str());
fprintf(out, "%5d\n", mtop->natoms);
- const char *format = get_hconf_format(v != nullptr);
+ const char* format = get_hconf_format(v != nullptr);
- aloop = gmx_mtop_atomloop_all_init(mtop);
- while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
+ for (const AtomProxy atomP : AtomRange(*mtop))
{
- gmx_mtop_atomloop_all_names(aloop, &atomname, &resnr, &resname);
+ int i = atomP.globalAtomNumber();
+ int residueNumber = atomP.residueNumber();
+ const char* atomName = atomP.atomName();
+ const char* residueName = atomP.residueName();
- fprintf(out, "%5d%-5.5s%5.5s%5d",
- resnr%100000, resname, atomname, (i+1)%100000);
+ fprintf(out, "%5d%-5.5s%5.5s%5d", residueNumber % 100000, residueName, 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]);
+ 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]);
+ fprintf(out, format, x[i][XX], x[i][YY], x[i][ZZ]);
}
}
fflush(out);
}
-void write_hconf_p(FILE *out, const char *title, const t_atoms *atoms,
- const rvec *x, const rvec *v, const matrix box)
+void write_hconf_p(FILE* out, const char* title, const t_atoms* atoms, const rvec* x, const rvec* v, const matrix box)
{
- int *aa;
- int i;
+ int* aa;
+ int i;
snew(aa, atoms->nr);
for (i = 0; (i < atoms->nr); i++)
sfree(aa);
}
-void write_conf_p(const char *outfile, const char *title,
- const t_atoms *atoms,
- const rvec *x, const rvec *v, const matrix box)
+void write_conf_p(const char* outfile,
+ const char* title,
+ const t_atoms* atoms,
+ const rvec* x,
+ const rvec* v,
+ const matrix box)
{
- FILE *out;
+ FILE* out;
out = gmx_fio_fopen(outfile, "w");
write_hconf_p(out, title, atoms, x, v, box);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff