static int get_xyz_coordnum(const char *infile)
{
- FILE *fp;
- int n;
-
- fp = gmx_fio_fopen(infile,"r");
- if (fscanf(fp,"%d",&n) != 1)
- gmx_fatal(FARGS,"Can not read number of atoms from %s",infile);
- gmx_fio_fclose(fp);
-
- return n;
+ FILE *fp;
+ int n;
+
+ fp = gmx_fio_fopen(infile, "r");
+ if (fscanf(fp, "%d", &n) != 1)
+ {
+ gmx_fatal(FARGS, "Can not read number of atoms from %s", infile);
+ }
+ gmx_fio_fclose(fp);
+
+ return n;
}
-static void read_xyz_conf(const char *infile,char *title,
- t_atoms *atoms,rvec *x)
+static void read_xyz_conf(const char *infile, char *title,
+ t_atoms *atoms, rvec *x)
{
- FILE *fp;
- int i,n;
- double xx,yy,zz;
- t_symtab *tab;
- char atomnm[32],buf[STRLEN];
-
- snew(tab,1);
- fp = gmx_fio_fopen(infile,"r");
- fgets2(buf,STRLEN-1,fp);
- if (sscanf(buf,"%d",&n) != 1)
- gmx_fatal(FARGS,"Can not read number of atoms from %s",infile);
- fgets2(buf,STRLEN-1,fp);
- strcpy(title,buf);
- for(i=0; (i<n); i++) {
- fgets2(buf,STRLEN-1,fp);
- if (sscanf(buf,"%s%lf%lf%lf",atomnm,&xx,&yy,&zz) != 4)
- gmx_fatal(FARGS,"Can not read coordinates from %s",infile);
- atoms->atomname[i] = put_symtab(tab,atomnm);
- x[i][XX] = xx*0.1;
- x[i][YY] = yy*0.1;
- x[i][ZZ] = zz*0.1;
- }
- gmx_fio_fclose(fp);
+ FILE *fp;
+ int i, n;
+ double xx, yy, zz;
+ t_symtab *tab;
+ char atomnm[32], buf[STRLEN];
+
+ snew(tab, 1);
+ fp = gmx_fio_fopen(infile, "r");
+ fgets2(buf, STRLEN-1, fp);
+ if (sscanf(buf, "%d", &n) != 1)
+ {
+ gmx_fatal(FARGS, "Can not read number of atoms from %s", infile);
+ }
+ fgets2(buf, STRLEN-1, fp);
+ strcpy(title, buf);
+ for (i = 0; (i < n); i++)
+ {
+ fgets2(buf, STRLEN-1, fp);
+ if (sscanf(buf, "%s%lf%lf%lf", atomnm, &xx, &yy, &zz) != 4)
+ {
+ gmx_fatal(FARGS, "Can not read coordinates from %s", infile);
+ }
+ atoms->atomname[i] = put_symtab(tab, atomnm);
+ x[i][XX] = xx*0.1;
+ x[i][YY] = yy*0.1;
+ x[i][ZZ] = zz*0.1;
+ }
+ gmx_fio_fclose(fp);
}
-void get_stx_coordnum(const char *infile,int *natoms)
+void get_stx_coordnum(const char *infile, int *natoms)
{
- FILE *in;
- int ftp,tpxver,tpxgen;
- t_trxframe fr;
- char g96_line[STRLEN+1];
-
- ftp=fn2ftp(infile);
- range_check(ftp,0,efNR);
- switch (ftp) {
- case efGRO:
- get_coordnum(infile, natoms);
- break;
- case efG96:
- in=gmx_fio_fopen(infile,"r");
- fr.title = NULL;
- fr.natoms = -1;
- fr.atoms = NULL;
- fr.x = NULL;
- fr.v = NULL;
- fr.f = NULL;
- *natoms=read_g96_conf(in,infile,&fr,g96_line);
- gmx_fio_fclose(in);
- break;
- case efXYZ:
- *natoms = get_xyz_coordnum(infile);
- break;
- case efPDB:
- case efBRK:
- case efENT:
- in=gmx_fio_fopen(infile,"r");
- get_pdb_coordnum(in, natoms);
- gmx_fio_fclose(in);
- break;
- case efESP:
- *natoms = get_espresso_coordnum(infile);
- break;
- case efTPA:
- case efTPB:
- case efTPR: {
- t_tpxheader tpx;
-
- read_tpxheader(infile,&tpx,TRUE,&tpxver,&tpxgen);
- *natoms = tpx.natoms;
- break;
- }
- default:
- gmx_fatal(FARGS,"File type %s not supported in get_stx_coordnum",
- ftp2ext(ftp));
- }
+ FILE *in;
+ int ftp, tpxver, tpxgen;
+ t_trxframe fr;
+ char g96_line[STRLEN+1];
+
+ ftp = fn2ftp(infile);
+ range_check(ftp, 0, efNR);
+ switch (ftp)
+ {
+ case efGRO:
+ get_coordnum(infile, natoms);
+ break;
+ case efG96:
+ in = gmx_fio_fopen(infile, "r");
+ fr.title = NULL;
+ fr.natoms = -1;
+ fr.atoms = NULL;
+ fr.x = NULL;
+ fr.v = NULL;
+ fr.f = NULL;
+ *natoms = read_g96_conf(in, infile, &fr, g96_line);
+ gmx_fio_fclose(in);
+ break;
+ case efXYZ:
+ *natoms = get_xyz_coordnum(infile);
+ break;
+ case efPDB:
+ case efBRK:
+ case efENT:
+ in = gmx_fio_fopen(infile, "r");
+ get_pdb_coordnum(in, natoms);
+ gmx_fio_fclose(in);
+ break;
+ case efESP:
+ *natoms = get_espresso_coordnum(infile);
+ break;
+ case efTPA:
+ case efTPB:
+ case efTPR:
+ {
+ t_tpxheader tpx;
+
+ read_tpxheader(infile, &tpx, TRUE, &tpxver, &tpxgen);
+ *natoms = tpx.natoms;
+ break;
+ }
+ default:
+ gmx_fatal(FARGS, "File type %s not supported in get_stx_coordnum",
+ ftp2ext(ftp));
+ }
}
-void read_stx_conf(const char *infile,char *title,t_atoms *atoms,
- rvec x[],rvec *v,int *ePBC,matrix box)
+void read_stx_conf(const char *infile, char *title, t_atoms *atoms,
+ rvec x[], rvec *v, int *ePBC, matrix box)
{
- FILE *in;
- char buf[256];
- gmx_mtop_t *mtop;
- t_topology top;
- t_trxframe fr;
- int i,ftp,natoms;
- real d;
- char g96_line[STRLEN+1];
-
- if (atoms->nr == 0)
- fprintf(stderr,"Warning: Number of atoms in %s is 0\n",infile);
- else if (atoms->atom == NULL)
- gmx_mem("Uninitialized array atom");
-
- if (ePBC)
- *ePBC = -1;
-
- ftp=fn2ftp(infile);
- switch (ftp) {
- case efGRO:
- read_whole_conf(infile, title, atoms, x, v, box);
- break;
- case efXYZ:
- read_xyz_conf(infile,title,atoms,x);
- break;
- case efG96:
- fr.title = NULL;
- fr.natoms = atoms->nr;
- fr.atoms = atoms;
- fr.x = x;
- fr.v = v;
- fr.f = NULL;
- in = gmx_fio_fopen(infile,"r");
- read_g96_conf(in, infile, &fr, g96_line);
- gmx_fio_fclose(in);
- copy_mat(fr.box,box);
- strncpy(title, fr.title, STRLEN);
- break;
- case efPDB:
- case efBRK:
- case efENT:
- read_pdb_conf(infile, title, atoms, x, ePBC, box, TRUE, NULL);
- break;
- case efESP:
- read_espresso_conf(infile,atoms,x,v,box);
- break;
- case efTPR:
- case efTPB:
- case efTPA:
- snew(mtop,1);
- i = read_tpx(infile,NULL,box,&natoms,x,v,NULL,mtop);
+ FILE *in;
+ char buf[256];
+ gmx_mtop_t *mtop;
+ t_topology top;
+ t_trxframe fr;
+ int i, ftp, natoms;
+ real d;
+ char g96_line[STRLEN+1];
+
+ if (atoms->nr == 0)
+ {
+ fprintf(stderr, "Warning: Number of atoms in %s is 0\n", infile);
+ }
+ else if (atoms->atom == NULL)
+ {
+ gmx_mem("Uninitialized array atom");
+ }
+
if (ePBC)
- *ePBC = i;
-
- strcpy(title,*(mtop->name));
-
- /* Free possibly allocated memory */
- done_atom(atoms);
-
- *atoms = gmx_mtop_global_atoms(mtop);
- top = gmx_mtop_t_to_t_topology(mtop);
- tpx_make_chain_identifiers(atoms,&top.mols);
-
- sfree(mtop);
- /* The strings in the symtab are still in use in the returned t_atoms
- * structure, so we should not free them. But there is no place to put the
- * symbols; the only choice is to leak the memory...
- * So we clear the symbol table before freeing the topology structure. */
- free_symtab(&top.symtab);
- done_top(&top);
-
- break;
- default:
- gmx_incons("Not supported in read_stx_conf");
- }
-}
+ {
+ *ePBC = -1;
+ }
- fr.title = title;
+ ftp = fn2ftp(infile);
+ switch (ftp)
+ {
+ case efGRO:
+ read_whole_conf(infile, title, atoms, x, v, box);
+ break;
+ case efXYZ:
+ read_xyz_conf(infile, title, atoms, x);
+ break;
+ case efG96:
++ fr.title = NULL;
+ fr.natoms = atoms->nr;
+ fr.atoms = atoms;
+ fr.x = x;
+ fr.v = v;
+ fr.f = NULL;
+ in = gmx_fio_fopen(infile, "r");
+ read_g96_conf(in, infile, &fr, g96_line);
+ gmx_fio_fclose(in);
+ copy_mat(fr.box, box);
++ strncpy(title, fr.title, STRLEN);
+ break;
+ case efPDB:
+ case efBRK:
+ case efENT:
+ read_pdb_conf(infile, title, atoms, x, ePBC, box, TRUE, NULL);
+ break;
+ case efESP:
+ read_espresso_conf(infile, atoms, x, v, box);
+ break;
+ case efTPR:
+ case efTPB:
+ case efTPA:
+ snew(mtop, 1);
+ i = read_tpx(infile, NULL, box, &natoms, x, v, NULL, mtop);
+ if (ePBC)
+ {
+ *ePBC = i;
+ }
+
+ strcpy(title, *(mtop->name));
+
+ /* Free possibly allocated memory */
+ done_atom(atoms);
+
+ *atoms = gmx_mtop_global_atoms(mtop);
+ top = gmx_mtop_t_to_t_topology(mtop);
+ tpx_make_chain_identifiers(atoms, &top.mols);
+
+ sfree(mtop);
+ /* The strings in the symtab are still in use in the returned t_atoms
+ * structure, so we should not free them. But there is no place to put the
+ * symbols; the only choice is to leak the memory...
+ * So we clear the symbol table before freeing the topology structure. */
+ free_symtab(&top.symtab);
+ done_top(&top);
+
+ break;
+ default:
+ gmx_incons("Not supported in read_stx_conf");
+ }
+}
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff