static gmx_bool pdb_next_x(t_trxstatus *status, FILE *fp, t_trxframe *fr)
{
t_atoms atoms;
t_symtab *symtab;
matrix boxpdb;
// Initiate model_nr to -1 rather than NOTSET.
// It is not worthwhile introducing extra variables in the
// read_pdbfile call to verify that a model_nr was read.
int ePBC, model_nr = -1, na;
char title[STRLEN], *time, *step;
double dbl;
atoms.nr = fr->natoms;
atoms.atom = nullptr;
atoms.pdbinfo = nullptr;
/* the other pointers in atoms should not be accessed if these are NULL */
snew(symtab, 1);
open_symtab(symtab);
na = read_pdbfile(fp, title, &model_nr, &atoms, symtab, fr->x, &ePBC, boxpdb, TRUE, nullptr);
free_symtab(symtab);
sfree(symtab);
set_trxframe_ePBC(fr, ePBC);
if (nframes_read(status) == 0)
{
fprintf(stderr, " '%s', %d atoms\n", title, fr->natoms);
}
fr->bPrec = TRUE;
fr->prec = 10000;
fr->bX = TRUE;
fr->bBox = (boxpdb[XX][XX] != 0.0);
if (fr->bBox)
{
copy_mat(boxpdb, fr->box);
}
fr->step = 0;
step = std::strstr(title, " step= ");
fr->bStep = ((step != nullptr) && sscanf(step+7, "%" SCNd64, &fr->step) == 1);
dbl = 0.0;
time = std::strstr(title, " t= ");
fr->bTime = ((time != nullptr) && sscanf(time+4, "%lf", &dbl) == 1);
fr->time = dbl;
if (na == 0)
{
return FALSE;
}
else
{
if (na != fr->natoms)
{
gmx_fatal(FARGS, "Number of atoms in pdb frame %d is %d instead of %d",
nframes_read(status), na, fr->natoms);
}
return TRUE;
}
}
void gmx_pdb_read_conf(const char *infile,
t_topology *top, rvec x[], int *ePBC, matrix box)
{
FILE *in = gmx_fio_fopen(infile, "r");
char title[STRLEN];
read_pdbfile(in, title, NULL, &top->atoms, &top->symtab, x, ePBC, box, TRUE, NULL);
top->name = put_symtab(&top->symtab, title);
gmx_fio_fclose(in);
}
void read_pdb_conf(char *infile,char *title,
t_atoms *atoms,rvec x[],int *ePBC,matrix box,bool bChange,
gmx_conect conect)
{
FILE *in;
in = gmx_fio_fopen(infile,"r");
read_pdbfile(in,title,NULL,atoms,x,ePBC,box,bChange,conect);
gmx_fio_fclose(in);
}
void gmx_pdb_read_conf(const char *infile,
t_symtab *symtab, char ***name, t_atoms *atoms,
rvec x[], int *ePBC, matrix box)
{
FILE *in = gmx_fio_fopen(infile, "r");
char title[STRLEN];
read_pdbfile(in, title, NULL, atoms, symtab, x, ePBC, box, TRUE, NULL);
*name = put_symtab(symtab, title);
gmx_fio_fclose(in);
}
static gmx_bool pdb_next_x(t_trxstatus *status, FILE *fp,t_trxframe *fr)
{
t_atoms atoms;
matrix boxpdb;
int ePBC,model_nr,na;
char title[STRLEN],*time;
double dbl;
atoms.nr = fr->natoms;
atoms.atom=NULL;
atoms.pdbinfo=NULL;
/* the other pointers in atoms should not be accessed if these are NULL */
model_nr=NOTSET;
na=read_pdbfile(fp,title,&model_nr,&atoms,fr->x,&ePBC,boxpdb,TRUE,NULL);
set_trxframe_ePBC(fr,ePBC);
if (nframes_read(status)==0)
fprintf(stderr," '%s', %d atoms\n",title, fr->natoms);
fr->bPrec = TRUE;
fr->prec = 10000;
fr->bX = TRUE;
fr->bBox = (boxpdb[XX][XX] != 0.0);
if (fr->bBox) {
copy_mat(boxpdb,fr->box);
}
if (model_nr!=NOTSET) {
fr->bStep = TRUE;
fr->step = model_nr;
}
time=strstr(title," t= ");
if (time) {
fr->bTime = TRUE;
sscanf(time+4,"%lf",&dbl);
fr->time=(real)dbl;
} else {
fr->bTime = FALSE;
/* this is a bit dirty, but it will work: if no time is read from
comment line in pdb file, set time to current frame number */
if (fr->bStep)
fr->time=(real)fr->step;
else
fr->time=(real)nframes_read(status);
}
if (na == 0) {
return FALSE;
} else {
if (na != fr->natoms)
gmx_fatal(FARGS,"Number of atoms in pdb frame %d is %d instead of %d",
nframes_read(status),na,fr->natoms);
return TRUE;
}
}
static gmx_bool pdb_next_x(t_trxstatus *status, FILE *fp, t_trxframe *fr)
{
t_atoms atoms;
t_symtab *symtab;
matrix boxpdb;
// Initiate model_nr to -1 rather than NOTSET.
// It is not worthwhile introducing extra variables in the
// read_pdbfile call to verify that a model_nr was read.
int ePBC, model_nr = -1, na;
char title[STRLEN], *time;
double dbl;
atoms.nr = fr->natoms;
atoms.atom = NULL;
atoms.pdbinfo = NULL;
/* the other pointers in atoms should not be accessed if these are NULL */
snew(symtab, 1);
open_symtab(symtab);
na = read_pdbfile(fp, title, &model_nr, &atoms, symtab, fr->x, &ePBC, boxpdb, TRUE, NULL);
free_symtab(symtab);
sfree(symtab);
set_trxframe_ePBC(fr, ePBC);
if (nframes_read(status) == 0)
{
fprintf(stderr, " '%s', %d atoms\n", title, fr->natoms);
}
fr->bPrec = TRUE;
fr->prec = 10000;
fr->bX = TRUE;
fr->bBox = (boxpdb[XX][XX] != 0.0);
if (fr->bBox)
{
copy_mat(boxpdb, fr->box);
}
if (model_nr != -1)
{
fr->bStep = TRUE;
fr->step = model_nr;
}
time = std::strstr(title, " t= ");
if (time)
{
fr->bTime = TRUE;
sscanf(time+4, "%lf", &dbl);
fr->time = (real)dbl;
}
else
{
fr->bTime = FALSE;
/* this is a bit dirty, but it will work: if no time is read from
comment line in pdb file, set time to current frame number */
if (fr->bStep)
{
fr->time = (real)fr->step;
}
else
{
fr->time = (real)nframes_read(status);
}
}
if (na == 0)
{
return FALSE;
}
else
{
if (na != fr->natoms)
{
gmx_fatal(FARGS, "Number of atoms in pdb frame %d is %d instead of %d",
nframes_read(status), na, fr->natoms);
}
return TRUE;
}
}
