int read_ter_db(const char *ffdir, char ter,
t_hackblock **tbptr, gpp_atomtype_t atype)
{
char ext[STRLEN];
int ntb;
sprintf(ext, ".%c.tdb", ter);
/* Search for termini database files.
* Do not generate an error when none are found.
*/
std::vector<std::string> tdbf = fflib_search_file_end(ffdir, ext, FALSE);
ntb = 0;
*tbptr = nullptr;
for (const auto &filename : tdbf)
{
read_ter_db_file(filename.c_str(), &ntb, tbptr, atype);
}
if (debug)
{
print_ter_db("new", ter, ntb, *tbptr, atype);
}
return ntb;
}
t_nm2type *rd_nm2type(const char *ffdir, int *nnm)
{
std::vector<std::string> ff = fflib_search_file_end(ffdir, ".n2t", FALSE);
*nnm = 0;
t_nm2type *nm = nullptr;
for (const auto &filename : ff)
{
rd_nm2type_file(filename, nnm, &nm);
}
return nm;
}
gpp_atomtype_t read_atype(const char *ffdir, t_symtab *tab)
{
int nfile, f;
char **file;
FILE *in;
char buf[STRLEN], name[STRLEN];
double m;
int nratt = 0;
gpp_atomtype_t at;
t_atom *a;
t_param *nb;
nfile = fflib_search_file_end(ffdir, ".atp", TRUE, &file);
at = init_atomtype();
snew(a, 1);
snew(nb, 1);
for (f = 0; f < nfile; f++)
{
in = fflib_open(file[f]);
while (!feof(in))
{
/* Skip blank or comment-only lines */
do
{
if (fgets2(buf, STRLEN, in) != NULL)
{
strip_comment(buf);
trim(buf);
}
}
while (!feof(in) && strlen(buf) == 0);
if (sscanf(buf, "%s%lf", name, &m) == 2)
{
a->m = m;
add_atomtype(at, tab, a, name, nb, 0, 0.0, 0.0, 0.0, 0, 0.0, 0.0 );
fprintf(stderr, "\rAtomtype %d", ++nratt);
fflush(stderr);
}
else
{
fprintf(stderr, "\nInvalid format: %s\n", buf);
}
}
gmx_ffclose(in);
sfree(file[f]);
}
fprintf(stderr, "\n");
sfree(file);
return at;
}
t_nm2type *rd_nm2type(const char *ffdir,int *nnm)
{
int nff,f;
char **ff;
t_nm2type *nm;
nff = fflib_search_file_end(ffdir,".n2t",FALSE,&ff);
*nnm = 0;
nm = NULL;
for(f=0; f<nff; f++) {
rd_nm2type_file(ff[f],nnm,&nm);
sfree(ff[f]);
}
sfree(ff);
return nm;
}
int read_h_db(const char *ffdir,t_hackblock **ah)
{
int nhdbf,f;
char **hdbf;
int nah;
FILE *fp;
/* Read the hydrogen database file(s).
* Do not generate an error when no files are found.
*/
nhdbf = fflib_search_file_end(ffdir,".hdb",FALSE,&hdbf);
nah = 0;
*ah = NULL;
for(f=0; f<nhdbf; f++) {
read_h_db_file(hdbf[f],&nah,ah);
sfree(hdbf[f]);
}
sfree(hdbf);
return nah;
}
void rename_atoms(const char *xlfile,const char *ffdir,
t_atoms *atoms,t_symtab *symtab,const t_restp *restp,
gmx_bool bResname,gmx_residuetype_t rt,gmx_bool bReorderNum,
gmx_bool bVerbose)
{
FILE *fp;
int nxlate,a,i,resind;
t_xlate_atom *xlatom;
int nf;
char **f;
char c,*rnm,atombuf[32],*ptr0,*ptr1;
gmx_bool bReorderedNum,bRenamed,bMatch;
nxlate = 0;
xlatom = NULL;
if (xlfile != NULL)
{
fp = libopen(xlfile);
get_xlatoms(xlfile,fp,&nxlate,&xlatom);
fclose(fp);
}
else
{
nf = fflib_search_file_end(ffdir,".arn",FALSE,&f);
for(i=0; i<nf; i++)
{
fp = fflib_open(f[i]);
get_xlatoms(f[i],fp,&nxlate,&xlatom);
fclose(fp);
sfree(f[i]);
}
sfree(f);
}
for(a=0; (a<atoms->nr); a++)
{
resind = atoms->atom[a].resind;
if (bResname)
{
rnm = *(atoms->resinfo[resind].name);
}
else
{
rnm = *(atoms->resinfo[resind].rtp);
}
strcpy(atombuf,*(atoms->atomname[a]));
bReorderedNum = FALSE;
if (bReorderNum)
{
if (isdigit(atombuf[0]))
{
c = atombuf[0];
for (i=0; ((size_t)i<strlen(atombuf)-1); i++)
{
atombuf[i] = atombuf[i+1];
}
atombuf[i] = c;
bReorderedNum = TRUE;
}
}
bRenamed = FALSE;
for(i=0; (i<nxlate) && !bRenamed; i++) {
/* Check if the base file name of the rtp and arn entry match */
if (restp == NULL ||
gmx_strcasecmp(restp[resind].filebase,xlatom[i].filebase) == 0)
{
/* Match the residue name */
bMatch = (xlatom[i].res == NULL ||
(gmx_strcasecmp("protein",xlatom[i].res) == 0 &&
gmx_residuetype_is_protein(rt,rnm)) ||
(gmx_strcasecmp("DNA",xlatom[i].res) == 0 &&
gmx_residuetype_is_dna(rt,rnm)) ||
(gmx_strcasecmp("RNA",xlatom[i].res) == 0 &&
gmx_residuetype_is_rna(rt,rnm)));
if (!bMatch)
{
ptr0 = rnm;
ptr1 = xlatom[i].res;
while (ptr0[0] != '\0' && ptr1[0] != '\0' &&
(ptr0[0] == ptr1[0] || ptr1[0] == '?'))
{
ptr0++;
ptr1++;
}
bMatch = (ptr0[0] == '\0' && ptr1[0] == '\0');
}
if (bMatch && strcmp(atombuf,xlatom[i].atom) == 0)
{
/* We have a match. */
/* Don't free the old atomname,
* since it might be in the symtab.
*/
ptr0 = strdup(xlatom[i].replace);
if (bVerbose)
{
printf("Renaming atom '%s' in residue %d %s to '%s'\n",
*atoms->atomname[a],
atoms->resinfo[resind].nr,
*atoms->resinfo[resind].name,
ptr0);
}
atoms->atomname[a] = put_symtab(symtab,ptr0);
bRenamed = TRUE;
}
}
}
if (bReorderedNum && !bRenamed)
{
atoms->atomname[a] = put_symtab(symtab,atombuf);
}
}
done_xlatom(nxlate,xlatom);
}
