int read_h_db(char *fn,t_hackblock **ah)
{
FILE *in;
char hfn[STRLEN], line[STRLEN], buf[STRLEN];
int i, n, nab, nah;
t_hackblock *aah;
sprintf(hfn,"%s.hdb",fn);
in=libopen(hfn);
if (debug) fprintf(debug,"Hydrogen Database (%s):\n",hfn);
nah=0;
aah=NULL;
while (fgets2(line,STRLEN-1,in)) {
if (sscanf(line,"%s%n",buf,&n) != 1) {
fprintf(stderr,"Error in hdb file: nah = %d\nline = '%s'\n",
nah,line);
break;
}
if (debug) fprintf(debug,"%s",buf);
srenew(aah,nah+1);
clear_t_hackblock(&aah[nah]);
aah[nah].name=strdup(buf);
if (sscanf(line+n,"%d",&nab) == 1) {
if (debug) fprintf(debug," %d\n",nab);
snew(aah[nah].hack,nab);
aah[nah].nhack = nab;
for(i=0; (i<nab); i++) {
if (feof(in))
gmx_fatal(FARGS, "Expected %d lines of hydrogens, found only %d "
"while reading Hydrogen Database %s residue %s",
nab, i-1, aah[nah].name, hfn);
if(NULL==fgets(buf, STRLEN, in))
{
gmx_fatal(FARGS,"Error reading from file %s",fn);
}
read_ab(buf,hfn,&(aah[nah].hack[i]));
}
}
nah++;
}
fclose(in);
/* Sort the list (necessary to be able to use bsearch */
qsort(aah,nah,(size_t)sizeof(**ah),compaddh);
if (debug)
dump_h_db(fn,nah,aah);
*ah=aah;
return nah;
}
int read_ter_db(char *FF,char ter,t_hackblock **tbptr,gpp_atomtype_t atype)
{
FILE *in;
char inf[STRLEN],header[STRLEN],buf[STRLEN],line[STRLEN];
t_hackblock *tb;
int i,j,n,ni,kwnr,nb,maxnb,nh;
sprintf(inf,"%s-%c.tdb",FF,ter);
in=libopen(inf);
if (debug)
fprintf(debug,"Opened %s\n",inf);
tb=NULL;
nb=-1;
maxnb=0;
kwnr=NOTSET;
get_a_line(in,line,STRLEN);
while (!feof(in)) {
if (get_header(line,header)) {
/* this is a new block, or a new keyword */
kwnr=find_kw(header);
if (kwnr == NOTSET) {
nb++;
/* here starts a new block */
if ( nb >= maxnb ) {
maxnb+=100;
srenew(tb,maxnb);
}
clear_t_hackblock(&tb[nb]);
tb[nb].name=strdup(header);
}
} else {
if (nb < 0)
gmx_fatal(FARGS,"reading termini database: "
"directive expected before line:\n%s\n"
"This might be a file in an old format.",line);
/* this is not a header, so it must be data */
if (kwnr >= ebtsNR) {
/* this is a hack: add/rename/delete atoms */
/* make space for hacks */
if (tb[nb].nhack >= tb[nb].maxhack) {
tb[nb].maxhack+=10;
srenew(tb[nb].hack, tb[nb].maxhack);
}
nh=tb[nb].nhack;
clear_t_hack(&(tb[nb].hack[nh]));
for(i=0; i<4; i++)
tb[nb].hack[nh].a[i]=NULL;
tb[nb].nhack++;
/* get data */
n=0;
if ( kwnr==ekwRepl || kwnr==ekwDel ) {
if (sscanf(line, "%s%n", buf, &n) != 1)
gmx_fatal(FARGS,"Reading Termini Database: "
"expected atom name on line\n%s",line);
tb[nb].hack[nh].oname = strdup(buf);
/* we only replace or delete one atom at a time */
tb[nb].hack[nh].nr = 1;
} else if ( kwnr==ekwAdd ) {
read_ab(line, inf, &(tb[nb].hack[nh]));
get_a_line(in, line, STRLEN);
} else
gmx_fatal(FARGS,"unimplemented keyword number %d (%s:%d)",
kwnr,__FILE__,__LINE__);
if ( kwnr==ekwRepl || kwnr==ekwAdd ) {
snew(tb[nb].hack[nh].atom, 1);
read_atom(line+n, tb[nb].hack[nh].atom, atype,
&tb[nb].hack[nh].cgnr);
if (!tb[nb].hack[nh].nname) {
if (tb[nb].hack[nh].oname)
tb[nb].hack[nh].nname = strdup(tb[nb].hack[nh].oname);
else
gmx_fatal(FARGS,"Don't know which name the new atom should have");
}
}
} else if (kwnr >= 0 && kwnr < ebtsNR) {
/* this is bonded data: bonds, angles, dihedrals or impropers */
srenew(tb[nb].rb[kwnr].b,tb[nb].rb[kwnr].nb+1);
n=0;
for(j=0; j<btsNiatoms[kwnr]; j++) {
if ( sscanf(line+n, "%s%n", buf, &ni) == 1 )
tb[nb].rb[kwnr].b[tb[nb].rb[kwnr].nb].a[j] = strdup(buf);
else
gmx_fatal(FARGS,"Reading Termini Database: expected %d atom names (found %d) on line\n%s", btsNiatoms[kwnr], j-1, line);
n+=ni;
}
for( ; j<MAXATOMLIST; j++)
tb[nb].rb[kwnr].b[tb[nb].rb[kwnr].nb].a[j] = NULL;
strcpy(buf, "");
sscanf(line+n, "%s", buf);
tb[nb].rb[kwnr].b[tb[nb].rb[kwnr].nb].s = strdup(buf);
tb[nb].rb[kwnr].nb++;
} else
gmx_fatal(FARGS,"Reading Termini Database: Expecting a header at line\n"
"%s",line);
}
get_a_line(in,line,STRLEN);
}
nb++;
srenew(tb,nb);
fclose(in);
if (debug)
print_ter_db(FF,ter,nb,tb,atype);
*tbptr=tb;
return nb;
}
static void read_h_db_file(const char *hfn,int *nahptr,t_hackblock **ah)
{
FILE *in;
char filebase[STRLEN],line[STRLEN], buf[STRLEN];
int i, n, nab, nah;
t_hackblock *aah;
if (debug) fprintf(debug,"Hydrogen Database (%s):\n",hfn);
fflib_filename_base(hfn,filebase,STRLEN);
/* Currently filebase is read and set, but not used.
* hdb entries from any hdb file and be applied to rtp entries
* in any rtp file.
*/
in = fflib_open(hfn);
nah = *nahptr;
aah = *ah;
while (fgets2(line,STRLEN-1,in)) {
if (sscanf(line,"%s%n",buf,&n) != 1) {
fprintf(stderr,"Error in hdb file: nah = %d\nline = '%s'\n",
nah,line);
break;
}
if (debug) fprintf(debug,"%s",buf);
srenew(aah,nah+1);
clear_t_hackblock(&aah[nah]);
aah[nah].name = strdup(buf);
aah[nah].filebase = strdup(filebase);
if (sscanf(line+n,"%d",&nab) == 1) {
if (debug) fprintf(debug," %d\n",nab);
snew(aah[nah].hack,nab);
aah[nah].nhack = nab;
for(i=0; (i<nab); i++) {
if (feof(in))
gmx_fatal(FARGS, "Expected %d lines of hydrogens, found only %d "
"while reading Hydrogen Database %s residue %s",
nab, i-1, aah[nah].name, hfn);
if(NULL==fgets(buf, STRLEN, in))
{
gmx_fatal(FARGS,"Error reading from file %s",hfn);
}
read_ab(buf,hfn,&(aah[nah].hack[i]));
}
}
nah++;
}
ffclose(in);
/* Sort the list (necessary to be able to use bsearch */
qsort(aah,nah,(size_t)sizeof(**ah),compaddh);
/*
if (debug)
dump_h_db(hfn,nah,aah);
*/
*nahptr = nah;
*ah = aah;
}
static void read_ter_db_file(const char *fn,
int *ntbptr, t_hackblock **tbptr,
gpp_atomtype_t atype)
{
char filebase[STRLEN], *ptr;
FILE *in;
char header[STRLEN], buf[STRLEN], line[STRLEN];
t_hackblock *tb;
int i, j, n, ni, kwnr, nb, maxnb, nh;
fflib_filename_base(fn, filebase, STRLEN);
/* Remove the C/N termini extension */
ptr = strrchr(filebase, '.');
if (ptr != nullptr)
{
ptr[0] = '\0';
}
in = fflib_open(fn);
tb = *tbptr;
nb = *ntbptr - 1;
maxnb = 0;
kwnr = NOTSET;
get_a_line(in, line, STRLEN);
while (!feof(in))
{
if (get_header(line, header))
{
/* this is a new block, or a new keyword */
kwnr = find_kw(header);
if (kwnr == NOTSET)
{
nb++;
/* here starts a new block */
if (nb >= maxnb)
{
maxnb = nb + 100;
srenew(tb, maxnb);
}
clear_t_hackblock(&tb[nb]);
tb[nb].name = gmx_strdup(header);
tb[nb].filebase = gmx_strdup(filebase);
}
}
else
{
if (nb < 0)
{
gmx_fatal(FARGS, "reading termini database: "
"directive expected before line:\n%s\n"
"This might be a file in an old format.", line);
}
/* this is not a header, so it must be data */
if (kwnr >= ebtsNR)
{
/* this is a hack: add/rename/delete atoms */
/* make space for hacks */
if (tb[nb].nhack >= tb[nb].maxhack)
{
tb[nb].maxhack += 10;
srenew(tb[nb].hack, tb[nb].maxhack);
}
nh = tb[nb].nhack;
clear_t_hack(&(tb[nb].hack[nh]));
for (i = 0; i < 4; i++)
{
tb[nb].hack[nh].a[i] = nullptr;
}
tb[nb].nhack++;
/* get data */
n = 0;
if (kwnr == ekwRepl || kwnr == ekwDel)
{
if (sscanf(line, "%s%n", buf, &n) != 1)
{
gmx_fatal(FARGS, "Reading Termini Database '%s': "
"expected atom name on line\n%s", fn, line);
}
tb[nb].hack[nh].oname = gmx_strdup(buf);
/* we only replace or delete one atom at a time */
tb[nb].hack[nh].nr = 1;
}
else if (kwnr == ekwAdd)
{
read_ab(line, fn, &(tb[nb].hack[nh]));
get_a_line(in, line, STRLEN);
}
else
{
gmx_fatal(FARGS, "unimplemented keyword number %d (%s:%d)",
kwnr, __FILE__, __LINE__);
}
if (kwnr == ekwRepl || kwnr == ekwAdd)
{
snew(tb[nb].hack[nh].atom, 1);
read_atom(line+n, kwnr == ekwAdd,
&tb[nb].hack[nh].nname, tb[nb].hack[nh].atom, atype,
&tb[nb].hack[nh].cgnr);
if (tb[nb].hack[nh].nname == nullptr)
{
if (tb[nb].hack[nh].oname != nullptr)
{
tb[nb].hack[nh].nname = gmx_strdup(tb[nb].hack[nh].oname);
}
else
{
gmx_fatal(FARGS, "Reading Termini Database '%s': don't know which name the new atom should have on line\n%s", fn, line);
}
}
}
}
else if (kwnr >= 0 && kwnr < ebtsNR)
{
/* this is bonded data: bonds, angles, dihedrals or impropers */
srenew(tb[nb].rb[kwnr].b, tb[nb].rb[kwnr].nb+1);
n = 0;
for (j = 0; j < btsNiatoms[kwnr]; j++)
{
if (sscanf(line+n, "%s%n", buf, &ni) == 1)
{
tb[nb].rb[kwnr].b[tb[nb].rb[kwnr].nb].a[j] = gmx_strdup(buf);
}
else
{
gmx_fatal(FARGS, "Reading Termini Database '%s': expected %d atom names (found %d) on line\n%s", fn, btsNiatoms[kwnr], j-1, line);
}
n += ni;
}
for (; j < MAXATOMLIST; j++)
{
tb[nb].rb[kwnr].b[tb[nb].rb[kwnr].nb].a[j] = nullptr;
}
strcpy(buf, "");
sscanf(line+n, "%s", buf);
tb[nb].rb[kwnr].b[tb[nb].rb[kwnr].nb].s = gmx_strdup(buf);
tb[nb].rb[kwnr].nb++;
}
else
{
gmx_fatal(FARGS, "Reading Termini Database: Expecting a header at line\n"
"%s", line);
}
}
get_a_line(in, line, STRLEN);
}
nb++;
srenew(tb, nb);
gmx_ffclose(in);
*ntbptr = nb;
*tbptr = tb;
}