void copy_t_restp(t_restp *s, t_restp *d)
{
int i;
*d = *s;
d->resname = safe_strdup(s->resname);
snew(d->atom, s->natom);
for (i = 0; i < s->natom; i++)
{
d->atom[i] = s->atom[i];
}
snew(d->atomname, s->natom);
for (i = 0; i < s->natom; i++)
{
snew(d->atomname[i], 1);
*d->atomname[i] = safe_strdup(*s->atomname[i]);
}
snew(d->cgnr, s->natom);
for (i = 0; i < s->natom; i++)
{
d->cgnr[i] = s->cgnr[i];
}
for (i = 0; i < ebtsNR; i++)
{
d->rb[i].type = s->rb[i].type;
d->rb[i].nb = 0;
d->rb[i].b = NULL;
}
merge_t_bondeds(s->rb, d->rb, FALSE, FALSE);
}
void get_hackblocks_rtp(t_hackblock **hb, t_restp **restp,
int nrtp, t_restp rtp[],
int nres, t_resinfo *resinfo,
int nterpairs,
t_hackblock **ntdb, t_hackblock **ctdb,
int *rn, int *rc)
{
int i, j, k, l;
char *key;
t_restp *res;
char buf[STRLEN];
const char *Hnum="123456";
int tern,terc;
gmx_bool bN,bC,bRM;
snew(*hb,nres);
snew(*restp,nres);
/* first the termini */
for(i=0; i<nterpairs; i++) {
if (rn[i] >= 0 && ntdb[i] != NULL) {
copy_t_hackblock(ntdb[i], &(*hb)[rn[i]]);
}
if (rc[i] >= 0 && ctdb[i] != NULL) {
merge_t_hackblock(ctdb[i], &(*hb)[rc[i]]);
}
}
/* then the whole rtp */
for(i=0; i < nres; i++) {
/* Here we allow a mismatch of one character when looking for the rtp entry.
* For such a mismatch there should be only one mismatching name.
* This is mainly useful for small molecules such as ions.
* Note that this will usually not work for protein, DNA and RNA,
* since there the residue names should be listed in residuetypes.dat
* and an error will have been generated earlier in the process.
*/
key = *resinfo[i].rtp;
snew(resinfo[i].rtp,1);
*resinfo[i].rtp = search_rtp(key,nrtp,rtp);
res = get_restp(*resinfo[i].rtp,nrtp,rtp);
copy_t_restp(res, &(*restp)[i]);
/* Check that we do not have different bonded types in one molecule */
check_restp_types(&(*restp)[0],&(*restp)[i]);
tern = -1;
for(j=0; j<nterpairs && tern==-1; j++) {
if (i == rn[j]) {
tern = j;
}
}
terc = -1;
for(j=0; j<nterpairs && terc == -1; j++) {
if (i == rc[j]) {
terc = j;
}
}
bRM = merge_t_bondeds(res->rb, (*hb)[i].rb,tern>=0,terc>=0);
if (bRM && ((tern >= 0 && ntdb[tern] == NULL) ||
(terc >= 0 && ctdb[terc] == NULL))) {
gmx_fatal(FARGS,"There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb file.");
}
if (bRM && ((tern >= 0 && ntdb[tern]->nhack == 0) ||
(terc >= 0 && ctdb[terc]->nhack == 0))) {
gmx_fatal(FARGS,"There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry.");
}
}
/* now perform t_hack's on t_restp's,
i.e. add's and deletes from termini database will be
added to/removed from residue topology
we'll do this on one big dirty loop, so it won't make easy reading! */
for(i=0; i < nres; i++)
{
for(j=0; j < (*hb)[i].nhack; j++)
{
if ( (*hb)[i].hack[j].nr )
{
/* find atom in restp */
for(l=0; l < (*restp)[i].natom; l++)
if ( ( (*hb)[i].hack[j].oname==NULL &&
strcmp((*hb)[i].hack[j].AI, *(*restp)[i].atomname[l])==0 ) ||
( (*hb)[i].hack[j].oname!=NULL &&
strcmp((*hb)[i].hack[j].oname,*(*restp)[i].atomname[l])==0 ) )
break;
if (l == (*restp)[i].natom)
{
/* If we are doing an atom rename only, we don't need
* to generate a fatal error if the old name is not found
* in the rtp.
*/
/* Deleting can happen also only on the input atoms,
* not necessarily always on the rtp entry.
*/
if (!((*hb)[i].hack[j].oname != NULL &&
(*hb)[i].hack[j].nname != NULL) &&
!((*hb)[i].hack[j].oname != NULL &&
(*hb)[i].hack[j].nname == NULL))
{
gmx_fatal(FARGS,
"atom %s not found in buiding block %d%s "
"while combining tdb and rtp",
(*hb)[i].hack[j].oname!=NULL ?
(*hb)[i].hack[j].oname : (*hb)[i].hack[j].AI,
i+1,*resinfo[i].rtp);
}
}
else
{
if ( (*hb)[i].hack[j].oname==NULL ) {
/* we're adding: */
add_atom_to_restp(&(*restp)[i],resinfo[i].nr,l,
&(*hb)[i].hack[j]);
}
else
{
/* oname != NULL */
if ( (*hb)[i].hack[j].nname==NULL ) {
/* we're deleting */
if (debug)
fprintf(debug, "deleting atom %s from res %d%s in rtp\n",
*(*restp)[i].atomname[l],
i+1,(*restp)[i].resname);
/* shift the rest */
(*restp)[i].natom--;
for(k=l; k < (*restp)[i].natom; k++) {
(*restp)[i].atom [k] = (*restp)[i].atom [k+1];
(*restp)[i].atomname[k] = (*restp)[i].atomname[k+1];
(*restp)[i].cgnr [k] = (*restp)[i].cgnr [k+1];
}
/* give back space */
srenew((*restp)[i].atom, (*restp)[i].natom);
srenew((*restp)[i].atomname, (*restp)[i].natom);
srenew((*restp)[i].cgnr, (*restp)[i].natom);
} else { /* nname != NULL */
/* we're replacing */
if (debug)
fprintf(debug, "replacing atom %s by %s in res %d%s in rtp\n",
*(*restp)[i].atomname[l], (*hb)[i].hack[j].nname,
i+1,(*restp)[i].resname);
snew( (*restp)[i].atomname[l], 1);
(*restp)[i].atom[l] = *(*hb)[i].hack[j].atom;
*(*restp)[i].atomname[l] = strdup((*hb)[i].hack[j].nname);
if ( (*hb)[i].hack[j].cgnr != NOTSET )
(*restp)[i].cgnr [l] = (*hb)[i].hack[j].cgnr;
}
}
}
}
}
}
}
void merge_t_hackblock(t_hackblock *s, t_hackblock *d)
{
merge_hacks(s, d);
merge_t_bondeds(s->rb, d->rb, FALSE, FALSE);
}