void pdb2top(FILE *top_file, char *posre_fn, char *molname,
t_atoms *atoms, rvec **x, gpp_atomtype_t atype, t_symtab *tab,
int nrtp, t_restp rtp[],
t_restp *restp, t_hackblock *hb,
int nterpairs,t_hackblock **ntdb, t_hackblock **ctdb,
gmx_bool bAllowMissing,
gmx_bool bVsites, gmx_bool bVsiteAromatics,
const char *ff, const char *ffdir,
real mHmult,
int nssbonds, t_ssbond *ssbonds,
real long_bond_dist, real short_bond_dist,
gmx_bool bDeuterate, gmx_bool bChargeGroups, gmx_bool bCmap,
gmx_bool bRenumRes,gmx_bool bRTPresname)
{
/*
t_hackblock *hb;
t_restp *restp;
*/
t_params plist[F_NRE];
t_excls *excls;
t_nextnb nnb;
int *cgnr;
int *vsite_type;
int i,nmissat;
int bts[ebtsNR];
init_plist(plist);
if (debug) {
print_resall(debug, atoms->nres, restp, atype);
dump_hb(debug, atoms->nres, hb);
}
/* Make bonds */
at2bonds(&(plist[F_BONDS]), hb,
atoms->nr, atoms->atom, atoms->atomname, atoms->nres, *x,
long_bond_dist, short_bond_dist, bAllowMissing);
/* specbonds: disulphide bonds & heme-his */
do_ssbonds(&(plist[F_BONDS]),
atoms->nr, atoms->atom, atoms->atomname, nssbonds, ssbonds,
bAllowMissing);
nmissat = name2type(atoms, &cgnr, atype, restp);
if (nmissat) {
if (bAllowMissing)
fprintf(stderr,"There were %d missing atoms in molecule %s\n",
nmissat,molname);
else
gmx_fatal(FARGS,"There were %d missing atoms in molecule %s, if you want to use this incomplete topology anyhow, use the option -missing",
nmissat,molname);
}
/* Cleanup bonds (sort and rm doubles) */
clean_bonds(&(plist[F_BONDS]));
snew(vsite_type,atoms->nr);
for(i=0; i<atoms->nr; i++)
vsite_type[i]=NOTSET;
if (bVsites) {
/* determine which atoms will be vsites and add dummy masses
also renumber atom numbers in plist[0..F_NRE]! */
do_vsites(nrtp, rtp, atype, atoms, tab, x, plist,
&vsite_type, &cgnr, mHmult, bVsiteAromatics, ffdir);
}
/* Make Angles and Dihedrals */
fprintf(stderr,"Generating angles, dihedrals and pairs...\n");
snew(excls,atoms->nr);
init_nnb(&nnb,atoms->nr,4);
gen_nnb(&nnb,plist);
print_nnb(&nnb,"NNB");
gen_pad(&nnb,atoms,restp[0].nrexcl,restp[0].HH14,
plist,excls,hb,restp[0].bAlldih,restp[0].bRemoveDih,
bAllowMissing);
done_nnb(&nnb);
/* Make CMAP */
if (TRUE == bCmap)
{
gen_cmap(&(plist[F_CMAP]), restp, atoms->nr, atoms->atom, atoms->atomname, atoms->nres);
if (plist[F_CMAP].nr > 0)
{
fprintf(stderr, "There are %4d cmap torsion pairs\n",
plist[F_CMAP].nr);
}
}
/* set mass of all remaining hydrogen atoms */
if (mHmult != 1.0)
do_h_mass(&(plist[F_BONDS]),vsite_type,atoms,mHmult,bDeuterate);
sfree(vsite_type);
/* Cleanup bonds (sort and rm doubles) */
/* clean_bonds(&(plist[F_BONDS]));*/
fprintf(stderr,
"There are %4d dihedrals, %4d impropers, %4d angles\n"
" %4d pairs, %4d bonds and %4d virtual sites\n",
plist[F_PDIHS].nr, plist[F_IDIHS].nr, plist[F_ANGLES].nr,
plist[F_LJ14].nr, plist[F_BONDS].nr,
plist[F_VSITE2].nr +
plist[F_VSITE3].nr +
plist[F_VSITE3FD].nr +
plist[F_VSITE3FAD].nr +
plist[F_VSITE3OUT].nr +
plist[F_VSITE4FD].nr +
plist[F_VSITE4FDN].nr );
print_sums(atoms, FALSE);
if (FALSE == bChargeGroups)
{
scrub_charge_groups(cgnr, atoms->nr);
}
if (bRenumRes)
{
for(i=0; i<atoms->nres; i++)
{
atoms->resinfo[i].nr = i + 1;
atoms->resinfo[i].ic = ' ';
}
}
if (top_file) {
fprintf(stderr,"Writing topology\n");
/* We can copy the bonded types from the first restp,
* since the types have to be identical for all residues in one molecule.
*/
for(i=0; i<ebtsNR; i++) {
bts[i] = restp[0].rb[i].type;
}
write_top(top_file, posre_fn, molname,
atoms, bRTPresname,
bts, plist, excls, atype, cgnr, restp[0].nrexcl);
}
/* cleaning up */
free_t_hackblock(atoms->nres, &hb);
free_t_restp(atoms->nres, &restp);
/* we should clean up hb and restp here, but that is a *L*O*T* of work! */
sfree(cgnr);
for (i=0; i<F_NRE; i++)
sfree(plist[i].param);
for (i=0; i<atoms->nr; i++)
sfree(excls[i].e);
sfree(excls);
}
static int add_h_low(t_atoms **pdbaptr, rvec *xptr[],
int nah, t_hackblock ah[],
int nterpairs, t_hackblock **ntdb, t_hackblock **ctdb,
int *rN, int *rC, gmx_bool bCheckMissing,
int **nabptr, t_hack ***abptr,
gmx_bool bUpdate_pdba, gmx_bool bKeep_old_pdba)
{
t_atoms *newpdba = NULL, *pdba = NULL;
int nadd;
int i, newi, j, d, natoms, nalreadypresent;
int *nab = NULL;
t_hack **ab = NULL;
t_hackblock *hb;
rvec *xn;
gmx_bool bKeep_ab;
/* set flags for adding hydrogens (according to hdb) */
pdba = *pdbaptr;
natoms = pdba->nr;
if (nabptr && abptr)
{
/* the first time these will be pointers to NULL, but we will
return in them the completed arrays, which we will get back
the second time */
nab = *nabptr;
ab = *abptr;
bKeep_ab = TRUE;
if (debug)
{
fprintf(debug, "pointer to ab found\n");
}
}
else
{
bKeep_ab = FALSE;
}
if (nab && ab)
{
/* WOW, everything was already figured out */
bUpdate_pdba = FALSE;
if (debug)
{
fprintf(debug, "pointer to non-null ab found\n");
}
}
else
{
/* We'll have to do all the hard work */
bUpdate_pdba = TRUE;
/* first get all the hackblocks for each residue: */
hb = get_hackblocks(pdba, nah, ah, nterpairs, ntdb, ctdb, rN, rC);
if (debug)
{
dump_hb(debug, pdba->nres, hb);
}
/* expand the hackblocks to atom level */
snew(nab, natoms);
snew(ab, natoms);
expand_hackblocks(pdba, hb, nab, ab, nterpairs, rN, rC);
free_t_hackblock(pdba->nres, &hb);
}
if (debug)
{
fprintf(debug, "before calc_all_pos\n");
dump_ab(debug, natoms, nab, ab, TRUE);
}
/* Now calc the positions */
calc_all_pos(pdba, *xptr, nab, ab, bCheckMissing);
if (debug)
{
fprintf(debug, "after calc_all_pos\n");
dump_ab(debug, natoms, nab, ab, TRUE);
}
if (bUpdate_pdba)
{
/* we don't have to add atoms that are already present in pdba,
so we will remove them from the ab (t_hack) */
nadd = check_atoms_present(pdba, nab, ab);
if (debug)
{
fprintf(debug, "removed add hacks that were already in pdba:\n");
dump_ab(debug, natoms, nab, ab, TRUE);
fprintf(debug, "will be adding %d atoms\n", nadd);
}
/* Copy old atoms, making space for new ones */
snew(newpdba, 1);
init_t_atoms(newpdba, natoms+nadd, FALSE);
newpdba->nres = pdba->nres;
sfree(newpdba->resinfo);
newpdba->resinfo = pdba->resinfo;
}
else
{
nadd = 0;
}
if (debug)
{
fprintf(debug, "snew xn for %d old + %d new atoms %d total)\n",
natoms, nadd, natoms+nadd);
}
if (nadd == 0)
{
/* There is nothing to do: return now */
if (!bKeep_ab)
{
free_ab(natoms, nab, ab);
}
return natoms;
}
snew(xn, natoms+nadd);
newi = 0;
for (i = 0; (i < natoms); i++)
{
/* check if this atom wasn't scheduled for deletion */
if (nab[i] == 0 || (ab[i][0].nname != NULL) )
{
if (newi >= natoms+nadd)
{
/*gmx_fatal(FARGS,"Not enough space for adding atoms");*/
nadd += 10;
srenew(xn, natoms+nadd);
if (bUpdate_pdba)
{
srenew(newpdba->atom, natoms+nadd);
srenew(newpdba->atomname, natoms+nadd);
}
debug_gmx();
}
if (debug)
{
fprintf(debug, "(%3d) %3d %4s %4s%3d %3d",
i+1, newi+1, *pdba->atomname[i],
*pdba->resinfo[pdba->atom[i].resind].name,
pdba->resinfo[pdba->atom[i].resind].nr, nab[i]);
}
if (bUpdate_pdba)
{
copy_atom(pdba, i, newpdba, newi);
}
copy_rvec((*xptr)[i], xn[newi]);
/* process the hacks for this atom */
nalreadypresent = 0;
for (j = 0; j < nab[i]; j++)
{
if (ab[i][j].oname == NULL) /* add */
{
newi++;
if (newi >= natoms+nadd)
{
/* gmx_fatal(FARGS,"Not enough space for adding atoms");*/
nadd += 10;
srenew(xn, natoms+nadd);
if (bUpdate_pdba)
{
srenew(newpdba->atom, natoms+nadd);
srenew(newpdba->atomname, natoms+nadd);
}
debug_gmx();
}
if (bUpdate_pdba)
{
newpdba->atom[newi].resind = pdba->atom[i].resind;
}
if (debug)
{
fprintf(debug, " + %d", newi+1);
}
}
if (ab[i][j].nname != NULL &&
(ab[i][j].oname == NULL ||
strcmp(ab[i][j].oname, *newpdba->atomname[newi]) == 0))
{
/* add or replace */
if (ab[i][j].oname == NULL && ab[i][j].bAlreadyPresent)
{
/* This atom is already present, copy it from the input. */
nalreadypresent++;
if (bUpdate_pdba)
{
copy_atom(pdba, i+nalreadypresent, newpdba, newi);
}
copy_rvec((*xptr)[i+nalreadypresent], xn[newi]);
}
else
{
if (bUpdate_pdba)
{
if (gmx_debug_at)
{
fprintf(debug, "Replacing %d '%s' with (old name '%s') %s\n",
newi,
(newpdba->atomname[newi] && *newpdba->atomname[newi]) ? *newpdba->atomname[newi] : "",
ab[i][j].oname ? ab[i][j].oname : "",
ab[i][j].nname);
}
snew(newpdba->atomname[newi], 1);
*newpdba->atomname[newi] = strdup(ab[i][j].nname);
if (ab[i][j].oname != NULL && ab[i][j].atom) /* replace */
{ /* newpdba->atom[newi].m = ab[i][j].atom->m; */
/* newpdba->atom[newi].q = ab[i][j].atom->q; */
/* newpdba->atom[newi].type = ab[i][j].atom->type; */
}
}
if (ab[i][j].bXSet)
{
copy_rvec(ab[i][j].newx, xn[newi]);
}
}
if (bUpdate_pdba && debug)
{
fprintf(debug, " %s %g %g", *newpdba->atomname[newi],
newpdba->atom[newi].m, newpdba->atom[newi].q);
}
}
}
newi++;
i += nalreadypresent;
if (debug)
{
fprintf(debug, "\n");
}
}
}
if (bUpdate_pdba)
{
newpdba->nr = newi;
}
if (bKeep_ab)
{
*nabptr = nab;
*abptr = ab;
}
else
{
/* Clean up */
free_ab(natoms, nab, ab);
}
if (bUpdate_pdba)
{
if (!bKeep_old_pdba)
{
for (i = 0; i < natoms; i++)
{
/* Do not free the atomname string itself, it might be in symtab */
/* sfree(*(pdba->atomname[i])); */
/* sfree(pdba->atomname[i]); */
}
sfree(pdba->atomname);
sfree(pdba->atom);
sfree(pdba->pdbinfo);
sfree(pdba);
}
*pdbaptr = newpdba;
}
else
{
nadd = newi-natoms;
}
sfree(*xptr);
*xptr = xn;
return newi;
}
int add_h(t_atoms **pdbaptr, rvec *xptr[],
int nah, t_hackblock ah[],
int nterpairs, t_hackblock **ntdb, t_hackblock **ctdb,
int *rN, int *rC, bool bMissing,
int **nabptr, t_hack ***abptr,
bool bUpdate_pdba, bool bKeep_old_pdba)
{
t_atoms *newpdba=NULL,*pdba=NULL;
bool bSet;
int nadd;
int i,newi,j,d,natoms;
int *nab=NULL;
t_hack **ab=NULL;
t_hackblock *hb;
rvec *xn;
bool bKeep_ab;
/* set flags for adding hydrogens (according to hdb) */
pdba=*pdbaptr;
natoms=pdba->nr;
if (nabptr && abptr) {
/* the first time these will be pointers to NULL, but we will
return in them the completed arrays, which we will get back
the second time */
nab = *nabptr;
ab = *abptr;
bKeep_ab=TRUE;
if (debug) fprintf(debug,"pointer to ab found\n");
} else
bKeep_ab=FALSE;
if (nab && ab) {
/* WOW, everything was already figured out */
bUpdate_pdba = FALSE;
if (debug) fprintf(debug,"pointer to non-null ab found\n");
} else {
/* We'll have to do all the hard work */
bUpdate_pdba = TRUE;
/* first get all the hackblocks for each residue: */
hb = get_hackblocks(pdba, nah, ah, nterpairs, ntdb, ctdb, rN, rC);
if (debug) dump_hb(debug, pdba->nres, hb);
/* expand the hackblocks to atom level */
snew(nab,natoms);
snew(ab,natoms);
expand_hackblocks(pdba, hb, nab, ab, nterpairs, rN, rC);
free_t_hackblock(pdba->nres, &hb);
}
if (debug) {
fprintf(debug,"before calc_all_pos\n");
dump_ab(debug, natoms, nab, ab, TRUE);
}
/* Now calc the positions */
calc_all_pos(pdba, *xptr, nab, ab, bMissing);
if (debug) {
fprintf(debug,"after calc_all_pos\n");
dump_ab(debug, natoms, nab, ab, TRUE);
}
if (bUpdate_pdba) {
/* we don't have to add atoms that are already present in pdba,
so we will remove them from the ab (t_hack) */
nadd = check_atoms_present(pdba, nab, ab, bMissing);
if (debug) {
fprintf(debug, "removed add hacks that were already in pdba:\n");
dump_ab(debug, natoms, nab, ab, TRUE);
fprintf(debug, "will be adding %d atoms\n",nadd);
}
/* Copy old atoms, making space for new ones */
snew(newpdba,1);
init_t_atoms(newpdba,natoms+nadd,FALSE);
newpdba->nres = pdba->nres;
sfree(newpdba->resname);
newpdba->resname = pdba->resname;
} else {
nadd = 0;
}
if (debug) fprintf(debug,"snew xn for %d old + %d new atoms %d total)\n",
natoms, nadd, natoms+nadd);
snew(xn,natoms+nadd);
newi=0;
for(i=0; (i<natoms); i++) {
/* check if this atom wasn't scheduled for deletion */
if ( nab[i]==0 || (ab[i][0].nname != NULL) ) {
if (newi >= natoms+nadd) {
/*gmx_fatal(FARGS,"Not enough space for adding atoms");*/
nadd+=10;
srenew(xn,natoms+nadd);
if (bUpdate_pdba) {
srenew(newpdba->atom,natoms+nadd);
srenew(newpdba->atomname,natoms+nadd);
}
debug_gmx();
}
if (debug) fprintf(debug,"(%3d) %3d %4s %4s%3d %3d",
i+1, newi+1, *pdba->atomname[i],
*pdba->resname[pdba->atom[i].resnr],
pdba->atom[i].resnr+1, nab[i]);
if (bUpdate_pdba)
copy_atom(pdba,i, newpdba,newi);
copy_rvec((*xptr)[i],xn[newi]);
/* process the hacks for this atom */
for(j=0; j<nab[i]; j++) {
if ( ab[i][j].oname==NULL ) { /* add */
newi++;
if (newi >= natoms+nadd) {
/* gmx_fatal(FARGS,"Not enough space for adding atoms");*/
nadd+=10;
srenew(xn,natoms+nadd);
if (bUpdate_pdba) {
srenew(newpdba->atom,natoms+nadd);
srenew(newpdba->atomname,natoms+nadd);
}
debug_gmx();
}
if (bUpdate_pdba) {
newpdba->atom[newi].resnr=pdba->atom[i].resnr;
}
if (debug) fprintf(debug," + %d",newi+1);
}
if ( ab[i][j].nname!=NULL ) { /* add or replace */
if (bUpdate_pdba) {
snew(newpdba->atomname[newi],1);
*newpdba->atomname[newi]=strdup(ab[i][j].nname);
if ( ab[i][j].oname!=NULL && ab[i][j].atom ) { /* replace */
/* newpdba->atom[newi].m = ab[i][j].atom->m; */
/* newpdba->atom[newi].q = ab[i][j].atom->q; */
/* newpdba->atom[newi].type = ab[i][j].atom->type; */
}
}
bSet=TRUE;
for(d=0; d<DIM; d++)
bSet = bSet && ab[i][j].newx[d]!=NOTSET;
if (bSet)
copy_rvec(ab[i][j].newx, xn[newi]);
if (bUpdate_pdba && debug)
fprintf(debug," %s %g %g",*newpdba->atomname[newi],
newpdba->atom[newi].m,newpdba->atom[newi].q);
}
}
newi++;
if (debug) fprintf(debug,"\n");
}
}
if (bUpdate_pdba)
newpdba->nr = newi;
if ( bKeep_ab ) {
*nabptr=nab;
*abptr=ab;
} else {
/* Clean up */
for(i=0; i<natoms; i++)
free_t_hack(nab[i], &ab[i]);
sfree(nab);
sfree(ab);
}
if ( bUpdate_pdba ) {
if ( !bKeep_old_pdba ) {
for(i=0; i < natoms; i++) {
sfree(*(pdba->atomname[i]));
/* sfree(pdba->atomname[i]); */
}
sfree(pdba->atomname);
sfree(pdba->atom);
sfree(pdba->pdbinfo);
sfree(pdba);
}
*pdbaptr=newpdba;
} else
nadd = newi-natoms;
sfree(*xptr);
*xptr=xn;
return newi;
}