static void gen_excls(t_atoms *atoms, t_excls *excls, t_hackblock hb[],
gmx_bool bAllowMissing)
{
int r;
atom_id a, astart, i1, i2, itmp;
t_rbondeds *hbexcl;
int e;
char *anm;
astart = 0;
for (a = 0; a < atoms->nr; a++)
{
r = atoms->atom[a].resind;
if (a == atoms->nr-1 || atoms->atom[a+1].resind != r)
{
hbexcl = &hb[r].rb[ebtsEXCLS];
for (e = 0; e < hbexcl->nb; e++)
{
anm = hbexcl->b[e].a[0];
i1 = search_atom(anm, astart, atoms,
"exclusion", bAllowMissing);
anm = hbexcl->b[e].a[1];
i2 = search_atom(anm, astart, atoms,
"exclusion", bAllowMissing);
if (i1 != NO_ATID && i2 != NO_ATID)
{
if (i1 > i2)
{
itmp = i1;
i1 = i2;
i2 = itmp;
}
srenew(excls[i1].e, excls[i1].nr+1);
excls[i1].e[excls[i1].nr] = i2;
excls[i1].nr++;
}
}
astart = a+1;
}
}
for (a = 0; a < atoms->nr; a++)
{
if (excls[a].nr > 1)
{
qsort(excls[a].e, excls[a].nr, (size_t)sizeof(atom_id), atom_id_comp);
}
}
}
void gen_cmap(t_params *psb, t_restp *restp, int natoms, t_atom atom[], char **aname[], int nres)
{
int residx,i,ii,j,k;
atom_id ai,aj,ak,al,am;
const char *ptr;
if (debug)
ptr = "cmap";
else
ptr = "check";
fprintf(stderr,"Making cmap torsions...");
i=0;
/* End loop at nres-1, since the very last residue does not have a +N atom, and
* therefore we get a valgrind invalid 4 byte read error with atom am */
for(residx=0; residx<nres-1; residx++)
{
/* Add CMAP terms from the list of CMAP interactions */
for(j=0;j<restp[residx].rb[ebtsCMAP].nb; j++)
{
ai=search_atom(restp[residx].rb[ebtsCMAP].b[j].a[0],i,natoms,atom,aname,
ptr,TRUE);
aj=search_atom(restp[residx].rb[ebtsCMAP].b[j].a[1],i,natoms,atom,aname,
ptr,TRUE);
ak=search_atom(restp[residx].rb[ebtsCMAP].b[j].a[2],i,natoms,atom,aname,
ptr,TRUE);
al=search_atom(restp[residx].rb[ebtsCMAP].b[j].a[3],i,natoms,atom,aname,
ptr,TRUE);
am=search_atom(restp[residx].rb[ebtsCMAP].b[j].a[4],i,natoms,atom,aname,
ptr,TRUE);
/* The first and last residues no not have cmap torsions */
if(ai!=NO_ATID && aj!=NO_ATID && ak!=NO_ATID && al!=NO_ATID && am!=NO_ATID)
{
add_cmap_param(psb,ai,aj,ak,al,am,restp[residx].rb[ebtsCMAP].b[j].s);
}
}
if(residx<nres-1)
{
while(atom[i].resind<residx+1)
{
i++;
}
}
}
/* Start the next residue */
}
static int get_impropers(t_atoms *atoms, t_hackblock hb[], t_param **improper,
gmx_bool bAllowMissing)
{
t_rbondeds *impropers;
int nimproper, i, j, k, start, ninc, nalloc;
atom_id ai[MAXATOMLIST];
gmx_bool bStop;
ninc = 500;
nalloc = ninc;
snew(*improper, nalloc);
/* Add all the impropers from the residue database to the list. */
nimproper = 0;
start = 0;
if (hb != NULL)
{
for (i = 0; (i < atoms->nres); i++)
{
impropers = &hb[i].rb[ebtsIDIHS];
for (j = 0; (j < impropers->nb); j++)
{
bStop = FALSE;
for (k = 0; (k < 4) && !bStop; k++)
{
ai[k] = search_atom(impropers->b[j].a[k], start,
atoms,
"improper", bAllowMissing);
if (ai[k] == NO_ATID)
{
bStop = TRUE;
}
}
if (!bStop)
{
if (nimproper == nalloc)
{
nalloc += ninc;
srenew(*improper, nalloc);
}
/* Not broken out */
set_p(&((*improper)[nimproper]), ai, NULL, impropers->b[j].s);
nimproper++;
}
}
while ((start < atoms->nr) && (atoms->atom[start].resind == i))
{
start++;
}
}
}
return nimproper;
}
static atom_id pdbasearch_atom(const char *name,int resind,t_atoms *pdba,
const char *searchtype,gmx_bool bAllowMissing)
{
int i;
for(i=0; (i<pdba->nr) && (pdba->atom[i].resind != resind); i++)
;
return search_atom(name,i,pdba->nr,pdba->atom,pdba->atomname,
searchtype,bAllowMissing);
}
atom_id pdbasearch_atom(char *name,int resnr,t_atoms *pdba, char *searchtype,
bool bMissing)
{
int i;
for(i=0; (i<pdba->nr) && (pdba->atom[i].resnr != resnr); i++)
;
return search_atom(name,i,pdba->nr,pdba->atom,pdba->atomname,
searchtype,bMissing);
}
static atom_id search_res_atom(const char *type,int resind,
int natom,t_atom at[],
char ** const *aname,
const char *bondtype,gmx_bool bAllowMissing)
{
int i;
for(i=0; (i<natom); i++)
if (at[i].resind == resind)
return search_atom(type,i,natom,at,aname,bondtype,bAllowMissing);
return NO_ATID;
}
static int get_impropers(t_atoms *atoms,t_hackblock hb[],t_param **idih,
bool bMissing)
{
char *a0;
t_rbondeds *idihs;
t_rbonded *hbidih;
int nidih,i,j,k,r,start,ninc,nalloc;
atom_id ai[MAXATOMLIST];
bool bStop;
ninc = 500;
nalloc = ninc;
snew(*idih,nalloc);
/* Add all the impropers from the residue database to the list. */
nidih = 0;
start = 0;
if (hb != NULL) {
for(i=0; (i<atoms->nres); i++) {
idihs=&hb[i].rb[ebtsIDIHS];
for(j=0; (j<idihs->nb); j++) {
bStop=FALSE;
for(k=0; (k<4) && !bStop; k++) {
ai[k] = search_atom(idihs->b[j].a[k],start,
atoms->nr,atoms->atom,atoms->atomname,
"improper",bMissing);
if (ai[k] == NO_ATID)
bStop = TRUE;
}
if (!bStop) {
if (nidih == nalloc) {
nalloc += ninc;
srenew(*idih,nalloc);
}
/* Not broken out */
set_p(&((*idih)[nidih]),ai,NULL,idihs->b[j].s);
nidih++;
}
}
while ((start<atoms->nr) && (atoms->atom[start].resind == i))
start++;
}
}
return nidih;
}
int
search_res_atom(const char *type, int resind,
t_atoms *atoms,
const char *bondtype, bool bAllowMissing)
{
int i;
for (i = 0; (i < atoms->nr); i++)
{
if (atoms->atom[i].resind == resind)
{
return search_atom(type, i, atoms, bondtype, bAllowMissing);
}
}
return -1;
}
static void at2bonds(t_params *psb, t_hackblock *hb,
int natoms, t_atom atom[], char **aname[],
int nres, rvec x[],
real long_bond_dist, real short_bond_dist,
gmx_bool bAllowMissing)
{
int resind,i,j,k;
atom_id ai,aj;
real dist2, long_bond_dist2, short_bond_dist2;
const char *ptr;
long_bond_dist2 = sqr(long_bond_dist);
short_bond_dist2 = sqr(short_bond_dist);
if (debug)
ptr = "bond";
else
ptr = "check";
fprintf(stderr,"Making bonds...\n");
i=0;
for(resind=0; (resind < nres) && (i<natoms); resind++) {
/* add bonds from list of bonded interactions */
for(j=0; j < hb[resind].rb[ebtsBONDS].nb; j++) {
/* Unfortunately we can not issue errors or warnings
* for missing atoms in bonds, as the hydrogens and terminal atoms
* have not been added yet.
*/
ai=search_atom(hb[resind].rb[ebtsBONDS].b[j].AI,i,natoms,atom,aname,
ptr,TRUE);
aj=search_atom(hb[resind].rb[ebtsBONDS].b[j].AJ,i,natoms,atom,aname,
ptr,TRUE);
if (ai != NO_ATID && aj != NO_ATID) {
dist2 = distance2(x[ai],x[aj]);
if (dist2 > long_bond_dist2 )
{
fprintf(stderr,"Warning: Long Bond (%d-%d = %g nm)\n",
ai+1,aj+1,sqrt(dist2));
}
else if (dist2 < short_bond_dist2 )
{
fprintf(stderr,"Warning: Short Bond (%d-%d = %g nm)\n",
ai+1,aj+1,sqrt(dist2));
}
add_param(psb,ai,aj,NULL,hb[resind].rb[ebtsBONDS].b[j].s);
}
}
/* add bonds from list of hacks (each added atom gets a bond) */
while( (i<natoms) && (atom[i].resind == resind) ) {
for(j=0; j < hb[resind].nhack; j++)
if ( ( hb[resind].hack[j].tp > 0 ||
hb[resind].hack[j].oname==NULL ) &&
strcmp(hb[resind].hack[j].AI,*(aname[i])) == 0 ) {
switch(hb[resind].hack[j].tp) {
case 9: /* COOH terminus */
add_param(psb,i,i+1,NULL,NULL); /* C-O */
add_param(psb,i,i+2,NULL,NULL); /* C-OA */
add_param(psb,i+2,i+3,NULL,NULL); /* OA-H */
break;
default:
for(k=0; (k<hb[resind].hack[j].nr); k++)
add_param(psb,i,i+k+1,NULL,NULL);
}
}
i++;
}
/* we're now at the start of the next residue */
}
}
