static void calc_all_pos(t_atoms *pdba, rvec x[], int nab[], t_hack *ab[],
gmx_bool bCheckMissing)
{
int i, j, ii, jj, m, ia, d, rnr,l=0;
#define MAXH 4
rvec xa[4]; /* control atoms for calc_h_pos */
rvec xh[MAXH]; /* hydrogen positions from calc_h_pos */
gmx_bool bFoundAll;
jj = 0;
for(i=0; i < pdba->nr; i++) {
rnr = pdba->atom[i].resind;
for(j=0; j < nab[i]; j+=ab[i][j].nr) {
/* check if we're adding: */
if (ab[i][j].oname==NULL && ab[i][j].tp > 0) {
bFoundAll = TRUE;
for(m=0; (m<ab[i][j].nctl && bFoundAll); m++) {
ia = pdbasearch_atom(ab[i][j].a[m], rnr, pdba,
bCheckMissing ? "atom" : "check",
!bCheckMissing);
if (ia < 0) {
/* not found in original atoms, might still be in t_hack (ab) */
hacksearch_atom(&ii, &jj, ab[i][j].a[m], nab, ab, rnr, pdba);
if (ii >= 0) {
copy_rvec(ab[ii][jj].newx, xa[m]);
} else {
bFoundAll = FALSE;
if (bCheckMissing) {
gmx_fatal(FARGS,"Atom %s not found in residue %s %d"
", rtp entry %s"
" while adding hydrogens",
ab[i][j].a[m],
*pdba->resinfo[rnr].name,
pdba->resinfo[rnr].nr,
*pdba->resinfo[rnr].rtp);
}
}
} else {
copy_rvec(x[ia], xa[m]);
}
}
if (bFoundAll) {
for(m=0; (m<MAXH); m++)
for(d=0; d<DIM; d++)
if (m<ab[i][j].nr)
xh[m][d] = 0;
else
xh[m][d] = NOTSET;
calc_h_pos(ab[i][j].tp, xa, xh, &l);
for(m=0; m<ab[i][j].nr; m++) {
copy_rvec(xh[m],ab[i][j+m].newx);
ab[i][j+m].bXSet = TRUE;
}
}
}
}
}
}
static int check_atoms_present(t_atoms *pdba, int nab[], t_hack *ab[])
{
int i, j, k, d, rnr, nadd;
nadd = 0;
for (i = 0; i < pdba->nr; i++)
{
rnr = pdba->atom[i].resind;
for (j = 0; j < nab[i]; j++)
{
if (ab[i][j].oname == NULL)
{
/* we're adding */
if (ab[i][j].nname == NULL)
{
gmx_incons("ab[i][j].nname not allocated");
}
/* check if the atom is already present */
k = pdbasearch_atom(ab[i][j].nname, rnr, pdba, "check", TRUE);
if (k != -1)
{
/* We found the added atom. */
ab[i][j].bAlreadyPresent = TRUE;
if (debug)
{
fprintf(debug, "Atom '%s' in residue '%s' %d is already present\n",
ab[i][j].nname,
*pdba->resinfo[rnr].name, pdba->resinfo[rnr].nr);
}
}
else
{
ab[i][j].bAlreadyPresent = FALSE;
/* count how many atoms we'll add */
nadd++;
}
}
else if (ab[i][j].nname == NULL)
{
/* we're deleting */
nadd--;
}
}
}
return nadd;
}
static void calc_all_pos(t_atoms *pdba, rvec x[], int nab[], t_hack *ab[],
bool bMissing)
{
int i, j, ii, jj, m, ia, d, rnr;
#define MAXH 4
rvec xa[4]; /* control atoms for calc_h_pos */
rvec xh[MAXH]; /* hydrogen positions from calc_h_pos */
jj = 0;
for(i=0; i < pdba->nr; i++) {
rnr = pdba->atom[i].resind;
for(j=0; j < nab[i]; j+=ab[i][j].nr) {
/* check if we're adding: */
if (ab[i][j].oname==NULL && ab[i][j].tp > 0) {
for(m=0; (m<ab[i][j].nctl); m++) {
ia = pdbasearch_atom(ab[i][j].a[m], rnr, pdba, "atom", bMissing);
if (ia < 0) {
/* not found in original atoms, might still be in t_hack (ab) */
hacksearch_atom(&ii, &jj, ab[i][j].a[m], nab, ab, rnr, pdba);
if (ii < 0)
gmx_fatal(FARGS,"Atom %s not found in residue %s%d"
" while adding hydrogens",
ab[i][j].a[m],
*pdba->resinfo[rnr].name,
pdba->resinfo[rnr].nr);
else
copy_rvec(ab[ii][jj].newx, xa[m]);
} else
copy_rvec(x[ia], xa[m]);
}
for(m=0; (m<MAXH); m++)
for(d=0; d<DIM; d++)
if (m<ab[i][j].nr)
xh[m][d] = 0;
else
xh[m][d] = NOTSET;
calc_h_pos(ab[i][j].tp, xa, xh);
for(m=0; m<ab[i][j].nr; m++)
copy_rvec(xh[m],ab[i][j+m].newx);
}
}
}
}
static int check_atoms_present(t_atoms *pdba, int nab[], t_hack *ab[],
bool bMissing)
{
int i, j, k, d, rnr, nadd;
nadd=0;
for(i=0; i < pdba->nr; i++) {
rnr = pdba->atom[i].resind;
for(j=0; j<nab[i]; j++)
if ( ab[i][j].oname==NULL ) {
/* we're adding */
if (ab[i][j].nname == NULL)
gmx_incons("ab[i][j].name not allocated");
/* check if the atom is already present */
k=pdbasearch_atom(ab[i][j].nname, rnr, pdba, "check", bMissing);
if ( k != -1 ) {
/* we found the added atom, so move the hack there: */
srenew(ab[k], nab[k]+1);
ab[k][nab[k]] = ab[i][j];
ab[k][nab[k]].oname = strdup(ab[k][nab[k]].nname);
/* reset any possible new coordinates: */
for(d=0; d<DIM; d++)
ab[k][nab[k]].newx[d]=NOTSET;
/* keep count */
nab[k]++;
/* remove the hack from this atom: */
for(k=j+1; k<nab[i]; k++)
ab[i][k-1] = ab[i][k];
/* keep count */
nab[i]--;
j--;
srenew(ab[i], nab[i]);
} else
/* count how many atoms we'll add */
nadd++;
} else if ( ab[i][j].nname==NULL )
/* we're deleting */
nadd--;
}
return nadd;
}
