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 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);
}
}
}
}
