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);
}
}
}
}
void calc_h_pos(int nht, rvec xa[], rvec xh[])
{
#define alfaH (acos(-1/3.0)) /* 109.47 degrees */
#define alfaHpl (2*M_PI/3) /* 120 degrees */
#define distH 0.1
#define alfaCOM (DEG2RAD*117)
#define alfaCO (DEG2RAD*121)
#define alfaCOA (DEG2RAD*115)
#define distO 0.123
#define distOA 0.125
#define distOM 0.136
rvec sa,sb,sij;
real s6,rij,ra,rb,xd;
int d;
s6=0.5*sqrt(3.e0);
/* common work for constructing one, two or three dihedral hydrogens */
switch (nht) {
case 2:
case 3:
case 4:
case 8:
case 9:
rij = 0.e0;
for(d=0; (d<DIM); d++) {
xd = xAJ[d];
sij[d] = xAI[d]-xd;
sb[d] = xd-xAK[d];
rij += sqr(sij[d]);
}
rij = sqrt(rij);
sa[XX] = sij[YY]*sb[ZZ]-sij[ZZ]*sb[YY];
sa[YY] = sij[ZZ]*sb[XX]-sij[XX]*sb[ZZ];
sa[ZZ] = sij[XX]*sb[YY]-sij[YY]*sb[XX];
ra = 0.e0;
for(d=0; (d<DIM); d++) {
sij[d] = sij[d]/rij;
ra += sqr(sa[d]);
}
ra = sqrt(ra);
for(d=0; (d<DIM); d++)
sa[d] = sa[d]/ra;
sb[XX] = sa[YY]*sij[ZZ]-sa[ZZ]*sij[YY];
sb[YY] = sa[ZZ]*sij[XX]-sa[XX]*sij[ZZ];
sb[ZZ] = sa[XX]*sij[YY]-sa[YY]*sij[XX];
break;
}/* end switch */
switch (nht) {
case 1: /* construct one planar hydrogen (peptide,rings) */
rij = 0.e0;
rb = 0.e0;
for(d=0; (d<DIM); d++) {
sij[d] = xAI[d]-xAJ[d];
sb[d] = xAI[d]-xAK[d];
rij += sqr(sij[d]);
rb += sqr(sb[d]);
}
rij = sqrt(rij);
rb = sqrt(rb);
ra = 0.e0;
for(d=0; (d<DIM); d++) {
sa[d] = sij[d]/rij+sb[d]/rb;
ra += sqr(sa[d]);
}
ra = sqrt(ra);
for(d=0; (d<DIM); d++)
xH1[d] = xAI[d]+distH*sa[d]/ra;
break;
case 2: /* one single hydrogen, e.g. hydroxyl */
for(d=0; (d<DIM); d++) {
xH1[d] = xAI[d]+distH*sin(alfaH)*sb[d]-distH*cos(alfaH)*sij[d];
}
break;
case 3: /* two planar hydrogens, e.g. -NH2 */
for(d=0; (d<DIM); d++) {
xH1[d] = xAI[d]-distH*sin(alfaHpl)*sb[d]-distH*cos(alfaHpl)*sij[d];
xH2[d] = xAI[d]+distH*sin(alfaHpl)*sb[d]-distH*cos(alfaHpl)*sij[d];
}
break;
case 4: /* two or three tetrahedral hydrogens, e.g. -CH3 */
for(d=0; (d<DIM); d++) {
xH1[d] = xAI[d]+distH*sin(alfaH)*sb[d]-distH*cos(alfaH)*sij[d];
xH2[d] = ( xAI[d]
- distH*sin(alfaH)*0.5*sb[d]
+ distH*sin(alfaH)*s6*sa[d]
- distH*cos(alfaH)*sij[d] );
if ( xH3[XX]!=NOTSET && xH3[YY]!=NOTSET && xH3[ZZ]!=NOTSET )
xH3[d] = ( xAI[d]
- distH*sin(alfaH)*0.5*sb[d]
- distH*sin(alfaH)*s6*sa[d]
- distH*cos(alfaH)*sij[d] );
}
break;
case 5: { /* one tetrahedral hydrogen, e.g. C3CH */
real center;
rvec dxc;
for(d=0; (d<DIM); d++) {
center=(xAJ[d]+xAK[d]+xAL[d])/3.0;
dxc[d]=xAI[d]-center;
}
center=norm(dxc);
for(d=0; (d<DIM); d++)
xH1[d]=xAI[d]+dxc[d]*distH/center;
break;
}
case 6: { /* two tetrahedral hydrogens, e.g. C-CH2-C */
rvec rBB,rCC1,rCC2,rNN;
real bb,nn;
for(d=0; (d<DIM); d++)
rBB[d]=xAI[d]-0.5*(xAJ[d]+xAK[d]);
bb=norm(rBB);
rvec_sub(xAI,xAJ,rCC1);
rvec_sub(xAI,xAK,rCC2);
cprod(rCC1,rCC2,rNN);
nn=norm(rNN);
for(d=0; (d<DIM); d++) {
xH1[d]=xAI[d]+distH*(cos(alfaH/2.0)*rBB[d]/bb+
sin(alfaH/2.0)*rNN[d]/nn);
xH2[d]=xAI[d]+distH*(cos(alfaH/2.0)*rBB[d]/bb-
sin(alfaH/2.0)*rNN[d]/nn);
}
break;
}
case 7: /* two water hydrogens */
gen_waterhydrogen(2, xa, xh);
break;
case 10: /* three water hydrogens */
gen_waterhydrogen(3, xa, xh);
break;
case 11: /* four water hydrogens */
gen_waterhydrogen(4, xa, xh);
break;
case 8: /* two carboxyl oxygens, -COO- */
for(d=0; (d<DIM); d++) {
xH1[d] = xAI[d]-distOM*sin(alfaCOM)*sb[d]-distOM*cos(alfaCOM)*sij[d];
xH2[d] = xAI[d]+distOM*sin(alfaCOM)*sb[d]-distOM*cos(alfaCOM)*sij[d];
}
break;
case 9: { /* carboxyl oxygens and hydrogen, -COOH */
rvec xa2[4]; /* i,j,k,l */
/* first add two oxygens */
for(d=0; (d<DIM); d++) {
xH1[d] = xAI[d]-distO *sin(alfaCO )*sb[d]-distO *cos(alfaCO )*sij[d];
xH2[d] = xAI[d]+distOA*sin(alfaCOA)*sb[d]-distOA*cos(alfaCOA)*sij[d];
}
/* now use rule 2 to add hydrogen to 2nd oxygen */
copy_rvec(xH2, xa2[0]); /* new i = n' */
copy_rvec(xAI, xa2[1]); /* new j = i */
copy_rvec(xAJ, xa2[2]); /* new k = j */
copy_rvec(xAK, xa2[3]); /* new l = k, not used */
calc_h_pos(2, xa2, (xh+2));
break;
}
default:
gmx_fatal(FARGS,"Invalid argument (%d) for nht in routine genh\n",nht);
} /* end switch */
}
