static void clean_dih(t_param *dih, int *ndih,t_param idih[],int nidih,
t_atoms *atoms,bool bAlldih, bool bRemoveDih)
{
int i,j,k,l;
int *index,nind;
bool bIsSet,bKeep;
int bestl,nh,minh;
snew(index,*ndih+1);
if (bAlldih) {
fprintf(stderr,"Keeping all generated dihedrals\n");
nind = *ndih;
for(i=0; i<nind; i++)
index[i] = i;
index[nind] = *ndih;
} else {
/* Make an index of all dihedrals over each bond */
nind = 0;
for(i=0; i<*ndih; i++)
if (!remove_dih(dih,i,*ndih))
index[nind++]=i;
index[nind] = *ndih;
}
/* if we don't want all dihedrals, we need to select the ones with the
* fewest hydrogens
*/
k=0;
for(i=0; i<nind; i++) {
bIsSet = (dih[index[i]].c[MAXFORCEPARAM-1] != NOTSET);
bKeep = TRUE;
if (!bIsSet && bRemoveDih)
/* remove the dihedral if there is an improper on the same bond */
for(j=0; (j<nidih) && bKeep; j++)
bKeep = !deq(&dih[index[i]],&idih[j]);
if (bKeep) {
/* Now select the "fittest" dihedral:
* the one with as few hydrogens as possible
*/
/* Best choice to get dihedral from */
bestl=index[i];
if (!bAlldih && !bIsSet) {
/* Minimum number of hydrogens for i and l atoms */
minh=2;
for(l=index[i]; (l<index[i+1]) && deq(&dih[index[i]],&dih[l]); l++) {
if ((nh=n_hydro(dih[l].a,atoms->atomname)) < minh) {
minh=nh;
bestl=l;
}
if (minh == 0)
break;
}
}
if (k != bestl)
cpparam(&(dih[k]),&dih[bestl]);
k++;
}
}
for (i=k; i<*ndih; i++)
strcpy(dih[i].s,"");
*ndih = k;
sfree(index);
}
/* Clean up the dihedrals (both generated and read from the .rtp
* file). */
static void clean_dih(t_param *dih, int *ndih, t_param improper[], int nimproper,
t_atoms *atoms, gmx_bool bKeepAllGeneratedDihedrals,
gmx_bool bRemoveDihedralIfWithImproper)
{
int i, j, k, l;
int *index, nind;
/* Construct the list of the indices of the dihedrals
* (i.e. generated or read) that might be kept. */
snew(index, *ndih+1);
if (bKeepAllGeneratedDihedrals)
{
fprintf(stderr, "Keeping all generated dihedrals\n");
nind = *ndih;
for (i = 0; i < nind; i++)
{
index[i] = i;
}
index[nind] = *ndih;
}
else
{
nind = 0;
/* Check if generated dihedral i should be removed. The
* dihedrals have been sorted by dcomp() above, so all those
* on the same two central atoms are together, with those from
* the .rtp file preceding those that were automatically
* generated. We remove the latter if the former exist. */
for (i = 0; i < *ndih; i++)
{
/* Keep the dihedrals that were defined in the .rtp file,
* and the dihedrals that were generated and different
* from the last one (whether it was generated or not). */
if (was_dihedral_set_in_rtp(&dih[i]) ||
0 == i ||
!is_dihedral_on_same_bond(&dih[i], &dih[i-1]))
{
index[nind++] = i;
}
}
index[nind] = *ndih;
}
k = 0;
for (i = 0; i < nind; i++)
{
gmx_bool bWasSetInRTP = was_dihedral_set_in_rtp(&dih[index[i]]);
gmx_bool bKeep = TRUE;
if (!bWasSetInRTP && bRemoveDihedralIfWithImproper)
{
/* Remove the dihedral if there is an improper on the same
* bond. */
for (j = 0; j < nimproper && bKeep; j++)
{
bKeep = !is_dihedral_on_same_bond(&dih[index[i]], &improper[j]);
}
}
if (bKeep)
{
/* If we don't want all dihedrals, we want to select the
* ones with the fewest hydrogens. Note that any generated
* dihedrals on the same bond as an .rtp dihedral may have
* been already pruned above in the construction of
* index[]. However, their parameters are still present,
* and l is looping over this dihedral and all of its
* pruned siblings. */
int bestl = index[i];
if (!bKeepAllGeneratedDihedrals && !bWasSetInRTP)
{
/* Minimum number of hydrogens for i and l atoms */
int minh = 2;
for (l = index[i];
(l < index[i+1] &&
is_dihedral_on_same_bond(&dih[index[i]], &dih[l]));
l++)
{
int nh = n_hydro(dih[l].a, atoms->atomname);
if (nh < minh)
{
minh = nh;
bestl = l;
}
if (0 == minh)
{
break;
}
}
}
if (k != bestl)
{
cpparam(&dih[k], &dih[bestl]);
}
k++;
}
}
for (i = k; i < *ndih; i++)
{
strcpy(dih[i].s, "");
}
*ndih = k;
sfree(index);
}
