Coordinate
_hDonCalcNormal(OpenBabel::OBAtom* a)
{
int nbrBonds(0);
Coordinate normal;
std::vector<OpenBabel::OBBond*>::iterator bi;
for (OpenBabel::OBBond* b = a->BeginBond(bi); b; b = a->NextBond(bi))
{
OpenBabel::OBAtom* aa = b->GetNbrAtom(a);
if (aa->GetAtomicNum() == 1)
{
continue;
}
++nbrBonds;
normal.x += (aa->x() - a->x());
normal.y += (aa->y() - a->y());
normal.z += (aa->z() - a->z());
}
double length(sqrt(normal.x*normal.x + normal.y*normal.y + normal.z*normal.z));
normal.x /= length;
normal.y /= length;
normal.z /= length;
normal.x = -normal.x;
normal.y = -normal.y;
normal.z = -normal.z;
normal.x += a->x();
normal.y += a->y();
normal.z += a->z();
return normal;
}
void
Fingerprint::_getFragments(std::vector<int> levels, std::vector<int>curfrag,
int level, OpenBabel::OBAtom* patom, OpenBabel::OBBond* pbond)
{
const int MaxFragSize = 7;
int bo(0);
if (pbond) bo = pbond->IsAromatic() ? 5 : pbond->GetBondOrder();
curfrag.push_back(bo);
curfrag.push_back(patom->GetAtomicNum());
levels[patom->GetIdx()] = level;
std::vector<OpenBabel::OBBond*>::iterator i;
OpenBabel::OBBond* pnewbond;
for (pnewbond = patom->BeginBond(i); pnewbond; pnewbond = patom->NextBond(i))
{
if (pnewbond == pbond)
{
continue;
}
OpenBabel::OBAtom* pnxtat = pnewbond->GetNbrAtom(patom);
int atlevel = levels[pnxtat->GetIdx()];
if (atlevel)
{
if (atlevel == 1)
{
curfrag[0] = bo;
_ringset.insert(curfrag);
}
}
else
{
if (level < MaxFragSize)
{
_getFragments(levels, curfrag, level + 1, pnxtat, pnewbond);
}
}
}
if ((curfrag[0] == 0) &&
((level > 1) || (patom->GetAtomicNum() > 8) || (patom->GetAtomicNum() < 6)))
{
_fragset.insert(curfrag);
}
}