int SetMM3Type(OBAtom *atom)
{
OBAtom *b; // neighbor
OBBondIterator i, j;
int countNeighborO, countNeighborS, countNeighborN, countNeighborC;
countNeighborO = countNeighborS = countNeighborN = countNeighborC = 0;
// The MM2 typing isn't very good, so we do this ourselves for the most common atom types
switch (atom->GetAtomicNum()) {
case 1: // Hydrogen
b = atom->BeginNbrAtom(j);
if (b->IsCarboxylOxygen())
return 24;
if (b->GetAtomicNum() == OBElements::Sulfur)
return 44;
if (b->GetAtomicNum() == OBElements::Nitrogen) {
if (b->IsAmideNitrogen())
return 28;
if (b->GetValence() > 3)
return 48;// ammonium
return 23; // default amine/imine
}
if (b->GetAtomicNum() == OBElements::Carbon && b->GetHyb() == 1)
return 124; // acetylene
if (b->GetAtomicNum() == OBElements::Oxygen) {
if (b->HasAlphaBetaUnsat())
return 73; // includes non-enol/phenol, but has the right spirit
return 21; // default alcohol
}
return 5; // default H
break;
case 2: // Helium
return 51; break;
case 3: // Li
return 163; break;
case 5: // B
if (atom->GetValence() >= 4)
return 27; // tetrahedral
return 26; break;
case 6: // C
if (atom->IsInRingSize(3)) { // cyclopropane / cyclopropene
if (atom->GetHyb() == 3)
return 22;
if (atom->GetHyb() == 2) {
if (atom->CountFreeOxygens() == 1) // propanone
return 67;
return 38; // propane
}
}
if (atom->IsInRingSize(4)) { // cyclobutane or cyclobutene
if (atom->GetHyb() == 3)
return 56;
if (atom->GetHyb() == 2) {
if (atom->CountFreeOxygens() == 1) // butanone
return 58;
return 57; // regular cyclobutane
}
}
if (atom->CountBondsOfOrder(2) == 2) { // allene
if (atom->CountFreeOxygens() == 1) // ketene
return 106;
return 68;
}
if (atom->GetFormalCharge() == +1)
return 30;
if (atom->GetSpinMultiplicity() == 2)
return 29;
if (atom->GetHyb() == 3)
return 1;
else if (atom->GetHyb() == 2) {
if (atom->CountFreeOxygens() >= 1)
return 3;
return 2;
}
else if (atom->GetHyb() == 1)
return 4;
break;
case 7: // N
// TODO
if (atom->IsAmideNitrogen())
return 151;
if (atom->IsAromatic()) {
if (atom->GetFormalCharge() == 1)
return 111;
if (atom->IsInRingSize(5)) // pyrrole
return 40;
if (atom->IsInRingSize(6)) // pyridine
return 37;
}
if (atom->CountFreeOxygens() == 2) // nitro
return 46;
if (atom->GetHyb() == 3) {
if (atom->GetValence() > 3)
return 39; // ammonium
return 8;
}
else if (atom->GetHyb() == 2)
return 9;
else if (atom->GetHyb() == 1)
return 10;
break;
case 8: // O
//TODO
if (atom->IsPhosphateOxygen())
return 159;
if (atom->IsCarboxylOxygen())
return 75;
if (atom->IsInRingSize(3))
return 49; // epoxy
b = atom->BeginNbrAtom(j);
if (atom->HasBondOfOrder(2) && b->GetAtomicNum() == OBElements::Carbon) { // O=C
return 7;
}
if (atom->IsAromatic())
return 41; // furan
return 6;
break;
case 9: // F
return 11; break;
case 10: // Ne
return 52; break;
case 12: // Mg
return 59; break;
case 14: // Si
return 19; break;
case 15: // P
if (atom->CountFreeOxygens() > 0)
return 153; // phosphate
if (atom->BOSum() > 3)
return 60; // phosphorus V
return 25; break;
case 16: // S
if (atom->IsAromatic())
return 42; // thiophene
if (atom->GetFormalCharge() == 1)
return 16; // sulfonium
// look at the neighbors
for (b = atom->BeginNbrAtom(j); b; b = atom->NextNbrAtom(j))
{
switch (b->GetAtomicNum()) {
case 6:
if (b->GetHyb() == 2) // S=C
countNeighborC++; break;
case 7:
countNeighborN++; break;
case 8:
if (b->GetHvyValence() == 1)
countNeighborO++;
break;
case 16:
countNeighborS++; break;
default:
continue;
}
}
if (countNeighborO == 1)
return 17; // sulfoxide
if (countNeighborO >= 2) {
if (countNeighborN)
return 154; // sulfonamide
return 18; // sulfone or sulfate
}
if (countNeighborC)
return 74; // S=C
if (countNeighborS == 1)
return 104; // S-S disulfide
else if (countNeighborS > 1)
return 105;
return 15; break;
case 17: // Cl
return 12; break;
case 18: // Ar
return 153; break;
case 20: // Ca
return 125; break;
case 26: // Fe
if (atom->GetFormalCharge() == 2)
return 61;
return 62; break;
case 27: // Co
if (atom->GetFormalCharge() == 2)
return 65;
return 66; break;
case 28: // Ni
if (atom->GetFormalCharge() == 2)
return 63;
return 64; break;
case 32: // Ge
return 31; break;
case 34: // Se
return 34; break;
case 35: // Br
return 13; break;
case 36: // Kr
return 54; break;
case 38: // Sr
return 126; break;
case 50: // Sn
return 32; break;
case 52: // Te
return 35; break;
case 53: // I
return 14; break;
case 54: // Xe
return 55; break;
case 56: // Ba
return 127; break;
case 57:
return 128; break;
case 58:
return 129; break;
case 59:
return 130; break;
case 60:
return 131; break;
case 61:
return 132; break;
case 62:
return 133; break;
case 63:
return 134; break;
case 64:
return 135; break;
case 65:
return 136; break;
case 66:
return 137; break;
case 67:
return 138; break;
case 68:
return 139; break;
case 69:
return 140; break;
case 70:
return 141; break;
case 71:
return 142; break;
case 82: // Pb
return 33; break;
default:
break;
}
return 0;
}
void OBAromaticTyper::AssignAromaticFlags(OBMol &mol)
{
if (!_init)
Init();
if (mol.HasAromaticPerceived())
return;
mol.SetAromaticPerceived();
obErrorLog.ThrowError(__FUNCTION__,
"Ran OpenBabel::AssignAromaticFlags", obAuditMsg);
_vpa.clear();
_vpa.resize(mol.NumAtoms()+1);
_velec.clear();
_velec.resize(mol.NumAtoms()+1);
_root.clear();
_root.resize(mol.NumAtoms()+1);
OBBond *bond;
OBAtom *atom;
vector<OBAtom*>::iterator i;
vector<OBBond*>::iterator j;
//unset all aromatic flags
for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
atom->UnsetAromatic();
for (bond = mol.BeginBond(j);bond;bond = mol.NextBond(j))
bond->UnsetAromatic();
int idx;
vector<vector<int> >::iterator m;
vector<OBSmartsPattern*>::iterator k;
//mark atoms as potentially aromatic
for (idx=0,k = _vsp.begin();k != _vsp.end();++k,++idx)
if ((*k)->Match(mol))
{
_mlist = (*k)->GetMapList();
for (m = _mlist.begin();m != _mlist.end();++m)
{
_vpa[(*m)[0]] = true;
_velec[(*m)[0]] = _verange[idx];
}
}
//sanity check - exclude all 4 substituted atoms and sp centers
for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
{
if (atom->GetImplicitValence() > 3)
{
_vpa[atom->GetIdx()] = false;
continue;
}
switch(atom->GetAtomicNum())
{
//phosphorus and sulfur may be initially typed as sp3
case 6:
case 7:
case 8:
if (atom->GetHyb() != 2)
_vpa[atom->GetIdx()] = false;
break;
}
}
//propagate potentially aromatic atoms
for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
if (_vpa[atom->GetIdx()])
PropagatePotentialAromatic(atom);
//select root atoms
SelectRootAtoms(mol);
ExcludeSmallRing(mol); //remove 3 membered rings from consideration
//loop over root atoms and look for aromatic rings
_visit.clear();
_visit.resize(mol.NumAtoms()+1);
for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
if (_root[atom->GetIdx()])
CheckAromaticity(atom,14);
//for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
// if (atom->IsAromatic())
// cerr << "aro = " <<atom->GetIdx() << endl;
//for (bond = mol.BeginBond(j);bond;bond = mol.NextBond(j))
//if (bond->IsAromatic())
//cerr << bond->GetIdx() << ' ' << bond->IsAromatic() << endl;
}