void
FilterRings::Calculate(OpenBabel::OBMol* mol)
{
// Are there rings?
bool rings(false);
OpenBabel::OBAtom* atom;
std::vector<OpenBabel::OBAtom*>::iterator i;
for (atom = mol->BeginAtom(i); atom; atom = mol->NextAtom(i))
{
if (atom->IsInRing())
{
rings = true;
break;
}
}
if (rings)
{
std::vector<OpenBabel::OBRing* > nrings = mol->GetSSSR();
_result = nrings.size();
}
else
{
_result = 0;
}
if ((_minLimit && (_result < _min)) || (_maxLimit && (_result > _max)))
{
_passed = false;
}
else
{
_passed = true;
}
}
void
FilterNonaromaticRingFraction::Calculate(OpenBabel::OBMol* mol)
{
// Are there atoms and rings?
unsigned int rings(0);
unsigned int natoms(0);
OpenBabel::OBAtom* atom;
std::vector<OpenBabel::OBAtom*>::iterator i;
for (atom = mol->BeginAtom(i); atom; atom = mol->NextAtom(i))
{
if (atom->IsHydrogen()) continue;
if (atom->IsInRing()) ++rings;
++natoms;
}
if (!natoms)
{
_result = 0.0;
_passed = false;
return;
}
std::set<int> uniqRingIdx;
if (rings)
{
std::vector<OpenBabel::OBRing*> nrings = mol->GetSSSR();
uniqRingIdx.clear();
std::vector<int>::iterator path;
std::vector<OpenBabel::OBRing*>::iterator ri;
for (ri = nrings.begin(); ri != nrings.end(); ++ri)
{
if (!(*ri)->IsAromatic())
{
for (path = (*ri)->_path.begin(); path != (*ri)->_path.end(); ++path)
{
uniqRingIdx.insert(*path);
}
}
}
}
unsigned int ar(uniqRingIdx.size());
if (ar)
{
_result = (double) ar / (double) natoms;
}
else
{
_result = 0.0;
}
if ((_minLimit && (_result < _min)) || (_maxLimit && (_result > _max)))
{
_passed = false;
}
else
{
_passed = true;
}
}
void
FilterCores::Calculate(OpenBabel::OBMol* mol)
{
// Any rings?
OpenBabel::OBAtom* atom;
std::vector<OpenBabel::OBAtom*>::iterator i;
bool rings(false);
for (atom = mol->BeginAtom(i); atom; atom = mol->NextAtom(i))
{
if (atom->IsInRing())
{
rings = true;
break;
}
}
if (rings)
{
// Make workcopy of original mol
OpenBabel::OBMol m = *mol; m.DeleteHydrogens();
// Iteratively remove all endstanding atoms until none are left
OpenBabel::OBAtom* atom;
std::vector<OpenBabel::OBAtom*>::iterator i;
bool endstanding(true);
while (endstanding && m.NumAtoms())
{
endstanding = false;
for (atom = m.BeginAtom(i); atom; atom = m.NextAtom(i))
{
if (atom->GetValence() < 2)
{
if (m.DeleteAtom(atom))
{
endstanding = true;
break;
}
}
}
}
if (m.NumAtoms()) _result = 1;
else _result = 0;
}
else
{
_result = 0;
}
if ((_minLimit && (_result < _min)) || (_maxLimit && (_result > _max)))
{
_passed = false;
}
else
{
_passed = true;
}
}
void
FilterAtomsInLargestNonaromaticRing::Calculate(OpenBabel::OBMol* mol)
{
// Are there rings?
bool rings(false);
OpenBabel::OBAtom* atom;
std::vector<OpenBabel::OBAtom*>::iterator i;
for (atom = mol->BeginAtom(i); atom; atom = mol->NextAtom(i))
{
if (atom->IsInRing())
{
rings = true;
break;
}
}
if (rings)
{
std::vector<OpenBabel::OBRing*> nrings = mol->GetSSSR();
_result = 0;
std::vector<OpenBabel::OBRing*>::iterator ri;
for (ri = nrings.begin(); ri != nrings.end(); ++ri)
{
if ( !(*ri)->IsAromatic() && ((*ri)->Size() > _result))
{
_result = (*ri)->Size();
}
}
if ((_minLimit && (_result < _min)) || (_maxLimit && (_result > _max)))
{
_passed = false;
}
else
{
_passed = true;
}
}
else
{
_result = 0;
_passed = true;
}
}
bool
Oprea_1::CalculateScaffold(const OpenBabel::OBMol& mol, Options* o)
{
OpenBabel::OBMol m(mol);
OpenBabel::OBAtom* atom;
OpenBabel::OBAtom* nbrAtom[2];
OpenBabel::OBBondIterator bi;
std::vector<OpenBabel::OBAtom*>::iterator avi;
OpenBabel::OBBond* bond;
std::vector<OpenBabel::OBBond*>::iterator bvi;
bool removed(true);
while (removed)
{
removed = false;
for (atom = m.BeginAtom(avi); atom; atom = m.NextAtom(avi))
{
if (IsEndStanding(atom, false, false))
{
m.DeleteAtom(atom);
removed = true;
break;
}
}
}
// Make all atoms as neutral C and all bond orders equal to 1
m.BeginModify();
for (atom = m.BeginAtom(avi); atom; atom = m.NextAtom(avi))
{
atom->SetAtomicNum(6);
atom->SetFormalCharge(0);
}
for (bond = m.BeginBond(bvi); bond; bond = m.NextBond(bvi))
{
bond->SetBondOrder(1);
}
m.EndModify();
// Transform all neighbouring linker atoms into a single bond
removed = true;
while (removed)
{
removed = false;
for (atom = m.BeginAtom(avi); atom; atom = m.NextAtom(avi))
{
if (!atom->IsInRing() && (atom->GetValence() == 2))
{
nbrAtom[0] = atom->BeginNbrAtom(bi);
nbrAtom[1] = atom->NextNbrAtom(bi);
if (nbrAtom[0] && nbrAtom[1])
{
m.BeginModify();
m.AddBond(nbrAtom[0]->GetIdx(), nbrAtom[1]->GetIdx(), 1);
m.DeleteAtom(atom);
m.EndModify();
removed = true;
break;
}
}
}
}
// Shrink all rings to their minimum size
removed = true;
while (removed)
{
removed = false;
for (atom = m.BeginAtom(avi); atom; atom = m.NextAtom(avi))
{
if ((atom->MemberOfRingSize() > 3) &&
(atom->GetValence() == 2))
{
nbrAtom[0] = atom->BeginNbrAtom(bi);
nbrAtom[1] = atom->NextNbrAtom(bi);
if (nbrAtom[0] && nbrAtom[1])
{
m.BeginModify();
m.AddBond(nbrAtom[0]->GetIdx(), nbrAtom[1]->GetIdx(), 1);
m.DeleteAtom(atom);
m.EndModify();
removed = true;
break;
}
}
}
}
if (!m.Empty())
{
_smiles = _mol2can.WriteString(&m, true);
}
else
{
_smiles = "-";
return false;
}
return true;
}
bool
Oprea_2::CalculateScaffold(const OpenBabel::OBMol& mol, Options* o)
{
OpenBabel::OBMol m(mol);
// Tag all HBD
std::vector<bool> hbd(m.NumAtoms() + 1);
for (OpenBabel::OBMolAtomIter atom(m); atom; ++atom)
{
if (atom->MatchesSMARTS("[NH,NH2,NH3,OH,nH]"))
{
hbd[atom->GetIdx()] = true;
}
else
{
hbd[atom->GetIdx()] = false;
}
}
// Tag all HBA
std::vector<bool> hba(m.NumAtoms() + 1);
for (OpenBabel::OBMolAtomIter atom(m); atom; ++atom)
{
if (!atom->IsAmideNitrogen() && // No amide nitrogen
!atom->IsAromatic() && // Not aromatic
(atom->GetFormalCharge() <= 0) && // No + charge
atom->MatchesSMARTS("[NH0]")) // No hydrogens
{
hba[atom->GetIdx()] = true;
}
else
if (atom->IsNitrogen() && // Nitrogen
atom->IsAromatic() && // Aromatic
atom->MatchesSMARTS("[nH0]") && // No hydrogens
(atom->GetHvyValence() <= 2) && // Maximal two non-H atoms connected
(atom->GetFormalCharge() <= 0)) // No + charge
{
hba[atom->GetIdx()] = true;
}
else
if (atom->IsOxygen() && // Oxygen
(atom->GetFormalCharge() <= 0)) // No + charge
{
hba[atom->GetIdx()] = true;
}
else
{
hba[atom->GetIdx()] = false;
}
}
// Mark the C(=O) or S(=O) also as HBA
for (OpenBabel::OBMolAtomIter atom(m); atom; ++atom)
{
if (atom->MatchesSMARTS("C=O"))
{
hba[atom->GetIdx()] = true;
}
else
if (atom->MatchesSMARTS("S=O"))
{
hba[atom->GetIdx()] = true;
}
}
// Make all atoms as neutral C, N (HBD), or O (HBA)
m.BeginModify();
std::vector<OpenBabel::OBAtom*>::iterator avi;
OpenBabel::OBAtom* atom;
for (atom = m.BeginAtom(avi); atom; atom = m.NextAtom(avi))
{
if (hba[atom->GetIdx()])
{
atom->SetAtomicNum(8);
}
else
if (hbd[atom->GetIdx()])
{
atom->SetAtomicNum(7);
}
else
{
atom->SetAtomicNum(6);
}
atom->SetFormalCharge(0);
}
m.EndModify();
// Remove all endstanding atoms
OpenBabel::OBBondIterator bi;
OpenBabel::OBBond* bond;
std::vector<OpenBabel::OBBond*>::iterator bvi;
bool removed(true);
while (removed)
{
removed = false;
for (atom = m.BeginAtom(avi); atom; atom = m.NextAtom(avi))
{
if (IsEndStanding(atom, false, false))
{
m.DeleteAtom(atom);
removed = true;
break;
}
}
}
// Set all bond orders equal to 1
m.BeginModify();
for (bond = m.BeginBond(bvi); bond; bond = m.NextBond(bvi))
{
bond->SetBondOrder(1);
}
m.EndModify();
// Transform all neighbouring linker atoms into a single bond
removed = true;
OpenBabel::OBAtom* nbrAtom[2];
while (removed)
{
removed = false;
for (atom = m.BeginAtom(avi); atom; atom = m.NextAtom(avi))
{
if (!atom->IsInRing() && (atom->GetValence() == 2))
{
m.BeginModify();
nbrAtom[0] = atom->BeginNbrAtom(bi);
nbrAtom[1] = atom->NextNbrAtom(bi);
if (nbrAtom[0] && nbrAtom[1])
{
m.AddBond(nbrAtom[0]->GetIdx(), nbrAtom[1]->GetIdx(), 1);
m.DeleteAtom(atom);
m.EndModify();
removed = true;
break;
}
}
}
}
// Shrink all rings to their minimum size
removed = true;
while (removed)
{
removed = false;
for (atom = m.BeginAtom(avi); atom; atom = m.NextAtom(avi))
{
if ((atom->MemberOfRingSize() > 3) && (atom->GetValence() == 2))
{
nbrAtom[0] = atom->BeginNbrAtom(bi);
nbrAtom[1] = atom->NextNbrAtom(bi);
if (nbrAtom[0] && nbrAtom[1])
{
if (nbrAtom[0]->GetAtomicNum() == atom->GetAtomicNum())
{
m.BeginModify();
m.AddBond(nbrAtom[0]->GetIdx(), nbrAtom[1]->GetIdx(), 1);
m.DeleteAtom(atom);
m.EndModify();
removed = true;
break;
}
else
if (nbrAtom[1]->GetAtomicNum() == atom->GetAtomicNum())
{
m.BeginModify();
m.AddBond(nbrAtom[0]->GetIdx(), nbrAtom[1]->GetIdx(), 1);
m.DeleteAtom(atom);
m.EndModify();
removed = true;
break;
}
}
}
}
}
if (!m.Empty())
{
_smiles = _mol2can.WriteString(&m, true);
}
else
{
_smiles = "-";
return false;
}
return true;
}
void
FilterBridgeFraction::Calculate(OpenBabel::OBMol* mol)
{
// Are there rings?
OpenBabel::OBAtom* atom;
std::vector<OpenBabel::OBAtom*>::iterator i;
bool rings(false);
for (atom = mol->BeginAtom(i); atom; atom = mol->NextAtom(i))
{
if (atom->IsInRing())
{
rings = true;
break;
}
}
if (rings)
{
// Make workcopy of original mol
OpenBabel::OBMol m = *mol; m.DeleteHydrogens();
unsigned int natoms(m.NumAtoms());
if (!natoms)
{
_result = 0.0;
_passed = false;
return;
}
// Iteratively remove all endstanding atoms until none are left
OpenBabel::OBAtom* atom;
std::vector<OpenBabel::OBAtom*>::iterator i;
bool endstanding(true);
while (endstanding && m.NumAtoms())
{
endstanding = false;
for (atom = m.BeginAtom(i); atom; atom = m.NextAtom(i))
{
if (atom->GetValence() < 2)
{
if (m.DeleteAtom(atom))
{
endstanding = true;
break;
}
}
}
}
// Now remove all ring atoms
rings = true;
while (rings && m.NumAtoms())
{
rings = false;
for (atom = m.BeginAtom(i); atom; atom = m.NextAtom(i))
{
if (atom->IsInRing())
{
if (m.DeleteAtom(atom))
{
rings = true;
break;
}
}
}
}
_result = (double) m.NumAtoms() / (double) natoms;
}
else
{
_result = 0.0;
}
if ((_minLimit && (_result < _min)) || (_maxLimit && (_result > _max)))
{
_passed = false;
}
else
{
_passed = true;
}
}
void
FilterAtomsInSmallestBridge::Calculate(OpenBabel::OBMol* mol)
{
// Are there rings?
OpenBabel::OBAtom* atom;
std::vector<OpenBabel::OBAtom*>::iterator i;
bool rings(false);
for (atom = mol->BeginAtom(i); atom; atom = mol->NextAtom(i))
{
if (atom->IsInRing())
{
rings = true;
break;
}
}
if (rings)
{
// Make workcopy of original mol
OpenBabel::OBMol m = *mol; m.DeleteHydrogens();
// Iteratively remove all endstanding atoms until none are left
OpenBabel::OBAtom* atom;
std::vector<OpenBabel::OBAtom*>::iterator i;
bool endstanding(true);
while (endstanding && m.NumAtoms())
{
endstanding = false;
for (atom = m.BeginAtom(i); atom; atom = m.NextAtom(i))
{
if (atom->GetValence() < 2)
{
if (m.DeleteAtom(atom))
{
endstanding = true;
break;
}
}
}
}
// Now remove all ring atoms
rings = true;
while (rings && m.NumAtoms())
{
rings = false;
for (atom = m.BeginAtom(i); atom; atom = m.NextAtom(i))
{
if (atom->IsInRing())
{
if (m.DeleteAtom(atom))
{
rings = true;
break;
}
}
}
}
// Separate into fragments
if (m.NumAtoms())
{
std::vector<std::vector<int> > bridges;
m.ContigFragList(bridges);
_result = bridges[0].size();
for (unsigned int i(1); i < bridges.size(); ++i)
{
if (bridges[i].size() < _result) _result = bridges[i].size();
}
}
if ((_minLimit && (_result < _min)) || (_maxLimit && (_result > _max)))
{
_passed = false;
}
else
{
_passed = true;
}
}
else
{
_result = 0;
_passed = true;
}
}
OpenBabel::OBMol
Schuffenhauer::Rule_11(OpenBabel::OBMol& oldMol)
{
// Return if the molecule contains an acyclic linker
std::vector<OpenBabel::OBAtom*>::iterator avi;
OpenBabel::OBAtom* atom;
for (atom = oldMol.BeginAtom(avi); atom; atom = oldMol.NextAtom(avi))
{
if (!atom->IsInRing() && atom->GetValence() >= 2)
{
return oldMol;
}
}
// Make sure we are dealing with a mixed aromatic/nonaromatic system
bool notaromatic(false);
bool aromatic(false);
for (atom = oldMol.BeginAtom(avi); atom; atom = oldMol.NextAtom(avi))
{
if (atom->IsAromatic())
{
aromatic = true;
}
else
{
notaromatic = true;
}
}
if (aromatic && notaromatic)
{
std::vector<OpenBabel::OBRing*> allrings(oldMol.GetSSSR());
if (allrings.size() <= _ringsToBeRetained)
{
return oldMol;
}
std::vector<OpenBabel::OBMol> mols;
std::vector<unsigned int> aromaticRings;
for (unsigned int i(0); i < allrings.size(); ++i)
{
if (allrings[i]->IsAromatic())
{
mols.push_back(oldMol);
aromaticRings.push_back(i);
}
}
std::vector<OpenBabel::OBMol> validMols;
for (unsigned int i(0); i < aromaticRings.size(); ++i)
{
mols[i] = RemoveRing(mols[i], allrings, aromaticRings[i]);
if (!mols[i].Empty())
{
validMols.push_back(mols[i]);
}
}
if (validMols.size() == 1)
{
return validMols[0];
}
}
return oldMol;
}
OpenBabel::OBMol
Schuffenhauer::Rule_7(OpenBabel::OBMol& oldMol)
{
std::vector<OpenBabel::OBRing*> allrings(oldMol.GetSSSR());
if (allrings.size() <= _ringsToBeRetained)
{
return oldMol;
}
// Are all atoms and bonds aromatic?
std::vector<OpenBabel::OBAtom*>::iterator avi;
OpenBabel::OBAtom* atom;
for (atom = oldMol.BeginAtom(avi); atom; atom = oldMol.NextAtom(avi))
{
if (!atom->IsAromatic())
{
return oldMol;
}
}
std::vector<OpenBabel::OBBond*>::iterator bvi;
OpenBabel::OBBond* bond;
for (bond = oldMol.BeginBond(bvi); bond; bond = oldMol.NextBond(bvi))
{
if (!bond->IsAromatic())
{
return oldMol;
}
}
std::vector<OpenBabel::OBMol> mols;
for (unsigned int i(0); i < allrings.size(); ++i)
{
mols.push_back(oldMol);
}
std::vector<OpenBabel::OBMol> validMols;
for (unsigned int i(0); i < mols.size(); ++i)
{
mols[i] = RemoveRing(mols[i], allrings, i);
if (!mols[i].Empty())
{
// Has aromaticity been broken?
bool broken(false);
for (atom = mols[i].BeginAtom(avi); atom; atom = mols[i].NextAtom(avi))
{
if (atom->IsInRing() && !atom->IsAromatic())
{
broken = true;
break;
}
}
if (!broken)
{
validMols.push_back(mols[i]);
}
}
}
if (validMols.size() == 1)
{
return validMols[0];
}
return oldMol;
}
void
FilterRingsystems::Calculate(OpenBabel::OBMol* mol)
{
// Are there rings?
bool rings(false);
OpenBabel::OBAtom* atom;
std::vector<OpenBabel::OBAtom*>::iterator i;
for (atom = mol->BeginAtom(i); atom; atom = mol->NextAtom(i))
{
if (atom->IsInRing())
{
rings = true;
break;
}
}
if (rings)
{
// Make workcopy of original mol
OpenBabel::OBMol m = *mol; m.DeleteHydrogens();
// Remove all atoms that are not part of ring
std::vector<OpenBabel::OBAtom*> nonRingAtoms;
nonRingAtoms.clear();
for (atom = m.BeginAtom(i); atom; atom = m.NextAtom(i))
{
if (!atom->IsInRing()) nonRingAtoms.push_back(atom);
}
for (unsigned int i(0); i < nonRingAtoms.size(); ++i)
{
m.DeleteAtom(nonRingAtoms[i]);
}
// Remove all bonds that are not part of a ring
std::vector<OpenBabel::OBBond*> nonRingBonds;
nonRingBonds.clear();
OpenBabel::OBBond* bond;
std::vector<OpenBabel::OBBond*>::iterator j;
for (bond = m.BeginBond(j); bond; bond = m.NextBond(j))
{
if (!bond->IsInRing()) nonRingBonds.push_back(bond);
}
for (unsigned int i(0); i < nonRingBonds.size(); ++i)
{
m.DeleteBond(nonRingBonds[i]);
}
// Count ringsystems
std::vector<std::vector< int > > ringsystems;
m.ContigFragList(ringsystems);
_result = ringsystems.size();
}
else
{
_result = 0;
}
if ((_minLimit && (_result < _min)) || (_maxLimit && (_result > _max)))
{
_passed = false;
}
else
{
_passed = true;
}
}