extern "C" int write_output_(char *out_filename, double *A, int *n)
{
std::ofstream ofs(out_filename);
OpenBabel::OBConversion ob(NULL, &ofs);
OpenBabel::OBAtom atom;
OpenBabel::OBMol mol;
int i;
ob.SetOutFormat("CML");
/* Atom is Iridium */
atom.SetAtomicNum(77);
for (i = 0; i < *n; i++)
{
atom.SetVector(A[i*3], A[i*3+1], A[i*3+2]);
mol.AddAtom(atom);
}
//for (i=0; i < *n; i++)
//{
//for (int j=i; j < *n; j++)
//{
//mol.AddBond(i+1, j+1, 0);
//}
//}
ob.Write(&mol);
ob.CloseOutFile();
}
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;
}