//--
// [rad] generate path and ident for bond
void RelationBond::GetPathAndIdentBond(const std::string& refMoleculeId, std::string& refPath, std::string& refIdent)
{
refPath = m_vecSatisfiedClasses.front()->GetPrefix() + ":" + m_vecSatisfiedClasses.front()->GetName();
std::stringstream ssConv;
OpenBabel::OBBond* pBond = m_pBond;
OpenBabel::OBAtom* pAtomStart = pBond->GetBeginAtom();
OpenBabel::OBAtom* pAtomEnd = pBond->GetEndAtom();
ssConv << m_vecSatisfiedClasses.front()->GetName() << "_" << refMoleculeId << "_" <<
pAtomStart->GetIdx() << "_" << pAtomEnd->GetIdx();
refIdent = "";
ssConv >> refIdent;
}
// [rad] generate path and ident for bond
void RelationBond::GetObjectPropertyPathAndIdentBond(int iPosition,
const std::string& refMoleculeId,
std::string& refPath,
std::string& refIdent)
{
refPath = m_vecSatisfiedObjectPropertiesBond[iPosition].first->GetPrefix() + ":" +
m_vecSatisfiedObjectPropertiesBond[iPosition].first->GetName();
std::stringstream ssConv;
OpenBabel::OBAtom* pAtomStart = m_vecSatisfiedObjectPropertiesBond[iPosition].second->m_pBond->GetBeginAtom();
OpenBabel::OBAtom* pAtomEnd = m_vecSatisfiedObjectPropertiesBond[iPosition].second->m_pBond->GetEndAtom();
ssConv << m_vecSatisfiedObjectPropertiesBond[iPosition].second->m_vecSatisfiedClasses.front()->GetName() << "_" << refMoleculeId << "_" <<
pAtomStart->GetIdx() << "_" << pAtomEnd->GetIdx();
refIdent = "";
ssConv >> refIdent;
}
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);
}
}
void Molecule::addHydrogens(Atom *a,
const QList<unsigned long> &atomIds,
const QList<unsigned long> &bondIds)
{
if (atomIds.size() != bondIds.size()) {
qDebug() << "Error, addHydrogens called with atom & bond id lists of different size!";
}
// Construct an OBMol, call AddHydrogens and translate the changes
OpenBabel::OBMol obmol = OBMol();
if (a) {
OpenBabel::OBAtom *obatom = obmol.GetAtom(a->index()+1);
// Set implicit valence for unusual elements not handled by OpenBabel
// PR#2803076
switch (obatom->GetAtomicNum()) {
case 3:
case 11:
case 19:
case 37:
case 55:
case 85:
case 87:
obatom->SetImplicitValence(1);
obatom->SetHyb(1);
obmol.SetImplicitValencePerceived();
break;
case 4:
case 12:
case 20:
case 38:
case 56:
case 88:
obatom->SetImplicitValence(2);
obatom->SetHyb(2);
obmol.SetImplicitValencePerceived();
break;
case 84: // Po
obatom->SetImplicitValence(2);
obatom->SetHyb(3);
obmol.SetImplicitValencePerceived();
break;
default: // do nothing
break;
}
obmol.AddHydrogens(obatom);
}
else
obmol.AddHydrogens();
// All new atoms in the OBMol must be the additional hydrogens
unsigned int numberAtoms = numAtoms();
int j = 0;
for (unsigned int i = numberAtoms+1; i <= obmol.NumAtoms(); ++i, ++j) {
if (obmol.GetAtom(i)->IsHydrogen()) {
OpenBabel::OBAtom *obatom = obmol.GetAtom(i);
Atom *atom;
if (atomIds.isEmpty())
atom = addAtom();
else if (j < atomIds.size())
atom = addAtom(atomIds.at(j));
else {
qDebug() << "Error - not enough unique ids in addHydrogens.";
break;
}
atom->setOBAtom(obatom);
// Get the neighbor atom
OpenBabel::OBBondIterator iter;
OpenBabel::OBAtom *next = obatom->BeginNbrAtom(iter);
Bond *bond;
if (bondIds.isEmpty())
bond = addBond();
else // Already confirmed by atom ids
bond = addBond(bondIds.at(j));
bond->setEnd(Molecule::atom(atom->index()));
bond->setBegin(Molecule::atom(next->GetIdx()-1));
}
}
for (unsigned int i = 1; i <= numberAtoms; ++i) {
// Warning -- OB atom index off-by-one here
atom(i-1)->setPartialCharge(obmol.GetAtom(i)->GetPartialCharge());
}
}
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;
}