void Seed::fillNewBonds(const ROMol& qmol) {
std::vector<bool> excludedBonds = ExcludedBonds;
for (unsigned srcAtomIdx = LastAddedAtomsBeginIdx; srcAtomIdx < getNumAtoms();
srcAtomIdx++) { // all atoms added on previous growing only
const Atom* atom = MoleculeFragment.Atoms[srcAtomIdx];
ROMol::OEDGE_ITER beg, end;
for (boost::tie(beg, end) = qmol.getAtomBonds(atom); beg != end;
beg++) { // all bonds from MoleculeFragment.Atoms[srcAtomIdx]
const Bond* bond = &*(qmol[*beg]);
if (!excludedBonds[bond->getIdx()]) {
// already in the seed or NewBonds list from another atom in a RING
excludedBonds[bond->getIdx()] = true;
unsigned ai = (atom == bond->getBeginAtom()) ? bond->getEndAtomIdx()
: bond->getBeginAtomIdx();
const Atom* end_atom = qmol.getAtomWithIdx(ai);
unsigned end_atom_idx = NotSet;
for (unsigned i = 0; i < getNumAtoms(); i++)
if (end_atom ==
MoleculeFragment.Atoms[i]) { // already exists in this seed
end_atom_idx = i;
break;
}
NewBonds.push_back(
NewBond(srcAtomIdx, bond->getIdx(), ai, end_atom_idx,
NotSet == end_atom_idx ? end_atom : nullptr));
}
}
}
}
void AtomContainer::addAtom(const double * pos, const std::vector<std::string>& atomProperties){
int iProperty;
//after adding the atom was successful, continue with adding additional properties
if(addAtom(pos)) {
//save additional properties
for (iProperty = 0; iProperty < atomProperties.size(); iProperty++){
if (!atomPropertyList.isPropertyInt(iProperty)) {
//property has float type
atomPropertyList.addFloatPropertyValue(iProperty, atof(atomProperties[iProperty].c_str()));
} else {
//property has integer type
if (isFloat(atomProperties[iProperty])) {
//but current value is of float type -> conversion
atomPropertyList.convertPropertyToFloat(iProperty);
atomPropertyList.addFloatPropertyValue(iProperty, atof(atomProperties[iProperty].c_str()));
} else {
//value has also integer type -> add value
atomPropertyList.addIntPropertyValue(iProperty,atoi(atomProperties[iProperty].c_str()));
}
}
}
} else {
std::cout << "WARNING: Adding atom " << getNumAtoms() <<" failed (placed outside container)" << std::endl;
}
}
void Seed::computeRemainingSize(const ROMol& qmol) {
RemainingBonds = RemainingAtoms = 0;
std::vector<unsigned> end_atom_stack;
std::vector<bool> visitedBonds = ExcludedBonds;
std::vector<bool> visitedAtoms(qmol.getNumAtoms());
for (auto&& visitedAtom : visitedAtoms) visitedAtom = false;
for (std::vector<unsigned>::const_iterator it =
MoleculeFragment.AtomsIdx.begin();
it != MoleculeFragment.AtomsIdx.end(); it++)
visitedAtoms[*it] = true;
// SDF all paths
// 1. direct neighbours
for (unsigned seedAtomIdx = LastAddedAtomsBeginIdx;
seedAtomIdx < getNumAtoms();
seedAtomIdx++) { // just now added new border vertices (candidates for
// future growing)
const Atom* atom = MoleculeFragment.Atoms[seedAtomIdx];
ROMol::OEDGE_ITER beg, end;
for (boost::tie(beg, end) = qmol.getAtomBonds(atom); beg != end;
beg++) { // all bonds from MoleculeFragment.Atoms[srcAtomIdx]
const Bond& bond = *(qmol[*beg]);
if (!visitedBonds[bond.getIdx()]) {
++RemainingBonds;
visitedBonds[bond.getIdx()] = true;
unsigned end_atom_idx =
(MoleculeFragment.AtomsIdx[seedAtomIdx] == bond.getBeginAtomIdx())
? bond.getEndAtomIdx()
: bond.getBeginAtomIdx();
if (!visitedAtoms[end_atom_idx]) { // check RING/CYCLE
++RemainingAtoms;
visitedAtoms[end_atom_idx] = true;
end_atom_stack.push_back(end_atom_idx);
}
}
}
}
// 2. go deep
while (!end_atom_stack.empty()) {
unsigned ai = end_atom_stack.back();
end_atom_stack.pop_back();
const Atom* atom = qmol.getAtomWithIdx(ai);
ROMol::OEDGE_ITER beg, end;
for (boost::tie(beg, end) = qmol.getAtomBonds(atom); beg != end;
beg++) { // all bonds from end_atom
const Bond& bond = *(qmol[*beg]);
if (!visitedBonds[bond.getIdx()]) {
++RemainingBonds;
visitedBonds[bond.getIdx()] = true;
unsigned end_atom_idx = (ai == bond.getBeginAtomIdx())
? bond.getEndAtomIdx()
: bond.getBeginAtomIdx();
if (!visitedAtoms[end_atom_idx]) { // check RING/CYCLE
++RemainingAtoms;
visitedAtoms[end_atom_idx] = true;
end_atom_stack.push_back(end_atom_idx);
}
}
}
}
}
