void MoleculeInChI::_normalizeMolecule(Molecule &mol)
{
QS_DEF(Array<int>, ignored);
ignored.clear_resize(mol.vertexEnd());
ignored.zerofill();
for (int i = mol.vertexBegin(); i < mol.vertexEnd(); i = mol.vertexNext(i))
if (mol.convertableToImplicitHydrogen(i))
ignored[i] = 1;
for (int i = mol.edgeBegin(); i != mol.edgeEnd(); i = mol.edgeNext(i))
if (mol.getBondTopology(i) == TOPOLOGY_RING)
mol.cis_trans.setParity(i, 0);
MoleculeAutomorphismSearch of;
of.detect_invalid_cistrans_bonds = true;
of.detect_invalid_stereocenters = true;
of.find_canonical_ordering = false;
of.ignored_vertices = ignored.ptr();
of.process(mol);
for (int i = mol.edgeBegin(); i != mol.edgeEnd(); i = mol.edgeNext(i))
if (mol.cis_trans.getParity(i) != 0 && of.invalidCisTransBond(i))
mol.cis_trans.setParity(i, 0);
for (int i = mol.vertexBegin(); i != mol.vertexEnd(); i = mol.vertexNext(i))
if (mol.stereocenters.getType(i) > MoleculeStereocenters::ATOM_ANY && of.invalidStereocenter(i))
mol.stereocenters.remove(i);
}
void CanonicalSmilesSaver::saveMolecule (Molecule &mol_) const
{
if (mol_.vertexCount() < 1)
return;
QS_DEF(Array<int>, ignored);
QS_DEF(Array<int>, order);
QS_DEF(Array<int>, ranks);
QS_DEF(Molecule, mol);
int i;
if (mol_.repeating_units.size() > 0)
throw Error("can not canonicalize a polymer");
// Detect hydrogens configuration if aromatic but not ambiguous
bool found_invalid_h = false;
for (i = mol_.vertexBegin(); i != mol_.vertexEnd(); i = mol_.vertexNext(i))
{
if (mol_.isRSite(i) || mol_.isPseudoAtom(i))
continue;
if (mol_.getImplicitH_NoThrow(i, -1) == -1)
found_invalid_h = true;
}
if (found_invalid_h)
{
AromaticityOptions options;
options.method = AromaticityOptions::GENERIC;
options.unique_dearomatization = true;
MoleculeDearomatizer::restoreHydrogens(mol_, options);
}
mol.clone(mol_, 0, 0);
// TODO: canonicalize allenes properly
mol.allene_stereo.clear();
ignored.clear_resize(mol.vertexEnd());
ignored.zerofill();
for (i = mol.vertexBegin(); i < mol.vertexEnd(); i = mol.vertexNext(i))
if (mol.convertableToImplicitHydrogen(i))
ignored[i] = 1;
for (i = mol.edgeBegin(); i != mol.edgeEnd(); i = mol.edgeNext(i))
if (mol.getBondTopology(i) == TOPOLOGY_RING && mol.cis_trans.getParity(i) != 0)
{
// we save cis/trans ring bonds into SMILES, but only those who
// do not participate in bigger ring systems
const Edge &edge = mol.getEdge(i);
if (mol.getAtomRingBondsCount(edge.beg) != 2 ||
mol.getAtomRingBondsCount(edge.end) != 2)
{
mol.cis_trans.setParity(i, 0);
continue;
}
// also, discard the cis-trans bonds that have been converted to aromatic
const Vertex &beg = mol.getVertex(edge.beg);
const Vertex &end = mol.getVertex(edge.end);
bool have_singlebond_beg = false;
bool have_singlebond_end = false;
int j;
for (j = beg.neiBegin(); j != beg.neiEnd(); j = beg.neiNext(j))
if (mol.getBondOrder(beg.neiEdge(j)) == BOND_SINGLE)
have_singlebond_beg = true;
for (j = end.neiBegin(); j != end.neiEnd(); j = end.neiNext(j))
if (mol.getBondOrder(end.neiEdge(j)) == BOND_SINGLE)
have_singlebond_end = true;
if (!have_singlebond_beg || !have_singlebond_end)
{
mol.cis_trans.setParity(i, 0);
continue;
}
}
MoleculeAutomorphismSearch of;
of.detect_invalid_cistrans_bonds = find_invalid_stereo;
of.detect_invalid_stereocenters = find_invalid_stereo;
of.find_canonical_ordering = true;
of.ignored_vertices = ignored.ptr();
of.process(mol);
of.getCanonicalNumbering(order);
for (i = mol.edgeBegin(); i != mol.edgeEnd(); i = mol.edgeNext(i))
if (mol.cis_trans.getParity(i) != 0 && of.invalidCisTransBond(i))
mol.cis_trans.setParity(i, 0);
for (i = mol.vertexBegin(); i != mol.vertexEnd(); i = mol.vertexNext(i))
if (mol.stereocenters.getType(i) > MoleculeStereocenters::ATOM_ANY && of.invalidStereocenter(i))
mol.stereocenters.remove(i);
ranks.clear_resize(mol.vertexEnd());
for (i = 0; i < order.size(); i++)
ranks[order[i]] = i;
SmilesSaver saver(_output);
saver.ignore_invalid_hcount = false;
saver.vertex_ranks = ranks.ptr();
saver.ignore_hydrogens = true;
saver.canonize_chiralities = true;
saver.saveMolecule(mol);
}
void CanonicalSmilesSaver::saveMolecule (Molecule &mol_)
{
if (mol_.vertexCount() < 1)
return;
QS_DEF(Array<int>, ignored);
QS_DEF(Array<int>, order);
QS_DEF(Array<int>, ranks);
QS_DEF(Molecule, mol);
int i;
if (mol_.sgroups.isPolimer())
throw Error("can not canonicalize a polymer");
// Detect hydrogens configuration if aromatic but not ambiguous
// We can store this infromation in the original structure mol_.
mol_.restoreAromaticHydrogens();
mol.clone(mol_, 0, 0);
// TODO: canonicalize allenes properly
mol.allene_stereo.clear();
ignored.clear_resize(mol.vertexEnd());
ignored.zerofill();
for (i = mol.vertexBegin(); i < mol.vertexEnd(); i = mol.vertexNext(i))
if (mol.convertableToImplicitHydrogen(i))
ignored[i] = 1;
// Try to save into ordinary smiles and find what cis-trans bonds were used
NullOutput null_output;
SmilesSaver saver_cistrans(null_output);
saver_cistrans.ignore_hydrogens = true;
saver_cistrans.saveMolecule(mol);
// Then reset cis-trans infromation that is not saved into SMILES
const Array<int>& parities = saver_cistrans.getSavedCisTransParities();
for (i = mol.edgeBegin(); i < mol.edgeEnd(); i = mol.edgeNext(i))
{
if (mol.cis_trans.getParity(i) != 0 && parities[i] == 0)
mol.cis_trans.setParity(i, 0);
}
MoleculeAutomorphismSearch of;
of.detect_invalid_cistrans_bonds = find_invalid_stereo;
of.detect_invalid_stereocenters = find_invalid_stereo;
of.find_canonical_ordering = true;
of.ignored_vertices = ignored.ptr();
of.process(mol);
of.getCanonicalNumbering(order);
for (i = mol.edgeBegin(); i != mol.edgeEnd(); i = mol.edgeNext(i))
if (mol.cis_trans.getParity(i) != 0 && of.invalidCisTransBond(i))
mol.cis_trans.setParity(i, 0);
for (i = mol.vertexBegin(); i != mol.vertexEnd(); i = mol.vertexNext(i))
if (mol.stereocenters.getType(i) > MoleculeStereocenters::ATOM_ANY && of.invalidStereocenter(i))
mol.stereocenters.remove(i);
ranks.clear_resize(mol.vertexEnd());
for (i = 0; i < order.size(); i++)
ranks[order[i]] = i;
vertex_ranks = ranks.ptr();
_actual_atom_atom_mapping.clear_resize(mol.vertexCount());
_actual_atom_atom_mapping.zerofill();
for (int i = 0; i < order.size(); ++i) {
int aam = mol.reaction_atom_mapping[order[i]];
if (aam) {
if (!_initial_to_actual.find(aam)) {
_initial_to_actual.insert(aam, ++_aam_counter);
_actual_atom_atom_mapping[order[i]] = _aam_counter;
}
else {
_actual_atom_atom_mapping[order[i]] = _initial_to_actual.at(aam);
}
}
}
mol.reaction_atom_mapping.copy(_actual_atom_atom_mapping);
SmilesSaver::saveMolecule(mol);
}