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 CmfSaver::_encodeBond (Molecule &mol, int idx, const int *mapping)
{
int order = mol.getBondOrder(idx);
if (order == BOND_SINGLE)
{
if (mol.getBondTopology(idx) == TOPOLOGY_RING)
_encode(CMF_BOND_SINGLE_RING);
else
_encode(CMF_BOND_SINGLE_CHAIN);
}
else if (order == BOND_DOUBLE)
{
int parity = mol.cis_trans.getParity(idx);
if (parity != 0)
{
int mapped_parity =
MoleculeCisTrans::applyMapping(parity, mol.cis_trans.getSubstituents(idx), mapping, true);
if (mapped_parity == MoleculeCisTrans::CIS)
{
if (mol.getBondTopology(idx) == TOPOLOGY_RING)
_encode(CMF_BOND_DOUBLE_RING_CIS);
else
_encode(CMF_BOND_DOUBLE_CHAIN_CIS);
}
else // mapped_parity == MoleculeCisTrans::TRANS
{
if (mol.getBondTopology(idx) == TOPOLOGY_RING)
_encode(CMF_BOND_DOUBLE_RING_TRANS);
else
_encode(CMF_BOND_DOUBLE_CHAIN_TRANS);
}
}
else if (mol.cis_trans.isIgnored(idx))
{
if (mol.getBondTopology(idx) == TOPOLOGY_RING)
_encode(CMF_BOND_DOUBLE_IGNORED_CIS_TRANS_RING);
else
_encode(CMF_BOND_DOUBLE_IGNORED_CIS_TRANS_CHAIN);
}
else
{
if (mol.getBondTopology(idx) == TOPOLOGY_RING)
_encode(CMF_BOND_DOUBLE_RING);
else
_encode(CMF_BOND_DOUBLE_CHAIN);
}
}
else if (order == BOND_TRIPLE)
{
if (mol.getBondTopology(idx) == TOPOLOGY_RING)
_encode(CMF_BOND_TRIPLE_RING);
else
_encode(CMF_BOND_TRIPLE_CHAIN);
}
else if (order == BOND_AROMATIC)
_encode(CMF_BOND_AROMATIC);
else
throw Error("bad bond order: %d", order);
if (bond_flags != 0)
{
int i, flags = bond_flags[idx];
for (i = 0; i < CMF_NUM_OF_BOND_FLAGS; i++)
if (flags & (1 << i))
_encode(CMF_BOND_FLAGS + i);
}
if (save_highlighting)
if (mol.isBondHighlighted(idx))
_encode(CMF_HIGHLIGHTED);
}
