bool MoleculeAutomorphismSearch::_isCisTransBondMappedRigid (Molecule &mol, int i, const int *mapping)
{
int parity = mol.cis_trans.getParity(i);
int parity2 = MoleculeCisTrans::applyMapping(parity, mol.cis_trans.getSubstituents(i), mapping, false);
const Edge &edge = mol.getEdge(i);
int i2 = mol.findEdgeIndex(mapping[edge.beg], mapping[edge.end]);
if (mol.cis_trans.getParity(i2) != parity2)
return false;
return true;
}
void IndigoInchi::parseInchiOutput (const inchi_OutputStruct &inchi_output, Molecule &mol)
{
mol.clear();
Array<int> atom_indices;
atom_indices.clear();
// Add atoms
for (AT_NUM i = 0; i < inchi_output.num_atoms; i ++)
{
const inchi_Atom &inchi_atom = inchi_output.atom[i];
int idx = mol.addAtom(Element::fromString(inchi_atom.elname));
atom_indices.push(idx);
}
// Add bonds
for (AT_NUM i = 0; i < inchi_output.num_atoms; i ++)
{
const inchi_Atom &inchi_atom = inchi_output.atom[i];
for (AT_NUM bi = 0; bi < inchi_atom.num_bonds; bi++)
{
AT_NUM nei = inchi_atom.neighbor[bi];
if (i > nei)
// Add bond only once
continue;
int bond_order = inchi_atom.bond_type[bi];
if (bond_order == INCHI_BOND_TYPE_NONE)
throw Molecule::Error("Indigo-InChI: NONE-typed bonds are not supported");
if (bond_order >= INCHI_BOND_TYPE_ALTERN)
throw Molecule::Error("Indigo-InChI: ALTERN-typed bonds are not supported");
int bond = mol.addBond(atom_indices[i], atom_indices[nei], bond_order);
}
}
// Add Hydrogen isotope atoms at the end to preserver
// the same atom ordering
for (AT_NUM i = 0; i < inchi_output.num_atoms; i ++)
{
const inchi_Atom &inchi_atom = inchi_output.atom[i];
int root_atom = atom_indices[i];
for (int iso = 1; iso <= NUM_H_ISOTOPES; iso++)
{
int count = inchi_atom.num_iso_H[iso];
while (count-- > 0)
{
int h = mol.addAtom(ELEM_H);
mol.setAtomIsotope(h, iso);
mol.addBond(root_atom, h, BOND_SINGLE);
}
}
}
// Set atom charges, radicals and etc.
for (int i = 0; i < inchi_output.num_atoms; i++)
{
const inchi_Atom &inchi_atom = inchi_output.atom[i];
int idx = atom_indices[i];
mol.setAtomCharge(idx, inchi_atom.charge);
if (inchi_atom.isotopic_mass)
mol.setAtomIsotope(idx, inchi_atom.isotopic_mass);
if (inchi_atom.radical)
mol.setAtomRadical(idx, inchi_atom.radical);
mol.setImplicitH(idx, inchi_atom.num_iso_H[0]);
}
neutralizeV5Nitrogen(mol);
// Process stereoconfiguration
for (int i = 0; i < inchi_output.num_stereo0D; i++)
{
inchi_Stereo0D &stereo0D = inchi_output.stereo0D[i];
if (stereo0D.type == INCHI_StereoType_DoubleBond)
{
if (stereo0D.parity != INCHI_PARITY_ODD && stereo0D.parity != INCHI_PARITY_EVEN)
continue;
int bond = mol.findEdgeIndex(stereo0D.neighbor[1], stereo0D.neighbor[2]);
bool valid = mol.cis_trans.registerBondAndSubstituents(bond);
if (!valid)
throw IndigoError("Indigo-InChI: Unsupported cis-trans configuration for "
"bond %d (atoms %d-%d-%d-%d)", bond, stereo0D.neighbor[0], stereo0D.neighbor[1],
stereo0D.neighbor[2], stereo0D.neighbor[3]);
int vb, ve;
const Edge &edge = mol.getEdge(bond);
if (edge.beg == stereo0D.neighbor[1])
{
vb = stereo0D.neighbor[0];
ve = stereo0D.neighbor[3];
}
else if (edge.beg == stereo0D.neighbor[2])
{
vb = stereo0D.neighbor[3];
ve = stereo0D.neighbor[0];
}
else
throw IndigoError("Indigo-InChI: Internal error: cannot find cis-trans bond indices");
const int *subst = mol.cis_trans.getSubstituents(bond);
bool same_side;
if (subst[0] == vb)
same_side = (subst[2] == ve);
else if (subst[1] == vb)
same_side = (subst[3] == ve);
else
throw IndigoError("Indigo-InChI: Internal error: cannot find cis-trans bond indices (#2)");
if (stereo0D.parity == INCHI_PARITY_EVEN)
same_side = !same_side;
mol.cis_trans.setParity(bond, same_side ? MoleculeCisTrans::CIS : MoleculeCisTrans::TRANS);
}
else if (stereo0D.type == INCHI_StereoType_Tetrahedral)
{
if (stereo0D.parity != INCHI_PARITY_ODD && stereo0D.parity != INCHI_PARITY_EVEN)
continue;
int pyramid[4];
if (stereo0D.central_atom == stereo0D.neighbor[0])
{
pyramid[1] = stereo0D.neighbor[1];
pyramid[0] = stereo0D.neighbor[2];
pyramid[2] = stereo0D.neighbor[3];
pyramid[3] = -1;
}
else
{
pyramid[0] = stereo0D.neighbor[0];
pyramid[1] = stereo0D.neighbor[1];
pyramid[2] = stereo0D.neighbor[2];
pyramid[3] = stereo0D.neighbor[3];
}
if (stereo0D.parity == INCHI_PARITY_ODD)
std::swap(pyramid[0], pyramid[1]);
mol.stereocenters.add(stereo0D.central_atom, MoleculeStereocenters::ATOM_ABS, 0, pyramid);
}
}
}
