int QueryMolecule::parseQueryAtom (QueryMolecule& qm, int aid, Array<int>& list) {
QueryMolecule::Atom& qa = qm.getAtom(aid);
QueryMolecule::Atom* qc = stripKnownAttrs(qa);
if (qc != NULL && isNotAtom(*qc, ELEM_H))
return QUERY_ATOM_A;
bool notList = false;
if (collectAtomList(qa, list, notList) ||
(qa.type == QueryMolecule::OP_NOT && collectAtomList(*qa.child(0), list, notList) && !notList)) { // !notList is to check there's no double negation
if (list.size() == 0)
return -1;
notList = notList || qa.type == QueryMolecule::OP_NOT;
if (!notList && list.size() == 5 && list[0] == ELEM_F && list[1] == ELEM_Cl && list[2] == ELEM_Br && list[3] == ELEM_I && list[4] == ELEM_At)
return QUERY_ATOM_X;
if (notList && list.size() == 2 && ((list[0] == ELEM_C && list[1] == ELEM_H) || (list[0] == ELEM_H && list[1] == ELEM_C)))
return QUERY_ATOM_Q;
return notList ? QUERY_ATOM_NOTLIST : QUERY_ATOM_LIST;
}
return -1;
}
bool MoleculePiSystemsMatcher::_fixAtoms (QueryMolecule &query, const int *mapping)
{
// Fix charges
for (int qv = query.vertexBegin();
qv != query.vertexEnd();
qv = query.vertexNext(qv))
{
int v = mapping[qv];
if (v < 0)
continue; // Such vertex must be ignored
int pi_system_idx = _atom_pi_system_idx[v];
if (pi_system_idx == _NOT_IN_PI_SYSTEM)
continue;
_Pi_System &pi_system = _pi_systems[pi_system_idx];
QueryMolecule::Atom &qatom = query.getAtom(qv);
int pv = pi_system.inv_mapping[v];
int charge = query.getAtomCharge(qv);
if (charge != CHARGE_UNKNOWN)
{
bool ret = pi_system.localizer->fixAtomCharge(pv, charge);
if (!ret)
return false;
}
else if (qatom.hasConstraint(QueryMolecule::ATOM_CHARGE))
throw Error("Unsupported atom charge specified");
int valence = query.getExplicitValence(qv);
if (valence != -1)
{
bool ret = pi_system.localizer->fixAtomConnectivity(pv, valence);
if (!ret)
return false;
}
else if (qatom.hasConstraint(QueryMolecule::ATOM_VALENCE))
throw Error("Unsupported atom charge specified");
}
return true;
}
bool QueryMolecule::queryAtomIsRegular (QueryMolecule& qm, int aid) {
QueryMolecule::Atom& qa = qm.getAtom(aid);
QueryMolecule::Atom* qc = stripKnownAttrs(qa);
return qc && qc->type == QueryMolecule::ATOM_NUMBER;
}
bool MoleculeSubstructureMatcher::_shouldUnfoldTargetHydrogens (QueryMolecule &query, bool is_fragment, bool disable_folding_query_h)
{
int i, j;
for (i = query.vertexBegin(); i != query.vertexEnd(); i = query.vertexNext(i))
{
// skip R-atoms
if (query.isRSite(i))
continue;
if (query.possibleAtomNumberAndIsotope(i, ELEM_H, 0))
{
const Vertex &vertex = query.getVertex(i);
// Degree 2 or higher => definilely not a hydrogen
if (vertex.degree() > 1)
continue;
// Can be lone hydrogen?
if (vertex.degree() == 0)
return true;
// degree is 1 at this point
int edge_idx = vertex.neiEdge(vertex.neiBegin());
// is it is double or triple bond => not hydrogen
if (query.getBondOrder(edge_idx) > 1)
continue;
// ring bond?
if (query.getBondTopology(edge_idx) == TOPOLOGY_RING)
continue;
// can be something other than hydrogen?
if (query.getAtomNumber(i) == -1)
return true;
if (is_fragment && i == query.vertexBegin())
// If first atom in a fragment is hydrogen then hydrogens should
// be unfolded because of the matching logic: when fragment will be
// matched this first hydrogen should match some atom.
// If hydrogens is not be unfolded in this case then
// [$([#1][N])]C will not match NC.
return true;
// If we need to find all embeddings then query hydrogens cannot be ignored:
// For example, if we are searching number of matcher for N-[#1] in N then
// it should 3 instead of 1
if (disable_folding_query_h)
return true;
// Check if hydrogen forms a cis-trans bond or stereocenter
int nei_vertex_idx = vertex.neiVertex(vertex.neiBegin());
if (query.stereocenters.exists(nei_vertex_idx))
return true;
// For example for this query hydrogens should be unfolded: [H]\\C=C/C
const Vertex &nei_vertex = query.getVertex(nei_vertex_idx);
for (int nei = nei_vertex.neiBegin(); nei != nei_vertex.neiEnd(); nei = nei_vertex.neiNext(nei))
{
int edge = nei_vertex.neiEdge(nei);
if (query.cis_trans.getParity(edge) != 0)
return true;
}
}
if (_shouldUnfoldTargetHydrogens_A(&query.getAtom(i), is_fragment, disable_folding_query_h))
return true;
}
MoleculeRGroups &rgroups = query.rgroups;
int n_rgroups = rgroups.getRGroupCount();
for (i = 1; i <= n_rgroups; i++)
{
PtrPool<BaseMolecule> &frags = rgroups.getRGroup(i).fragments;
for (j = frags.begin(); j != frags.end(); j = frags.next(j))
if (_shouldUnfoldTargetHydrogens(frags[j]->asQueryMolecule(), is_fragment, disable_folding_query_h))
return true;
}
return false;
}