bool MangoTautomer::matchBinary (Scanner &scanner)
{
CmfLoader loader(_context.cmf_dict, scanner);
loader.loadMolecule(_target);
_initTarget(true);
TautomerMethod m = RSMARTS;
MoleculeTautomerMatcher matcher(_target, _params.substructure);
matcher.setRulesList(&_context.tautomer_rules);
matcher.setRules(_params.conditions, _params.force_hydrogens, _params.ring_chain, m);
matcher.setQuery(_query.ref());
profTimerStart(temb, "match.embedding");
bool res = matcher.find();
profTimerStop(temb);
if (res)
{
profIncTimer("match.embedding_found", profTimerGetTime(temb));
}
else
{
profIncTimer("match.embedding_not_found", profTimerGetTime(temb));
}
return res;
}
bool MangoSubstructure::matchBinary (Scanner &scanner, Scanner *xyz_scanner)
{
_validateQueryExtraData();
profTimerStart(tcmf, "match.cmf");
cmf_loader.free();
cmf_loader.create(_context.cmf_dict, scanner);
if (!_query_has_stereocare_bonds)
cmf_loader->skip_cistrans = true;
if (!_query_has_stereocenters)
cmf_loader->skip_stereocenters = true;
cmf_loader->loadMolecule(_target);
if (xyz_scanner != 0)
cmf_loader->loadXyz(*xyz_scanner);
profTimerStop(tcmf);
profTimerStart(tinit, "match.init_target");
_initTarget(true);
profTimerStop(tinit);
return matchLoadedTarget();
}
void MangoExact::loadTarget (Scanner &scanner)
{
MoleculeAutoLoader loader(scanner);
_context.setLoaderSettings(loader);
loader.loadMolecule(_target);
Molecule::checkForConsistency(_target);
_initTarget(_target, false);
}
void MangoTautomer::loadTarget (Scanner &scanner)
{
MoleculeAutoLoader loader(scanner);
_context.setLoaderSettings(loader);
loader.loadMolecule(_target);
_initTarget(false);
}
void MangoSubstructure::loadTarget (Scanner &scanner)
{
MoleculeAutoLoader loader(scanner);
loader.treat_x_as_pseudoatom = _context.treat_x_as_pseudoatom;
loader.ignore_closing_bond_direction_mismatch =
_context.ignore_closing_bond_direction_mismatch;
loader.loadMolecule(_target);
_initTarget(false);
Molecule::checkForConsistency(_target);
}
bool MangoExact::matchBinary (Scanner &scanner, Scanner *xyz_scanner)
{
CmfLoader loader(_context.cmf_dict, scanner);
loader.loadMolecule(_target);
if (xyz_scanner != 0)
loader.loadXyz(*xyz_scanner);
_initTarget(_target, true);
/*
* Set up timeout for matching
*/
MoleculeExactMatcher matcher(_query, _target);
matcher.flags = _flags;
matcher.rms_threshold = _rms_threshold;
return matcher.find();
}
