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;
}
void RingoFastIndex::_match (OracleEnv &env, int idx)
{
_last_id = idx;
BingoStorage &storage = this->_context.context().context().storage;
QS_DEF(Array<char>, stored);
storage.get(idx, stored);
if (stored[0] != 0)
return; // reaction was removed from index
BufferScanner scanner(stored);
scanner.skip(1); // skip the deletion mark
scanner.skip(scanner.readByte()); // skip the compessed rowid
profTimerStart(tall, "match");
bool res = _context.substructure.matchBinary(scanner);
profTimerStop(tall);
if (res)
{
OraRowidText & rid = matched.at(matched.add());
_decompressRowid(stored, rid);
profIncTimer("match.found", profTimerGetTime(tall));
_matched++;
}
else
{
profIncTimer("match.not_found", profTimerGetTime(tall));
_unmatched++;
}
}
bool MangoSubstructure::matchLoadedTarget ()
{
MoleculeSubstructureMatcher matcher(_target);
matcher.match_3d = match_3d;
matcher.rms_threshold = rms_threshold;
matcher.highlight = true;
matcher.use_pi_systems_matcher = _use_pi_systems_matcher;
matcher.setNeiCounters(&_nei_query_counters, &_nei_target_counters);
matcher.fmcache = &_fmcache;
_fmcache.clear();
matcher.setQuery(_query);
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;
}
void MangoFastIndex::_match (OracleEnv &env, int idx)
{
_last_id = idx;
BingoStorage &storage = this->_context.context().context().storage;
QS_DEF(Array<char>, stored);
storage.get(idx, stored);
if (stored[0] != 0)
return; // molecule was removed from index
BufferScanner scanner(stored);
scanner.skip(1); // skip the deletion mark
scanner.skip(scanner.readByte()); // skip the compessed rowid
scanner.skip(2); // skip 'ord' bits count
bool res = false;
profTimerStart(tall, "match");
if (_fetch_type == _SUBSTRUCTURE)
{
QS_DEF(Array<char>, xyz_buf);
if (_context.substructure.needCoords())
{
OraRowidText rid;
_decompressRowid(stored, rid);
if (_loadCoords(env, rid.ptr(), xyz_buf))
{
BufferScanner xyz_scanner(xyz_buf);
res = _context.substructure.matchBinary(scanner, &xyz_scanner);
}
else
// no XYZ --> skip the molecule
res = false;
}
else
res = _context.substructure.matchBinary(scanner, 0);
}
else if (_fetch_type == _TAUTOMER_SUBSTRUCTURE)
res = _context.tautomer.matchBinary(scanner);
else // _fetch_type == _SIMILARITY
res = _context.similarity.matchBinary(scanner);
profTimerStop(tall);
if (res)
{
OraRowidText & rid = matched.at(matched.add());
_decompressRowid(stored, rid);
profIncTimer("match.found", profTimerGetTime(tall));
_matched++;
}
else
{
profIncTimer("match.not_found", profTimerGetTime(tall));
_unmatched++;
}
}