void MangoIndex::prepare (Scanner &molfile, Output &output,
OsLock *lock_for_exclusive_access)
{
QS_DEF(Molecule, mol);
QS_DEF(Array<int>, gross);
MoleculeAutoLoader loader(molfile);
loader.treat_x_as_pseudoatom = _context->treat_x_as_pseudoatom;
loader.ignore_closing_bond_direction_mismatch =
_context->ignore_closing_bond_direction_mismatch;
loader.loadMolecule(mol);
//Skip all SGroups
mol.clearSGroups();
Molecule::checkForConsistency(mol);
// Make aromatic molecule
MoleculeAromatizer::aromatizeBonds(mol, AromaticityOptions::BASIC);
MangoExact::calculateHash(mol, _hash);
if (!skip_calculate_fp)
{
MoleculeFingerprintBuilder builder(mol, _context->fp_parameters);
profTimerStart(tfing, "moleculeIndex.createFingerprint");
builder.process();
profTimerStop(tfing);
_fp.copy(builder.get(), _context->fp_parameters.fingerprintSize());
_fp_sim_bits_count = builder.countBits_Sim();
output.writeBinaryWord((word)_fp_sim_bits_count);
const byte *fp_sim_ptr = builder.getSim();
int fp_sim_size = _context->fp_parameters.fingerprintSizeSim();
ArrayOutput fp_sim_output(_fp_sim_str);
for (int i = 0; i < fp_sim_size; i++)
fp_sim_output.printf("%02X", fp_sim_ptr[i]);
fp_sim_output.writeChar(0);
}
ArrayOutput output_cmf(_cmf);
{
// CmfSaver modifies _context->cmf_dict and
// requires exclusive access for this
OsLockerNullable locker(lock_for_exclusive_access);
CmfSaver saver(_context->cmf_dict, output_cmf);
saver.saveMolecule(mol);
if (mol.have_xyz)
{
ArrayOutput output_xyz(_xyz);
saver.saveXyz(output_xyz);
}
else
_xyz.clear();
}
output.writeArray(_cmf);
// Save gross formula
GrossFormula::collect(mol, gross);
GrossFormula::toString(gross, _gross_str);
_counted_elems_str.clear();
_counted_elem_counters.clear();
ArrayOutput ce_output(_counted_elems_str);
for (int i = 0; i < (int)NELEM(counted_elements); i++)
{
_counted_elem_counters.push(gross[counted_elements[i]]);
ce_output.printf(", %d", gross[counted_elements[i]]);
}
ce_output.writeByte(0);
// Calculate molecular mass
MoleculeMass mass_calulator;
mass_calulator.relative_atomic_mass_map = &_context->relative_atomic_mass_map;
_molecular_mass = mass_calulator.molecularWeight(mol);
}
void MangoIndex::prepare (Scanner &molfile, Output &output,
OsLock *lock_for_exclusive_access)
{
QS_DEF(Molecule, mol);
QS_DEF(Array<int>, gross);
MoleculeAutoLoader loader(molfile);
_context->setLoaderSettings(loader);
loader.loadMolecule(mol);
// Skip all SGroups
mol.clearSGroups();
if (_context->allow_non_unique_dearomatization)
MoleculeDearomatizer::restoreHydrogens(mol, false);
if (_context->zero_unknown_aromatic_hydrogens)
{
mol.restoreAromaticHydrogens();
for (int i : mol.vertices())
{
if (mol.isRSite(i) || mol.isPseudoAtom(i))
continue;
if (mol.getAtomAromaticity(i) == ATOM_AROMATIC && mol.getImplicitH_NoThrow(i, -1) == -1)
mol.setImplicitH(i, 0);
}
}
Molecule::checkForConsistency(mol);
// Make aromatic molecule
MoleculeAromatizer::aromatizeBonds(mol, AromaticityOptions::BASIC);
MangoExact::calculateHash(mol, _hash);
if (!skip_calculate_fp)
{
MoleculeFingerprintBuilder builder(mol, _context->fp_parameters);
profTimerStart(tfing, "moleculeIndex.createFingerprint");
builder.process();
profTimerStop(tfing);
_fp.copy(builder.get(), _context->fp_parameters.fingerprintSize());
_fp_sim_bits_count = builder.countBits_Sim();
output.writeBinaryWord((word)_fp_sim_bits_count);
const byte *fp_sim_ptr = builder.getSim();
int fp_sim_size = _context->fp_parameters.fingerprintSizeSim();
ArrayOutput fp_sim_output(_fp_sim_str);
for (int i = 0; i < fp_sim_size; i++)
fp_sim_output.printf("%02X", fp_sim_ptr[i]);
fp_sim_output.writeChar(0);
}
ArrayOutput output_cmf(_cmf);
{
// CmfSaver modifies _context->cmf_dict and
// requires exclusive access for this
OsLockerNullable locker(lock_for_exclusive_access);
CmfSaver saver(_context->cmf_dict, output_cmf);
saver.saveMolecule(mol);
if (mol.have_xyz)
{
ArrayOutput output_xyz(_xyz);
saver.saveXyz(output_xyz);
}
else
_xyz.clear();
}
output.writeArray(_cmf);
// Save gross formula
GrossFormula::collect(mol, gross);
GrossFormula::toString(gross, _gross_str);
_counted_elems_str.clear();
_counted_elem_counters.clear();
ArrayOutput ce_output(_counted_elems_str);
for (int i = 0; i < (int)NELEM(counted_elements); i++)
{
_counted_elem_counters.push(gross[counted_elements[i]]);
ce_output.printf(", %d", gross[counted_elements[i]]);
}
ce_output.writeByte(0);
// Calculate molecular mass
MoleculeMass mass_calulator;
mass_calulator.relative_atomic_mass_map = &_context->relative_atomic_mass_map;
_molecular_mass = mass_calulator.molecularWeight(mol);
}