def build_benchmark_check_rdkmols_catalog(mmapdir, molit=read_labelled_only_smiles, checks=False, overwrite=False):
"""Builds a memmapped catalog {molid->rdkbytes} from a (molid, smiles) iterator.
tests it and compares to sequential recreation of the molecules from smiles.
"""
# Build the catalog
info('Building %s catalog...' % mmapdir)
start = time()
mmm = MemMappedMols(mmapdir)
if not overwrite and mmm.has_catalog():
info('Already computed, skipping.')
else:
mmm.save_from_smiles_iterator(molit())
info('Time taken to build the memmapped file: %.2f seconds' % (time() - start))
if not checks:
return
# Load the catalog
mmms = MemMappedMols(mmapdir)
# Lame benchmark - memmapped contiguous
info('Benchmarking contiguous memmap reading')
start = time()
molcount = 0
for molid in mmms.molids():
mmms.mol(molid)
molcount += 1
info('Time taken to read the memmapped %d mols (contiguous): %.2f seconds' % (molcount, time() - start))
info('Benchmarking random memmap reading')
start = time()
molcount = 0
for molid in set(mmms.molids()):
mmms.mol(molid)
molcount += 1
info('Time taken to read the memmapped %d mols (random): %.2f seconds' % (molcount, time() - start))
# Lame benchmark - from smiles
info('Benchmarking reading from the original file')
start = time()
molcount = 0
for _, smiles in molit():
Chem.MolFromSmiles(smiles)
molcount += 1
info('Time taken to read the smiled %d mols: %.2f seconds' % (molcount, time() - start))
# Exhaustive linear test that all mols are correctly stored
info('Making sure that all is OKish')
for molid, smiles in molit():
emol = Chem.MolFromSmiles(smiles)
if emol is None:
if not mmms.mol(molid) is None:
warning('Molecule %s with original smiles %s should not be parsed from the binary store' %
(molid, smiles))
else:
if not Chem.MolToSmiles(emol) == Chem.MolToSmiles(mmms.mol(molid)):
warning('Molecule %s with original smiles %s do not reconstruct properly: \n\t(%s != %s)' %
(molid, smiles, Chem.MolToSmiles(emol), Chem.MolToSmiles(mmms.mol(molid))))
info('All is OKish')
def to_rdkit_mol(smiles, molid=None, sanitize=True, to2D=False, to3D=False, toPropertyMol=False):
"""Converts a smiles string into an RDKit molecule."""
mol = Chem.MolFromSmiles(smiles, sanitize=sanitize)
if mol is None:
if molid is None:
warning('RDKit cannot create a molecule from smiles %s' % smiles)
else:
warning('RDKit cannot create molecule %s from smiles %s' % (molid, smiles))
return mol
if to3D:
AllChem.EmbedMolecule(mol)
AllChem.UFFOptimizeMolecule(mol)
elif to2D:
AllChem.Compute2DCoords(mol)
if toPropertyMol:
return PropertyMol(mol)
return mol
def to_rdkit_mol(mol_repr, molid=None, instantiator=Chem.MolFromSmiles, to2D=False, to3D=False, toPropertyMol=False):
"""
Converts a molecular representation (e.g. smiles string) into an RDKit molecule.
Allows to perform common postprocessing operations on the resulting molecule.
"""
if not isinstance(mol_repr, Chem.Mol):
mol = instantiator(mol_repr)
else:
mol = mol_repr
if mol is None:
if molid is None:
warning('RDKit cannot create a molecule from %r' % mol_repr)
else:
warning('RDKit cannot create molecule %s from %r' % (molid, mol_repr))
return mol
if to3D:
AllChem.EmbedMolecule(mol)
AllChem.UFFOptimizeMolecule(mol)
elif to2D:
AllChem.Compute2DCoords(mol)
if toPropertyMol:
return PropertyMol(mol)
return mol
