def add_mol(self, molid, rdkmol):
"""Serial, memory-conservative fingerprinter for building a fingerprints sparse matrix incrementally."""
try:
# Amazing DRY violation
counts, _ = unfolded_morgan_fingerprint(rdkmol,
max_radius=self.max_radius,
fcfp=self.fcfp,
use_hs=self.use_hs,
canonical=self.canonical,
isomeric=self.isomeric,
kekule=self.kekule,
all_bonds_explicit=self.all_bonds_explicit)
cols_vals = []
for smiles, count in counts.iteritems():
if smiles not in self._s2i:
self._s2i[smiles] = len(self._s2i)
self._rows.append(len(self._molids))
cols_vals.append((self._s2i[smiles], count))
cols_vals = sorted(cols_vals)
self._cols.extend(map(itemgetter(0), cols_vals))
self._vals.extend(map(itemgetter(1), cols_vals))
self._molids.append(molid)
except Exception, _:
warning('Could not compute unfolded fingerprint for molecule %s' % molid)
self._failed_moldids.append(molid)
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) # TODO: allow other formats, like sdf or inchi
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 iterate_records_in_text_file(
filename, record_terminator="$$$$", terminator_only_after_empty_line=True, verbose=True
):
"""Iterate over all molecule records in the given sdf file.
# NB: assume that the last record also includes terminator
# Must the record terminator be preceded by an empty line?
"""
# Let's detect compressed files just using the extension
if hasattr(filename, "next"):
fileh = filename
elif filename.endswith(".zip"):
fileh = zipfile.ZipFile(filename, "r")
elif filename.endswith(".gz"):
fileh = gzip.GzipFile(filename, "r")
else:
fileh = open(filename, "r")
notatend = True
partial_record = []
line_num = 0
while notatend:
notatend = fileh.next()
partial_record.append(notatend)
line_num += 1
if notatend.strip() == record_terminator:
if terminator_only_after_empty_line:
if len(partial_record) < 2 or partial_record[-2] != "\n":
if verbose:
warning(
"Warning: the terminator %s in line %d is not preceded by a blank line\n"
% (partial_record[-1].strip(), line_num)
)
continue # Do not yield yet, as the terminator is not preceded by an empty line
full_record = partial_record
partial_record = []
yield "".join(full_record).strip()
fileh.close()