def setUp(self):
"""
Set up for tests. Writes molecules and targets to files.
"""
self.temp_dir = tempfile.mkdtemp()
smiles = [
'CC(=O)OC1=CC=CC=C1C(=O)O', 'C[C@@H](C1=CC=C(C=C1)CC(C)C)C(=O)O'
]
self.names = ['aspirin', 'ibuprofen']
engine = conformers.ConformerGenerator(max_conformers=1)
self.mols = []
self.smiles = [] # use RDKit-generated SMILES
for i in xrange(len(smiles)):
mol = Chem.MolFromSmiles(smiles[i])
mol.SetProp('_Name', self.names[i])
self.mols.append(engine.generate_conformers(mol))
self.smiles.append(
Chem.MolToSmiles(mol, isomericSmiles=True, canonical=True))
# write mols
_, self.input_filename = tempfile.mkstemp(suffix='.sdf',
dir=self.temp_dir)
writer = serial.MolWriter()
writer.open(self.input_filename)
writer.write(self.mols)
writer.close()
# write targets
self.targets = [0, 1]
_, self.targets_filename = tempfile.mkstemp(suffix='.pkl',
dir=self.temp_dir)
write_pickle(self.targets, self.targets_filename)
def main(active_filename,
decoy_filename,
output_filename,
assign_stereo_from_3d=False):
"""
Construct target files for datasets with active/decoy labels.
Parameters
----------
active_filename : str
Active molecule filename.
decoy_filename : str
Decoy molecule filename.
output_filename : str
Output filename.
assign_stereo_from_3d : bool, optional (default False)
Assign stereochemistry from 3D coordinates.
"""
active_smiles = get_smiles(active_filename, assign_stereo_from_3d)
decoy_smiles = get_smiles(decoy_filename, assign_stereo_from_3d)
targets = np.concatenate(
(np.ones(len(active_smiles),
dtype=int), np.zeros(len(decoy_smiles), dtype=int)))
smiles = np.concatenate((active_smiles, decoy_smiles))
write_pickle({'smiles': smiles, 'targets': targets}, output_filename)
def main(input_filename, map_filename, output_filename, column_indices=None):
"""
Get regression targets.
Parameters
----------
input_filename : str
PCBA data filename.
map_filename : str
ID->SMILES map filename.
output_filename : str
Output filename.
column_indices : list, optional
Column indices to include. If None, compounds are classified by
activity.
"""
parser = PcbaParser(input_filename, map_filename,
column_indices=column_indices)
if column_indices is not None:
print "Extracting data from the following columns:"
for col in parser.get_column_names():
print '\t', col
smiles, targets = parser.get_targets()
# print the fraction of valid assay records that were found in the map
total = np.count_nonzero(~np.isnan(parser.read_data().PUBCHEM_CID))
print '{}/{} records matched'.format(len(targets), total)
# save SMILES and targets
write_pickle({'smiles': smiles, 'targets': targets}, output_filename)
def setUp(self):
"""
Set up for tests. Writes molecules and targets to files.
"""
self.temp_dir = tempfile.mkdtemp()
smiles = ['CC(=O)OC1=CC=CC=C1C(=O)O',
'C[C@@H](C1=CC=C(C=C1)CC(C)C)C(=O)O']
self.names = ['aspirin', 'ibuprofen']
engine = conformers.ConformerGenerator(max_conformers=1)
self.mols = []
self.smiles = [] # use RDKit-generated SMILES
for i in xrange(len(smiles)):
mol = Chem.MolFromSmiles(smiles[i])
mol.SetProp('_Name', self.names[i])
self.mols.append(engine.generate_conformers(mol))
self.smiles.append(Chem.MolToSmiles(mol, isomericSmiles=True,
canonical=True))
# write mols
_, self.input_filename = tempfile.mkstemp(suffix='.sdf',
dir=self.temp_dir)
writer = serial.MolWriter()
writer.open(self.input_filename)
writer.write(self.mols)
writer.close()
# write targets
self.targets = [0, 1]
_, self.targets_filename = tempfile.mkstemp(suffix='.pkl',
dir=self.temp_dir)
write_pickle(self.targets, self.targets_filename)
def main(input_filename, map_filename, directory='.', prefix='nci60',
suffix='pkl.gz'):
"""
Get regression targets.
Parameters
----------
input_filename : str
PCBA data filename.
map_filename : str
ID->SMILES map filename.
directory : str, optional (default '.')
Directory in which to write target files.
prefix : str, optional (default 'nci60')
Prefix for target files.
suffix : str, optional (default 'pkl.gz')
Suffix for target files.
"""
parser = Nci60Parser(input_filename, map_filename)
split_targets = parser.split_targets()
# get total record count
total = np.count_nonzero(~np.isnan(parser.read_data().NSC))
# write a separate file for each dataset
# note that split_targets is an OrderedDict
for i, name in enumerate(split_targets.keys()):
data = split_targets[name]
# print the fraction of valid assay records that were found in the map
print '{}\t{}/{} records matched'.format(
name, len(data['targets']), total)
write_pickle(
data,
os.path.join(directory,
'{}-{:02}-targets.{}'.format(prefix, i, suffix)))
def setUp(self):
"""
Set up tests.
"""
self.temp_dir = tempfile.mkdtemp()
self.map = {
'CID645443':
'Cc1ccc(-n2c3c(cc(C(=O)Nc4cccc(C)n4)c2=O)C(=O)CCC3)cc1',
'CID2997889': 'CC(C)(C)C(=O)Nc1ccc(-c2cn3ccsc3n2)cc1',
'CID2244': 'CC(=O)Oc1ccccc1C(=O)O',
'CID2662': 'Cc1ccc(-c2cc(C(F)(F)F)nn2-c2ccc(S(N)(=O)=O)cc2)cc1',
'CID3672': 'CC(C)Cc1ccc(C(C)C(=O)O)cc1'
}
_, self.map_filename = tempfile.mkstemp(dir=self.temp_dir,
suffix='.pkl')
write_pickle(self.map, self.map_filename)
# use a subset of AID588342
# note that CID 654924 is duplicated
this_dir = os.path.split(os.path.realpath(__file__))[0]
self.data_filename = os.path.join(this_dir, 'data/test_pcba_data.csv')
# set up parser
# settings match PcbaParser defaults
self.engine = AssayDataParser(self.data_filename,
self.map_filename,
delimiter=',',
primary_key='PUBCHEM_CID',
activity_key='PUBCHEM_ACTIVITY_OUTCOME',
activity_value='Active',
id_prefix='CID')
def setUp(self):
"""
Set up tests.
"""
self.temp_dir = tempfile.mkdtemp()
self.map = {
"CID645443": "Cc1ccc(-n2c3c(cc(C(=O)Nc4cccc(C)n4)c2=O)C(=O)CCC3)cc1",
"CID2997889": "CC(C)(C)C(=O)Nc1ccc(-c2cn3ccsc3n2)cc1",
"CID2244": "CC(=O)Oc1ccccc1C(=O)O",
"CID2662": "Cc1ccc(-c2cc(C(F)(F)F)nn2-c2ccc(S(N)(=O)=O)cc2)cc1",
"CID3672": "CC(C)Cc1ccc(C(C)C(=O)O)cc1",
}
_, self.map_filename = tempfile.mkstemp(dir=self.temp_dir, suffix=".pkl")
write_pickle(self.map, self.map_filename)
# use a subset of AID588342
# note that CID 654924 is duplicated
this_dir = os.path.split(os.path.realpath(__file__))[0]
self.data_filename = os.path.join(this_dir, "data/test_pcba_data.csv")
# set up parser
# settings match PcbaParser defaults
self.engine = AssayDataParser(
self.data_filename,
self.map_filename,
delimiter=",",
primary_key="PUBCHEM_CID",
activity_key="PUBCHEM_ACTIVITY_OUTCOME",
activity_value="Active",
id_prefix="CID",
)
def test_write_pickle_gz(self):
"""
Test write_pickle with gzipped pickle.
"""
_, filename = tempfile.mkstemp(dir=self.temp_dir, suffix='.pkl.gz')
write_pickle({'foo': 'bar'}, filename)
with gzip.open(filename) as f:
assert cPickle.load(f)['foo'] == 'bar'
def test_write_pickle_gz(self):
"""
Test write_pickle with gzipped pickle.
"""
_, filename = tempfile.mkstemp(dir=self.temp_dir, suffix='.pkl.gz')
write_pickle({'foo': 'bar'}, filename)
with gzip.open(filename) as f:
assert cPickle.load(f)['foo'] == 'bar'
def test_collate_mols3(self):
"""
Test collate_mols where targets are in a different order than
molecules.
"""
# write targets
targets = {'names': ['ibuprofen', 'aspirin'], 'y': [1, 0]}
write_pickle(targets, self.targets_filename)
# run script
self.check_output(['circular'], (2, 2048))
def test_collate_mols1(self):
"""
Test collate_mols where molecules are pruned.
"""
# write targets
targets = {'names': ['ibuprofen'], 'y': [0]}
write_pickle(targets, self.targets_filename)
# run script
self.check_output(['circular'], (1, 2048), targets=targets['y'],
names=targets['names'], smiles=[self.smiles[1]])
def test_collate_mols3(self):
"""
Test collate_mols where targets are in a different order than
molecules.
"""
# write targets
targets = {'names': ['ibuprofen', 'aspirin'], 'y': [1, 0]}
write_pickle(targets, self.targets_filename)
# run script
self.check_output(['circular'], (2, 2048))
def test_collate_mols1(self):
"""
Test collate_mols where molecules are pruned.
"""
# write targets
targets = {'names': ['ibuprofen'], 'y': [0]}
write_pickle(targets, self.targets_filename)
# run script
self.check_output(['circular'], (1, 2048),
targets=targets['y'],
names=targets['names'],
smiles=[self.smiles[1]])
def setUp(self):
"""
Set up tests.
"""
self.temp_dir = tempfile.mkdtemp()
self.map = {"NSC1": "CC1=CC(=O)C=CC1=O"}
_, self.map_filename = tempfile.mkstemp(dir=self.temp_dir, suffix=".pkl")
write_pickle(self.map, self.map_filename)
this_dir = os.path.split(os.path.realpath(__file__))[0]
self.data_filename = os.path.join(this_dir, "data/test_nci60_data.txt")
# set up parser
self.engine = Nci60Parser(self.data_filename, self.map_filename)
def setUp(self):
"""
Set up tests.
"""
self.temp_dir = tempfile.mkdtemp()
self.map = {'NSC1': 'CC1=CC(=O)C=CC1=O'}
_, self.map_filename = tempfile.mkstemp(dir=self.temp_dir,
suffix='.pkl')
write_pickle(self.map, self.map_filename)
this_dir = os.path.split(os.path.realpath(__file__))[0]
self.data_filename = os.path.join(this_dir, 'data/test_nci60_data.txt')
# set up parser
self.engine = Nci60Parser(self.data_filename, self.map_filename)
def main(input_filenames,
output_filename,
id_prefix=None,
allow_duplicates=True,
update=False,
assign_stereo_from_3d=False):
"""
Get SMILES for compounds and map to compound names.
Parameters
----------
input_filenames : list
Input molecule filenames.
output_filename : str
Output filename.
id_prefix : str, optional
Prefix to prepend to IDs.
allow_duplicates : bool, optional (default True)
Allow duplicate SMILES.
update : bool, optional (default False)
Update an existing map with the same output filename. If False, a new
map will be generated using only the input file(s).
assign_stereo_from_3d : bool, optional (default False)
Assign stereochemistry from 3D coordinates.
"""
smiles = SmilesMap(prefix=id_prefix,
allow_duplicates=allow_duplicates,
assign_stereo_from_3d=assign_stereo_from_3d)
# update existing map
if update:
smiles.map = read_pickle(output_filename)
for input_filename in input_filenames:
print input_filename
with serial.MolReader().open(input_filename) as reader:
for mol in reader:
try:
smiles.add_mol(mol)
except ValueError:
if mol.HasProp('_Name'):
print 'Skipping {}'.format(mol.GetProp('_Name'))
else:
print 'Skipping {}'.format(
Chem.MolToSmiles(mol, isomericSmiles=True))
write_pickle(smiles.get_map(), output_filename)
def test_collate_mols2(self):
"""
Test collate_mols where targets are pruned.
"""
# write targets
targets = {'names': ['aspirin', 'ibuprofen'], 'y': [0, 1]}
write_pickle(targets, self.targets_filename)
# write mols
writer = serial.MolWriter()
writer.open(self.input_filename)
writer.write([self.mols[0]])
writer.close()
# run script
self.check_output(['circular'], (1, 2048), targets=[0],
names=['aspirin'], smiles=[self.smiles[0]])
def write_output_file(data, output_filename, compression_level=3):
"""
Pickle output data, possibly to a compressed file.
Parameters
----------
data : object
Object to pickle in output file.
output_filename : str
Output filename. Should end with .joblib, .pkl, or .pkl.gz.
compression_level : int, optional (default 3)
Compression level (0-9) to use with joblib.dump.
"""
if output_filename.endswith('.pkl') or output_filename.endswith('.pkl.gz'):
write_pickle(data, output_filename)
elif output_filename.endswith('.joblib'):
joblib.dump(data, output_filename, compress=compression_level)
else:
raise NotImplementedError('Unrecognized output file extension.')
def test_collate_mols2(self):
"""
Test collate_mols where targets are pruned.
"""
# write targets
targets = {'names': ['aspirin', 'ibuprofen'], 'y': [0, 1]}
write_pickle(targets, self.targets_filename)
# write mols
writer = serial.MolWriter()
writer.open(self.input_filename)
writer.write([self.mols[0]])
writer.close()
# run script
self.check_output(['circular'], (1, 2048),
targets=[0],
names=['aspirin'],
smiles=[self.smiles[0]])
def main(input_filenames, output_filename, id_prefix=None,
allow_duplicates=True, update=False, assign_stereo_from_3d=False):
"""
Get SMILES for compounds and map to compound names.
Parameters
----------
input_filenames : list
Input molecule filenames.
output_filename : str
Output filename.
id_prefix : str, optional
Prefix to prepend to IDs.
allow_duplicates : bool, optional (default True)
Allow duplicate SMILES.
update : bool, optional (default False)
Update an existing map with the same output filename. If False, a new
map will be generated using only the input file(s).
assign_stereo_from_3d : bool, optional (default False)
Assign stereochemistry from 3D coordinates.
"""
smiles = SmilesMap(prefix=id_prefix, allow_duplicates=allow_duplicates,
assign_stereo_from_3d=assign_stereo_from_3d)
# update existing map
if update:
smiles.map = read_pickle(output_filename)
for input_filename in input_filenames:
print input_filename
with serial.MolReader().open(input_filename) as reader:
for mol in reader:
try:
smiles.add_mol(mol)
except ValueError:
if mol.HasProp('_Name'):
print 'Skipping {}'.format(mol.GetProp('_Name'))
else:
print 'Skipping {}'.format(
Chem.MolToSmiles(mol, isomericSmiles=True))
write_pickle(smiles.get_map(), output_filename)
def setUp(self):
"""
Set up tests.
"""
self.temp_dir = tempfile.mkdtemp()
self.map = {
"CID645443": "Cc1ccc(-n2c3c(cc(C(=O)Nc4cccc(C)n4)c2=O)C(=O)CCC3)cc1",
"CID2997889": "CC(C)(C)C(=O)Nc1ccc(-c2cn3ccsc3n2)cc1",
"CID2244": "CC(=O)Oc1ccccc1C(=O)O",
"CID2662": "Cc1ccc(-c2cc(C(F)(F)F)nn2-c2ccc(S(N)(=O)=O)cc2)cc1",
"CID3672": "CC(C)Cc1ccc(C(C)C(=O)O)cc1",
}
_, self.map_filename = tempfile.mkstemp(dir=self.temp_dir, suffix=".pkl")
write_pickle(self.map, self.map_filename)
# use a subset of AID588342
# note that CID 654924 is duplicated
this_dir = os.path.split(os.path.realpath(__file__))[0]
self.data_filename = os.path.join(this_dir, "data/test_pcba_data.csv")
# set up parser
self.engine = PcbaParser(self.data_filename, self.map_filename)
def main(active_filename, decoy_filename, output_filename,
assign_stereo_from_3d=False):
"""
Construct target files for datasets with active/decoy labels.
Parameters
----------
active_filename : str
Active molecule filename.
decoy_filename : str
Decoy molecule filename.
output_filename : str
Output filename.
assign_stereo_from_3d : bool, optional (default False)
Assign stereochemistry from 3D coordinates.
"""
active_smiles = get_smiles(active_filename, assign_stereo_from_3d)
decoy_smiles = get_smiles(decoy_filename, assign_stereo_from_3d)
targets = np.concatenate((np.ones(len(active_smiles), dtype=int),
np.zeros(len(decoy_smiles), dtype=int)))
smiles = np.concatenate((active_smiles, decoy_smiles))
write_pickle({'smiles': smiles, 'targets': targets}, output_filename)
def main(config_filename, output_filename, pdb_filename=None):
"""
Meta-information consists of a row for each target, with a column rach for
associated AIDs and PDBs (lists).
"""
# read target->PDB associations
pdb = {}
if pdb_filename is not None:
with open(pdb_filename) as f:
for line in f:
target, code = line.split()
pdb[target] = code.split(
',') # multiple PDBs can be separated by ','
config = pd.read_csv(config_filename)
# get AIDs for each target
targets = {}
for _, row in config.iterrows():
target = row['target']
try:
int(target)
target = 'gi_{}'.format(target) # add 'gi_' to integer targets
except ValueError:
pass
if target not in targets:
targets[target] = []
targets[target].append(row['aid'])
# construct dataframe
points = []
for target, aids in targets.iteritems():
points.append({
'target': target,
'aids': aids,
'pdbs': pdb.get(target)
})
df = pd.DataFrame(points)
write_pickle(df, output_filename)
def main(input_filename,
map_filename,
directory='.',
prefix='nci60',
suffix='pkl.gz'):
"""
Get regression targets.
Parameters
----------
input_filename : str
PCBA data filename.
map_filename : str
ID->SMILES map filename.
directory : str, optional (default '.')
Directory in which to write target files.
prefix : str, optional (default 'nci60')
Prefix for target files.
suffix : str, optional (default 'pkl.gz')
Suffix for target files.
"""
parser = Nci60Parser(input_filename, map_filename)
split_targets = parser.split_targets()
# get total record count
total = np.count_nonzero(~np.isnan(parser.read_data().NSC))
# write a separate file for each dataset
# note that split_targets is an OrderedDict
for i, name in enumerate(split_targets.keys()):
data = split_targets[name]
# print the fraction of valid assay records that were found in the map
print '{}\t{}/{} records matched'.format(name, len(data['targets']),
total)
write_pickle(
data,
os.path.join(directory,
'{}-{:02}-targets.{}'.format(prefix, i, suffix)))
def setUp(self):
"""
Set up tests.
"""
self.temp_dir = tempfile.mkdtemp()
self.map = {
'CID645443':
'Cc1ccc(-n2c3c(cc(C(=O)Nc4cccc(C)n4)c2=O)C(=O)CCC3)cc1',
'CID2997889': 'CC(C)(C)C(=O)Nc1ccc(-c2cn3ccsc3n2)cc1',
'CID2244': 'CC(=O)Oc1ccccc1C(=O)O',
'CID2662': 'Cc1ccc(-c2cc(C(F)(F)F)nn2-c2ccc(S(N)(=O)=O)cc2)cc1',
'CID3672': 'CC(C)Cc1ccc(C(C)C(=O)O)cc1'
}
_, self.map_filename = tempfile.mkstemp(dir=self.temp_dir,
suffix='.pkl')
write_pickle(self.map, self.map_filename)
# use a subset of AID588342
# note that CID 654924 is duplicated
this_dir = os.path.split(os.path.realpath(__file__))[0]
self.data_filename = os.path.join(this_dir, 'data/test_pcba_data.csv')
# set up parser
self.engine = PcbaParser(self.data_filename, self.map_filename)