def main(smiles_file,
params_file,
sdf_dir=None,
out_file="molecules.csv.bz2",
log=None,
num_proc=None,
parallel_mode=None,
verbose=False):
"""Fingerprint molecules."""
setup_logging(log, verbose=verbose)
parallelizer = Parallelizer(parallel_mode="processes")
# set conformer generation and fingerprinting parameters
confgen_params, fprint_params = params_to_dicts(params_file)
kwargs = {"save": False, "fprint_params": fprint_params}
smiles_dict = smiles_to_dict(smiles_file)
mol_num = len({x.split('-')[0] for x in smiles_dict})
if sdf_dir is not None:
sdf_files = glob.glob(os.path.join(sdf_dir, "*.sdf*"))
sdf_files = sorted(
[x for x in sdf_files if name_from_sdf_filename(x) in smiles_dict])
data_iter = make_data_iterator(sdf_files)
fp_method = native_tuples_from_sdf
logging.info("Using SDF files from {}".format(sdf_dir))
else:
kwargs["confgen_params"] = confgen_params
data_iter = ((smiles, name)
for name, smiles in smiles_dict.iteritems())
mol_num = len({x.split('-')[0] for x in smiles_dict})
fp_method = native_tuples_from_smiles
logging.info("Will generate conformers.")
logging.info(
"Conformer generation params: {!r}.".format(confgen_params))
logging.info("Fingerprinting params: {!r}.".format(fprint_params))
# fingerprint in parallel
logging.info("Fingerprinting {:d} molecules".format(mol_num))
mol_list_dict = {}
for result, data in parallelizer.run_gen(fp_method,
data_iter,
kwargs=kwargs):
if not result:
logging.warning("Fingerprinting failed for {}.".format(data[0]))
continue
try:
_, name = result[0]
name = name.split('_')[0]
except IndexError:
logging.warning("Fingerprinting failed for {}.".format(data[0]))
continue
mol_list_dict[name] = result
logging.info("Finished fingerprinting molecules")
# save to SEA molecules file
logging.info("Saving fingerprints to {}".format(out_file))
fp_type = fprint_params_to_fptype(**fprint_params)
lists_dicts_to_molecules(out_file, smiles_dict, mol_list_dict, fp_type)
logging.info("Finished!")
def params_to_molecules(params, smiles_file, conf_dir, out_dir,
parallelizer=None):
"""Generate molecules_file based on params dict."""
smiles_dict = smiles_to_dict(smiles_file)
logging.debug("SMILES file has {:d} unique smiles.".format(
len(smiles_dict)))
logging.debug("Example SMILES: {!r}".format(smiles_dict.items()[0]))
fprint_params = {"radius_multiplier": params["radius_multiplier"],
"stereo": STEREO, "bits": params["bits"],
"first": params['first'], "level": params['level']}
conf_dir_files = glob.glob("{!s}/*".format(conf_dir))
logging.debug("Found {:d} files in conformer directory.".format(
len(conf_dir_files)))
sdf_files = [x for x in conf_dir_files
if os.path.basename(x).split('.')[0] in smiles_dict]
logging.debug("{:d} conformer files match SMILES.".format(len(sdf_files)))
if len(sdf_files) == 0:
raise Exception("Directory {!s} does not contain any usable SDF "
"files.".format(conf_dir))
kwargs = {"save": False, "fprint_params": fprint_params}
data_iterator = make_data_iterator(sdf_files)
if parallelizer is not None:
results_iter = parallelizer.run_gen(native_tuples_from_sdf,
data_iterator, kwargs=kwargs)
else:
results_iter = (native_tuples_from_sdf(*x, **kwargs)
for x in data_iterator)
molecules_file = get_molecules_file(out_dir)
fp_type = fprint_params_to_fptype(**params)
with smart_open(molecules_file, "wb") as f:
writer = csv.writer(f)
fp_type.write(writer)
writer.writerow(("molecule id", "smiles", "fingerprint"))
for results in results_iter:
try:
fp_native_list, sdf_file = results
except ValueError:
logging.error("Results of fingerprinting did not look as "
"expected: {!r}".format(results))
proto_name = MolItemName.from_str(fp_native_list[0][1]).proto_name
smiles = smiles_dict[proto_name]
for fp_native, fp_name in fp_native_list:
writer.writerow((fp_name, smiles, fp_native))
del smiles_dict
filtered_smiles_dict, mol_lists_dict, fp_type = molecules_to_lists_dicts(
molecules_file)
return (filtered_smiles_dict, mol_lists_dict, fp_type)
def run(sdf_files,
bits=BITS,
first=FIRST_DEF,
level=LEVEL_DEF,
radius_multiplier=RADIUS_MULTIPLIER_DEF,
counts=COUNTS_DEF,
stereo=STEREO_DEF,
include_disconnected=INCLUDE_DISCONNECTED_DEF,
rdkit_invariants=RDKIT_INVARIANTS_DEF,
exclude_floating=EXCLUDE_FLOATING_DEF,
params=None,
out_dir_base=None,
out_ext=OUT_EXT_DEF,
db_file=None,
overwrite=False,
all_iters=False,
log=None,
num_proc=None,
parallel_mode=None,
verbose=False):
"""Generate E3FP fingerprints from SDF files."""
setup_logging(log, verbose=verbose)
if params is not None:
params = read_params(params, fill_defaults=True)
bits = get_value(params, "fingerprinting", "bits", int)
first = get_value(params, "fingerprinting", "first", int)
level = get_value(params, "fingerprinting", "level", int)
radius_multiplier = get_value(params, "fingerprinting",
"radius_multiplier", float)
counts = get_value(params, "fingerprinting", "counts", bool)
stereo = get_value(params, "fingerprinting", "stereo", bool)
include_disconnected = get_value(params, "fingerprinting",
"include_disconnected", bool)
rdkit_invariants = get_value(params, "fingerprinting",
"rdkit_invariants", bool)
exclude_floating = get_value(params, "fingerprinting",
"exclude_floating", bool)
para = Parallelizer(num_proc=num_proc, parallel_mode=parallel_mode)
if para.rank == 0:
logging.info("Initializing E3FP generation.")
logging.info("Getting SDF files")
if len(sdf_files) == 1 and os.path.isdir(sdf_files[0]):
from glob import glob
sdf_files = glob("{:s}/*sdf*".format(sdf_files[0]))
data_iterator = make_data_iterator(sdf_files)
logging.info("SDF File Number: {:d}".format(len(sdf_files)))
if out_dir_base is not None:
logging.info("Out Directory Basename: {:s}".format(out_dir_base))
logging.info("Out Extension: {:s}".format(out_ext))
if db_file is not None:
logging.info("Database File: {:s}".format(db_file))
if db_file is None and out_dir_base is None:
sys.exit('Either `db_file` or `out_dir_base` must be specified.')
logging.info("Max First Conformers: {:d}".format(first))
logging.info("Bits: {:d}".format(bits))
logging.info("Level/Max Iterations: {:d}".format(level))
logging.info(
"Shell Radius Multiplier: {:.4g}".format(radius_multiplier))
logging.info("Stereo Mode: {!s}".format(stereo))
if include_disconnected:
logging.info("Connected-only mode: on")
if rdkit_invariants:
logging.info("Invariant type: RDKit")
else:
logging.info("Invariant type: Daylight")
logging.info("Parallel Mode: {!s}".format(para.parallel_mode))
logging.info("Starting")
else:
data_iterator = iter([])
fp_kwargs = {
"first": first,
"bits": bits,
"level": level,
"radius_multiplier": radius_multiplier,
"stereo": stereo,
"counts": counts,
"include_disconnected": include_disconnected,
"rdkit_invariants": rdkit_invariants,
"exclude_floating": exclude_floating,
"out_dir_base": out_dir_base,
"out_ext": out_ext,
"all_iters": all_iters,
"overwrite": overwrite,
"save": False
}
if out_dir_base is not None:
fp_kwargs['save'] = True
run_kwargs = {"kwargs": fp_kwargs}
results_iter = para.run_gen(fprints_dict_from_sdf, data_iterator,
**run_kwargs)
if db_file is not None:
fprints = []
for result, data in results_iter:
try:
fprints.extend(result.get(level, result[max(result.keys())]))
except (AttributeError, ValueError):
# fprinting failed, assume logged in method
continue
if len(fprints) > 0:
db = FingerprintDatabase(fp_type=type(fprints[0]), level=level)
db.add_fingerprints(fprints)
db.save(db_file)
logging.info("Saved fingerprints to {:s}".format(db_file))
else:
list(results_iter)
def run(
mol2=None,
smiles=None,
standardise=STANDARDISE_DEF,
num_conf=NUM_CONF_DEF,
first=FIRST_DEF,
pool_multiplier=POOL_MULTIPLIER_DEF,
rmsd_cutoff=RMSD_CUTOFF_DEF,
max_energy_diff=MAX_ENERGY_DIFF_DEF,
forcefield=FORCEFIELD_DEF,
seed=SEED_DEF,
params=None,
prioritize=False,
out_dir=OUTDIR_DEF,
compress=COMPRESS_DEF,
overwrite=False,
values_file=None,
log=None,
num_proc=None,
parallel_mode=None,
verbose=False,
):
"""Run conformer generation."""
setup_logging(log, verbose=verbose)
if params is not None:
params = read_params(params)
standardise = get_value(params, "preprocessing", "standardise", bool)
num_conf = get_value(params, "conformer_generation", "num_conf", int)
first = get_value(params, "conformer_generation", "first", int)
pool_multiplier = get_value(params, "conformer_generation",
"pool_multiplier", int)
rmsd_cutoff = get_value(params, "conformer_generation", "rmsd_cutoff",
float)
max_energy_diff = get_value(params, "conformer_generation",
"max_energy_diff", float)
forcefield = get_value(params, "conformer_generation", "forcefield")
seed = get_value(params, "conformer_generation", "seed", int)
# check args
if forcefield not in FORCEFIELD_CHOICES:
raise ValueError(
"Specified forcefield {} is not in valid options {!r}".format(
forcefield, FORCEFIELD_CHOICES))
para = Parallelizer(num_proc=num_proc, parallel_mode=parallel_mode)
# Check to make sure args make sense
if mol2 is None and smiles is None:
if para.is_master():
parser.print_usage()
logging.error("Please provide mol2 file or a SMILES file.")
sys.exit()
if mol2 is not None and smiles is not None:
if para.is_master():
parser.print_usage()
logging.error("Please provide only a mol2 file OR a SMILES file.")
sys.exit()
if num_proc and num_proc < 1:
if para.is_master():
parser.print_usage()
logging.error(
"Please provide more than one processor with `--num_proc`.")
sys.exit()
# Set up input type
if mol2 is not None:
in_type = "mol2"
elif smiles is not None:
in_type = "smiles"
if para.is_master():
if in_type == "mol2":
logging.info("Input type: mol2 file(s)")
logging.info("Input file number: {:d}".format(len(mol2)))
mol_iter = (mol_from_mol2(_mol2_file,
_name,
standardise=standardise)
for _mol2_file, _name in mol2_generator(*mol2))
else:
logging.info("Input type: Detected SMILES file(s)")
logging.info("Input file number: {:d}".format(len(smiles)))
mol_iter = (mol_from_smiles(_smiles,
_name,
standardise=standardise)
for _smiles, _name in smiles_generator(*smiles))
if prioritize:
logging.info(("Prioritizing mols with low rotatable bond number"
" and molecular weight first."))
mols_with_properties = [(
AllChem.CalcNumRotatableBonds(mol),
AllChem.CalcExactMolWt(mol),
mol,
) for mol in mol_iter if mol is not None]
data_iterator = make_data_iterator(
(x[-1] for x in sorted(mols_with_properties)))
else:
data_iterator = make_data_iterator(
(x for x in mol_iter if x is not None))
# Set up parallel-specific options
logging.info("Parallel Type: {}".format(para.parallel_mode))
# Set other options
touch_dir(out_dir)
if not num_conf:
num_conf = -1
logging.info("Out Directory: {}".format(out_dir))
logging.info("Overwrite Existing Files: {}".format(overwrite))
if values_file is not None:
if os.path.exists(values_file) and overwrite is not True:
value_args = (values_file, "a")
logging.info("Values file: {} (append)".format((values_file)))
else:
value_args = (values_file, "w")
logging.info("Values file: {} (new file)".format(
(values_file)))
if num_conf is None or num_conf == -1:
logging.info("Target Conformer Number: auto")
else:
logging.info("Target Conformer Number: {:d}".format(num_conf))
if first is None or first == -1:
logging.info("First Conformers Number: all")
else:
logging.info("First Conformers Number: {:d}".format(first))
logging.info("Pool Multiplier: {:d}".format(pool_multiplier))
logging.info("RMSD Cutoff: {:.4g}".format(rmsd_cutoff))
if max_energy_diff is None:
logging.info("Maximum Energy Difference: None")
else:
logging.info("Maximum Energy Difference: {:.4g} kcal".format(
max_energy_diff))
logging.info("Forcefield: {}".format(forcefield.upper()))
if seed != -1:
logging.info("Seed: {:d}".format(seed))
logging.info("Starting.")
else:
data_iterator = iter([])
gen_conf_kwargs = {
"out_dir": out_dir,
"num_conf": num_conf,
"rmsd_cutoff": rmsd_cutoff,
"max_energy_diff": max_energy_diff,
"forcefield": forcefield,
"pool_multiplier": pool_multiplier,
"first": first,
"seed": seed,
"save": True,
"overwrite": overwrite,
"compress": compress,
}
run_kwargs = {"kwargs": gen_conf_kwargs}
results_iterator = para.run_gen(generate_conformers, data_iterator,
**run_kwargs)
if para.is_master() and values_file is not None:
hdf5_buffer = HDF5Buffer(*value_args)
for result, data in results_iterator:
if (para.is_master() and values_file is not None
and result is not False):
values_to_hdf5(hdf5_buffer, result)
if para.is_master() and values_file is not None:
hdf5_buffer.flush()
hdf5_buffer.close()
