Making changes for end of day (8e09e7a8) · Commits · 钟慕尧 / deepchem

deep_chem/scripts/process_dataset.py

+14 −0

Original line number	Diff line number	Diff line
		@@ -69,6 +69,7 @@ def parse_float_input(val):
		return np.nan

		def generate_fingerprints(name, out):
		"""Generates circular fingerprints for dataset."""
		dataset_dir = os.path.join(out, name)
		fingerprint_dir = os.path.join(dataset_dir, "fingerprints")
		shards_dir = os.path.join(dataset_dir, "shards")
		@@ -80,6 +81,19 @@ def generate_fingerprints(name, out):
		sdf, fingerprints,
		"circular", "--size", "1024"])

		def generate_descriptors(name, out):
		"""Generates molecular descriptors for dataset."""
		dataset_dir = os.path.join(out, name)
		fingerprint_dir = os.path.join(dataset_dir, "descriptors")
		shards_dir = os.path.join(dataset_dir, "shards")
		sdf = os.path.join(shards_dir, "%s-0.sdf.gz" % name)
		fingerprints = os.path.join(fingerprint_dir,
		"%s-fingerprints.pkl.gz" % name)
		subprocess.call(["python", "-m", "vs_utils.scripts.featurize",
		"--scaffolds", "--smiles",
		sdf, fingerprints,
		"descriptors"])

		def globavir_specs():
		fields = ["compound_name", "isomeric_smiles", "tdo_ic50_nm", "tdo_Ki_nm",
		"tdo_percent_activity_10_um", "tdo_percent_activity_1_um", "ido_ic50_nm",