Changing file load (9fed36f2) · Commits · 钟慕尧 / deepchem

deepchem/dock/docking.py

+0 −2

Original line number	Diff line number	Diff line
		@@ -81,6 +81,4 @@ class VinaGridDNNDocker(object):
		protein_docked, ligand_docked = self.pose_generator.generate_poses(
		protein_file, ligand_file)
		score = self.pose_scorer.score(protein_docked, ligand_docked)
		#score = self.pose_scorer.score(protein_file, ligand_file)
		return (score, (protein_docked, ligand_docked))
		#return (score, (protein_file, ligand_file))

+0 −16

Original line number	Diff line number	Diff line
		@@ -78,32 +78,16 @@ def hydrogenate_and_compute_partial_charges(input_file, input_format,
		print("Create pdb with hydrogens added")
		hyd_conversion = openbabel.OBConversion()
		hyd_conv = hyd_conversion.SetInAndOutFormats(str(input_format), str("pdb"))
		############################################################ DEBUG
		print("input_format")
		print(input_format)
		print("hyd_conv")
		print(hyd_conv)
		############################################################ DEBUG
		mol = openbabel.OBMol()
		hyd_conversion.ReadFile(mol, str(input_file))
		# AddHydrogens(not-polaronly, correctForPH, pH)
		mol.AddHydrogens(False, True, 7.4)
		hyd_out = hyd_conversion.WriteFile(mol, str(hyd_output))
		############################################################ DEBUG
		print("hyd_out")
		print(hyd_out)
		print("os.path.exists(hyd_output)")
		print(os.path.exists(hyd_output))
		############################################################ DEBUG

		if verbose:
		print("Create a pdbqt file from the hydrogenated pdb above.")
		charge_conversion = openbabel.OBConversion()
		charge_conv = charge_conversion.SetInAndOutFormats(str("pdb"), str("pdbqt"))
		############################################################ DEBUG
		print("charge_conv")
		print(charge_conv)
		############################################################ DEBUG

		if protein:
		print("Make protein rigid.")

+7 −3

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		@@ -6,8 +6,8 @@ from __future__ import division
		from __future__ import unicode_literals

		# TODO(rbharath): Use standard joblib once old-data has been regenerated.
		#import joblib
		from sklearn.externals import joblib
		import joblib
		from sklearn.externals import joblib as old_joblib
		import gzip
		import pickle
		import pandas as pd
		@@ -103,7 +103,11 @@ def load_from_disk(filename):
		if os.path.splitext(name)[1] == ".pkl":
		return load_pickle_from_disk(filename)
		elif os.path.splitext(name)[1] == ".joblib":
		try:
		return joblib.load(filename)
		except KeyError:
		# Try older joblib version for legacy files.
		return old_joblib.load(filename)
		elif os.path.splitext(name)[1] == ".csv":
		# First line of user-specified CSV must be header.
		df = pd.read_csv(filename, header=0)