bugfixes (4880f2aa) · Commits · 钟慕尧 / deepchem

deepchem/splits/splitters.py

+2 −0

Original line number	Diff line number	Diff line
		@@ -766,6 +766,7 @@ def ClusterFps(fps, cutoff=0.2):
		# (ytz): this is directly copypasta'd from Greg Landrum's clustering example.
		dists = []
		nfps = len(fps)
		from rdkit import DataStructs
		for i in range(1, nfps):
		sims = DataStructs.BulkTanimotoSimilarity(fps[i], fps[:i])
		dists.extend([1 - x for x in sims])
		@@ -909,6 +910,7 @@ class FingerprintSplitter(Splitter):
		fingerprints.append(fp)

		distances = np.ones(shape=(data_len, data_len))
		from rdkit import DataStructs
		for i in range(data_len):
		for j in range(data_len):
		distances[i][j] = 1 - DataStructs.FingerprintSimilarity(

+0 −1

Original line number	Diff line number	Diff line
		@@ -15,7 +15,6 @@ import tempfile
		import tarfile
		import zipfile


		try:
		from urllib.request import urlretrieve # Python 3
		except:

+11 −7

Original line number	Diff line number	Diff line
		@@ -8,6 +8,7 @@ __license__ = "3-clause BSD"

		import numpy as np


		class ConformerGenerator(object):
		"""
		Generate molecule conformers.
		@@ -43,7 +44,11 @@ class ConformerGenerator(object):
		minimization, increasing the size of the pool increases the chance
		of identifying max_conformers unique conformers.
		"""
		def __init__(self, max_conformers=1, rmsd_threshold=0.5, force_field='uff',

		def __init__(self,
		max_conformers=1,
		rmsd_threshold=0.5,
		force_field='uff',
		pool_multiplier=10):
		self.max_conformers = max_conformers
		if rmsd_threshold is None or rmsd_threshold < 0:
		@@ -124,8 +129,7 @@ class ConformerGenerator(object):
		"""
		from rdkit.Chem import AllChem
		if self.force_field == 'uff':
		ff = AllChem.UFFGetMoleculeForceField(
		mol, confId=conf_id, **kwargs)
		ff = AllChem.UFFGetMoleculeForceField(mol, confId=conf_id, **kwargs)
		elif self.force_field.startswith('mmff'):
		AllChem.MMFFSanitizeMolecule(mol)
		mmff_props = AllChem.MMFFGetMoleculeProperties(
		@@ -237,8 +241,8 @@ class ConformerGenerator(object):
		Molecule.
		"""
		from rdkit.Chem import AllChem
		rmsd = np.zeros((mol.GetNumConformers(), mol.GetNumConformers()),
		dtype=float)
		rmsd = np.zeros(
		(mol.GetNumConformers(), mol.GetNumConformers()), dtype=float)
		for i, ref_conf in enumerate(mol.GetConformers()):
		for j, fit_conf in enumerate(mol.GetConformers()):
		if i >= j:

+1 −2

Original line number	Diff line number	Diff line
		@@ -3,7 +3,6 @@ import logging
		import numpy as np
		import os


		try:
		from StringIO import StringIO
		except ImportError:
		@@ -217,7 +216,7 @@ def merge_molecules_xyz(protein_xyz, ligand_xyz):
		def merge_molecules(ligand, protein):
		"""Helper method to merge ligand and protein molecules."""
		from rdkit.Chem import rdmolops
		return Chem.rdmolops.CombineMols(ligand, protein)
		return rdmolops.CombineMols(ligand, protein)


		class PdbqtLigandWriter(object):