Merge pull request #428 from proteneer/isomorph (d63d15f7) · Commits · 钟慕尧 / deepchem

deepchem/data/data_loader.py

+8 −0

Original line number	Diff line number	Diff line
		@@ -11,6 +11,8 @@ import numpy as np
		import csv
		import numbers
		import tempfile
		from rdkit.Chem import rdmolfiles
		from rdkit.Chem import rdmolops
		from rdkit import Chem
		import time
		import sys
		@@ -63,6 +65,12 @@ def featurize_smiles_df(df, featurizer, field, log_every_N=1000, verbose=True):
		features = []
		for ind, elem in enumerate(sample_elems):
		mol = Chem.MolFromSmiles(elem)
		# TODO (ytz) this is a bandage solution to reorder the atoms so
		# that they're always in the same canonical order. Presumably this
		# should be correctly implemented in the future for graph mols.
		if mol:
		new_order = rdmolfiles.CanonicalRankAtoms(mol)
		mol = rdmolops.RenumberAtoms(mol, new_order)
		if ind % log_every_N == 0:
		log("Featurizing sample %d" % ind, verbose)
		features.append(featurizer.featurize([mol]))