Rolled back conversion to GetDistanceMatrix (2e6b5059) · Commits · 钟慕尧 / deepchem

deepchem/feat/molecule_featurizers/mat_featurizer.py

+10 −1

Original line number	Diff line number	Diff line
		@@ -49,7 +49,16 @@ class MATFeaturizer(MolecularFeaturizer):
		])

		adjacency_matrix = Chem.rdmolops.getAdjacencyMatrix(mol)
		distance_matrix = Chem.rdmolops.GetDistanceMatrix(mol)

		conformer = mol.GetConformer()
		positional_matrix = np.array([[
		conformer.GetAtomPosition(k).x,
		conformer.GetAtomPosition(k).y,
		conformer.GetAtomPosition(k).z
		] for k in range(mol.GetNumAtoms())])
		distance_matrix = pairwise_distances(positional_matrix)



		if self.add_dummy_node:
		m = np.zeros((node_features.shape[0] + 1, node_features.shape[1] + 1))