Merge pull request #883 from rbharath/warnings (027d03e7) · Commits · 钟慕尧 / deepchem

deepchem/feat/rdkit_grid_featurizer.py

+9 −4

Original line number	Diff line number	Diff line
		@@ -590,7 +590,11 @@ def compute_hydrogen_bonds(protein_xyz, protein, ligand_xyz, ligand,
		return (hbond_contacts)


		def convert_atom_to_voxel(molecule_xyz, atom_index, box_width, voxel_width):
		def convert_atom_to_voxel(molecule_xyz,
		atom_index,
		box_width,
		voxel_width,
		verbose=False):
		"""
		Converts an atom to an i,j,k grid index.
		"""
		@@ -600,6 +604,7 @@ def convert_atom_to_voxel(molecule_xyz, atom_index, box_width, voxel_width):
		(molecule_xyz[atom_index, :] + np.array([box_width, box_width, box_width]
		) / 2.0) / voxel_width).astype(int)
		if ((indices < 0) \| (indices >= box_width / voxel_width)).any():
		if verbose:
		warn(
		'Coordinates are outside of the box (atom id = %s, coords xyz = %s, coords in box = %s'
		% (atom_index, molecule_xyz[atom_index], indices))