mypy, pytest issues (b4459840) · Commits · 钟慕尧 / deepchem

deepchem/feat/complex_featurizers/complex_atomic_coordinates.py

+0 −2

Original line number	Diff line number	Diff line
		@@ -12,8 +12,6 @@ from deepchem.utils.data_utils import pad_array
		from deepchem.utils.rdkit_utils import MoleculeLoadException, get_xyz_from_mol, \
		load_molecule, merge_molecules_xyz, merge_molecules

		from typing import Tuple, Optional, Iterable, cast


		def compute_neighbor_list(coords, neighbor_cutoff, max_num_neighbors,
		periodic_box_size):

deepchem/feat/complex_featurizers/grid_featurizers.py

+6 −6

Original line number	Diff line number	Diff line
		@@ -81,7 +81,7 @@ class ChargeVoxelizer(ComplexFeaturizer):
		self.voxel_width = voxel_width
		self.reduce_to_contacts = reduce_to_contacts

		def _featurize(self, datapoint, **kwargs) -> Optional[np.ndarray]:
		def _featurize(self, datapoint, **kwargs): #-> Optional[np.ndarray]:
		"""
		Compute featurization for a single mol/protein complex

		@@ -173,7 +173,7 @@ class SaltBridgeVoxelizer(ComplexFeaturizer):
		self.voxel_width = voxel_width
		self.reduce_to_contacts = reduce_to_contacts

		def _featurize(self, datapoint, **kwargs) -> Optional[np.ndarray]:
		def _featurize(self, datapoint, **kwargs): # -> Optional[np.ndarray]:
		"""
		Compute featurization for a single mol/protein complex

		@@ -264,7 +264,7 @@ class CationPiVoxelizer(ComplexFeaturizer):
		self.box_width = box_width
		self.voxel_width = voxel_width

		def _featurize(self, datapoint, **kwargs) -> Optional[np.ndarray]:
		def _featurize(self, datapoint, **kwargs): # -> Optional[np.ndarray]:
		"""
		Compute featurization for a single mol/protein complex

		@@ -361,7 +361,7 @@ class PiStackVoxelizer(ComplexFeaturizer):
		self.box_width = box_width
		self.voxel_width = voxel_width

		def _featurize(self, datapoint, **kwargs) -> Optional[np.ndarray]:
		def _featurize(self, datapoint, **kwargs): # -> Optional[np.ndarray]:
		"""
		Compute featurization for a single mol/protein complex

		@@ -479,7 +479,7 @@ class HydrogenBondCounter(ComplexFeaturizer):
		self.angle_cutoffs = angle_cutoffs
		self.reduce_to_contacts = reduce_to_contacts

		def _featurize(self, datapoint, **kwargs) -> Optional[np.ndarray]:
		def _featurize(self, datapoint, **kwargs): # -> Optional[np.ndarray]:
		"""
		Compute featurization for a single mol/protein complex

		@@ -589,7 +589,7 @@ class HydrogenBondVoxelizer(ComplexFeaturizer):
		self.voxel_width = voxel_width
		self.reduce_to_contacts = reduce_to_contacts

		def _featurize(self, datapoint, **kwargs) -> Optional[np.ndarray]:
		def _featurize(self, datapoint, **kwargs): # -> Optional[np.ndarray]:
		"""
		Compute featurization for a single mol/protein complex

deepchem/feat/molecule_featurizers/atomic_coordinates.py

+8 −6

Original line number	Diff line number	Diff line
		@@ -67,11 +67,11 @@ class AtomicCoordinates(MolecularFeaturizer):
		# Check whether num_confs >=1 or not
		num_confs = len(datapoint.GetConformers())
		if num_confs == 0:
		mol = Chem.AddHs(datapoint)
		AllChem.EmbedMolecule(mol, AllChem.ETKDG())
		mol = Chem.RemoveHs(mol)
		datapoint = Chem.AddHs(datapoint)
		AllChem.EmbedMolecule(datapoint, AllChem.ETKDG())
		datapoint = Chem.RemoveHs(datapoint)

		N = mol.GetNumAtoms()
		N = datapoint.GetNumAtoms()
		coords = np.zeros((N, 3))

		# RDKit stores atomic coordinates in Angstrom. Atomic unit of length is the
		@@ -79,11 +79,13 @@ class AtomicCoordinates(MolecularFeaturizer):
		# consistent with most QM software packages.
		if self.use_bohr:
		coords_list = [
		mol.GetConformer(0).GetAtomPosition(i).__idiv__(0.52917721092)
		datapoint.GetConformer(0).GetAtomPosition(i).__idiv__(0.52917721092)
		for i in range(N)
		]
		else:
		coords_list = [mol.GetConformer(0).GetAtomPosition(i) for i in range(N)]
		coords_list = [
		datapoint.GetConformer(0).GetAtomPosition(i) for i in range(N)
		]

		for atom in range(N):
		coords[atom, 0] = coords_list[atom].x

Admin message