mypy change all to use datapoint (81521621) · Commits · 钟慕尧 / deepchem

deepchem/feat/base_classes.py

+44 −19

Original line number	Diff line number	Diff line
		@@ -4,7 +4,7 @@ Feature calculations.
		import inspect
		import logging
		import numpy as np
		from typing import Any, Dict, Iterable, Tuple, Union, cast
		from typing import Any, Dict, Iterable, Optional, Tuple, Union, cast

		from deepchem.utils import get_print_threshold
		from deepchem.utils.typing import PymatgenStructure
		@@ -44,7 +44,7 @@ class Featurizer(object):
		A numpy array containing a featurized representation of `datapoints`.
		"""
		datapoints = list(datapoints)
		features: list[any] = []
		features = []
		for i, point in enumerate(datapoints):
		if i % log_every_n == 0:
		logger.info("Featurizing datapoint %i" % i)
		@@ -158,7 +158,7 @@ class ComplexFeaturizer(Featurizer):
		"""

		def featurize(self,
		datapoints: Iterable[Tuple[str, str]] = None,
		datapoints: Optional[Iterable[Tuple[str, str]]] = None,
		log_every_n: int = 100,
		**kwargs) -> np.ndarray:
		"""
		@@ -212,7 +212,7 @@ class ComplexFeaturizer(Featurizer):

		return np.asarray(features)

		def _featurize(self, datapoints: Iterable[Tuple[str, str]] = None, **kwargs):
		def _featurize(self, datapoint: Optional[Tuple[str, str]] = None, **kwargs):
		"""
		Calculate features for single mol/protein complex.

		@@ -242,12 +242,12 @@ class MolecularFeaturizer(Featurizer):
		The subclasses of this class require RDKit to be installed.
		"""

		def featurize(self, molecules, log_every_n=1000, **kwargs) -> np.ndarray:
		def featurize(self, datapoints, log_every_n=1000, **kwargs) -> np.ndarray:
		"""Calculate features for molecules.

		Parameters
		----------
		molecules: rdkit.Chem.rdchem.Mol / SMILES string / iterable
		datapoints: rdkit.Chem.rdchem.Mol / SMILES string / iterable
		RDKit Mol, or SMILES string or iterable sequence of RDKit mols/SMILES
		strings.
		log_every_n: int, default 1000
		@@ -266,15 +266,21 @@ class MolecularFeaturizer(Featurizer):
		except ModuleNotFoundError:
		raise ImportError("This class requires RDKit to be installed.")

		if 'molecules' in kwargs:
		datapoints = kwargs.get("molecules")
		raise DeprecationWarning(
		'Molecules is being phased out as a parameter, please pass "datapoints" instead.'
		)

		# Special case handling of single molecule
		if isinstance(molecules, str) or isinstance(molecules, Mol):
		molecules = [molecules]
		if isinstance(datapoints, str) or isinstance(datapoints, Mol):
		datapoints = [datapoints]
		else:
		# Convert iterables to list
		molecules = list(molecules)
		datapoints = list(datapoints)

		features: list = []
		for i, mol in enumerate(molecules):
		for i, mol in enumerate(datapoints):
		if i % log_every_n == 0:
		logger.info("Featurizing datapoint %i" % i)

		@@ -323,14 +329,15 @@ class MaterialStructureFeaturizer(Featurizer):
		"""

		def featurize(self,
		structures: Iterable[Union[Dict[str, Any], PymatgenStructure]],
		datapoints: Optional[Iterable[Union[Dict[str, Any],
		PymatgenStructure]]] = None,
		log_every_n: int = 1000,
		**kwargs) -> np.ndarray:
		"""Calculate features for crystal structures.

		Parameters
		----------
		structures: Iterable[Union[Dict, pymatgen.core.Structure]]
		datapoints: Iterable[Union[Dict, pymatgen.core.Structure]]
		Iterable sequence of pymatgen structure dictionaries
		or pymatgen.core.Structure. Please confirm the dictionary representations
		of pymatgen.core.Structure from https://pymatgen.org/pymatgen.core.structure.html.
		@@ -341,16 +348,25 @@ class MaterialStructureFeaturizer(Featurizer):
		-------
		features: np.ndarray
		A numpy array containing a featurized representation of
		`structures`.
		`datapoints`.
		"""
		try:
		from pymatgen.core import Structure
		except ModuleNotFoundError:
		raise ImportError("This class requires pymatgen to be installed.")

		structures = list(structures)
		if 'structures' in kwargs:
		datapoints = kwargs.get("structures")
		raise DeprecationWarning(
		'Structures is being phased out as a parameter, please pass "datapoints" instead.'
		)

		if not isinstance(datapoints, Iterable):
		datapoints = [cast(Union[Dict[str, Any], PymatgenStructure], datapoints)]

		datapoints = list(datapoints)
		features = []
		for idx, structure in enumerate(structures):
		for idx, structure in enumerate(datapoints):
		if idx % log_every_n == 0:
		logger.info("Featurizing datapoint %i" % idx)
		try:
		@@ -389,14 +405,14 @@ class MaterialCompositionFeaturizer(Featurizer):
		"""

		def featurize(self,
		compositions: Iterable[str],
		datapoints: Optional[Iterable[str]] = None,
		log_every_n: int = 1000,
		**kwargs) -> np.ndarray:
		"""Calculate features for crystal compositions.

		Parameters
		----------
		compositions: Iterable[str]
		datapoints: Iterable[str]
		Iterable sequence of composition strings, e.g. "MoS2".
		log_every_n: int, default 1000
		Logging messages reported every `log_every_n` samples.
		@@ -412,9 +428,18 @@ class MaterialCompositionFeaturizer(Featurizer):
		except ModuleNotFoundError:
		raise ImportError("This class requires pymatgen to be installed.")

		compositions = list(compositions)
		if 'compositions' in kwargs and datapoints is None:
		datapoints = kwargs.get("compositions")
		raise DeprecationWarning(
		'Compositions is being phased out as a parameter, please pass "datapoints" instead.'
		)

		if not isinstance(datapoints, Iterable):
		datapoints = [cast(str, datapoints)]

		datapoints = list(datapoints)
		features = []
		for idx, composition in enumerate(compositions):
		for idx, composition in enumerate(datapoints):
		if idx % log_every_n == 0:
		logger.info("Featurizing datapoint %i" % idx)
		try:

deepchem/feat/complex_featurizers/complex_atomic_coordinates.py

+10 −4

Original line number	Diff line number	Diff line
		@@ -12,7 +12,7 @@ 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
		from typing import Tuple, Optional, Iterable, cast


		def compute_neighbor_list(coords, neighbor_cutoff, max_num_neighbors,
		@@ -118,16 +118,22 @@ class NeighborListComplexAtomicCoordinates(ComplexFeaturizer):
		# Type of data created by this featurizer
		self.dtype = object

		def _featurize(self, complex: Tuple[str, str], **kwargs):
		def _featurize(self, datapoint, **kwargs):
		"""
		Compute neighbor list for complex.

		Parameters
		----------
		complex: Tuple[str, str]
		datapoint: Tuple[str, str]
		Filenames for molecule and protein.
		"""
		mol_pdb_file, protein_pdb_file = complex
		if 'complex' in kwargs:
		datapoint = kwargs.get("complex")
		raise DeprecationWarning(
		'Complex is being phased out as a parameter, please pass "datapoint" instead.'
		)

		mol_pdb_file, protein_pdb_file = datapoint
		mol_coords, ob_mol = load_molecule(mol_pdb_file)
		protein_coords, protein_mol = load_molecule(protein_pdb_file)
		system_coords = merge_molecules_xyz([mol_coords, protein_coords])

deepchem/feat/complex_featurizers/contact_fingerprints.py

+9 −3

Original line number	Diff line number	Diff line
		@@ -93,17 +93,23 @@ class ContactCircularFingerprint(ComplexFeaturizer):
		self.radius = radius
		self.size = size

		def _featurize(self, complex: Tuple[str, str], **kwargs):
		def _featurize(self, datapoint, **kwargs):
		"""
		Compute featurization for a molecular complex

		Parameters
		----------
		complex: Tuple[str, str]
		datapoint: Tuple[str, str]
		Filenames for molecule and protein.
		"""
		if 'complex' in kwargs:
		datapoint = kwargs.get("complex")
		raise DeprecationWarning(
		'Complex is being phased out as a parameter, please pass "datapoint" instead.'
		)

		try:
		fragments = load_complex(complex, add_hydrogens=False)
		fragments = load_complex(datapoint, add_hydrogens=False)

		except MoleculeLoadException:
		logger.warning("This molecule cannot be loaded by Rdkit. Returning None")

deepchem/feat/complex_featurizers/grid_featurizers.py

+52 −23

Original line number	Diff line number	Diff line
		@@ -81,18 +81,23 @@ class ChargeVoxelizer(ComplexFeaturizer):
		self.voxel_width = voxel_width
		self.reduce_to_contacts = reduce_to_contacts

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

		Parameters
		----------
		complex: Tuple[str, str]
		datapoint: Tuple[str, str]
		Filenames for molecule and protein.
		"""
		if 'complex' in kwargs:
		datapoint = kwargs.get("complex")
		raise DeprecationWarning(
		'Complex is being phased out as a parameter, please pass "datapoint" instead.'
		)

		try:
		fragments = rdkit_utils.load_complex(complex, add_hydrogens=False)
		fragments = rdkit_utils.load_complex(datapoint, add_hydrogens=False)

		except MoleculeLoadException:
		logger.warning("This molecule cannot be loaded by Rdkit. Returning None")
		@@ -168,18 +173,23 @@ class SaltBridgeVoxelizer(ComplexFeaturizer):
		self.voxel_width = voxel_width
		self.reduce_to_contacts = reduce_to_contacts

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

		Parameters
		----------
		complex: Tuple[str, str]
		datapoint: Tuple[str, str]
		Filenames for molecule and protein.
		"""
		if 'complex' in kwargs:
		datapoint = kwargs.get("complex")
		raise DeprecationWarning(
		'Complex is being phased out as a parameter, please pass "datapoint" instead.'
		)

		try:
		fragments = rdkit_utils.load_complex(complex, add_hydrogens=False)
		fragments = rdkit_utils.load_complex(datapoint, add_hydrogens=False)

		except MoleculeLoadException:
		logger.warning("This molecule cannot be loaded by Rdkit. Returning None")
		@@ -254,18 +264,23 @@ class CationPiVoxelizer(ComplexFeaturizer):
		self.box_width = box_width
		self.voxel_width = voxel_width

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

		Parameters
		----------
		complex: Tuple[str, str]
		datapoint: Tuple[str, str]
		Filenames for molecule and protein.
		"""
		if 'complex' in kwargs:
		datapoint = kwargs.get("complex")
		raise DeprecationWarning(
		'Complex is being phased out as a parameter, please pass "datapoint" instead.'
		)

		try:
		fragments = rdkit_utils.load_complex(complex, add_hydrogens=False)
		fragments = rdkit_utils.load_complex(datapoint, add_hydrogens=False)

		except MoleculeLoadException:
		logger.warning("This molecule cannot be loaded by Rdkit. Returning None")
		@@ -346,17 +361,23 @@ class PiStackVoxelizer(ComplexFeaturizer):
		self.box_width = box_width
		self.voxel_width = voxel_width

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

		Parameters
		----------
		complex: Tuple[str, str]
		datapoint: Tuple[str, str]
		Filenames for molecule and protein.
		"""
		if 'complex' in kwargs:
		datapoint = kwargs.get("complex")
		raise DeprecationWarning(
		'Complex is being phased out as a parameter, please pass "datapoint" instead.'
		)

		try:
		fragments = rdkit_utils.load_complex(complex, add_hydrogens=False)
		fragments = rdkit_utils.load_complex(datapoint, add_hydrogens=False)

		except MoleculeLoadException:
		logger.warning("This molecule cannot be loaded by Rdkit. Returning None")
		@@ -458,18 +479,22 @@ class HydrogenBondCounter(ComplexFeaturizer):
		self.angle_cutoffs = angle_cutoffs
		self.reduce_to_contacts = reduce_to_contacts

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

		Parameters
		----------
		complex: Tuple[str, str]
		datapoint: Tuple[str, str]
		Filenames for molecule and protein.
		"""
		if 'complex' in kwargs:
		datapoint = kwargs.get("complex")
		raise DeprecationWarning(
		'Complex is being phased out as a parameter, please pass "datapoint" instead.'
		)
		try:
		fragments = rdkit_utils.load_complex(complex, add_hydrogens=False)
		fragments = rdkit_utils.load_complex(datapoint, add_hydrogens=False)

		except MoleculeLoadException:
		logger.warning("This molecule cannot be loaded by Rdkit. Returning None")
		@@ -564,18 +589,22 @@ class HydrogenBondVoxelizer(ComplexFeaturizer):
		self.voxel_width = voxel_width
		self.reduce_to_contacts = reduce_to_contacts

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

		Parameters
		----------
		complex: Tuple[str, str]
		datapoint: Tuple[str, str]
		Filenames for molecule and protein.
		"""
		if 'complex' in kwargs:
		datapoint = kwargs.get("complex")
		raise DeprecationWarning(
		'Complex is being phased out as a parameter, please pass "datapoint" instead.'
		)
		try:
		fragments = rdkit_utils.load_complex(complex, add_hydrogens=False)
		fragments = rdkit_utils.load_complex(datapoint, add_hydrogens=False)

		except MoleculeLoadException:
		logger.warning("This molecule cannot be loaded by Rdkit. Returning None")

deepchem/feat/complex_featurizers/splif_fingerprints.py

+18 −6

Original line number	Diff line number	Diff line
		@@ -146,17 +146,23 @@ class SplifFingerprint(ComplexFeaturizer):
		self.size = size
		self.radius = radius

		def _featurize(self, complex: Tuple[str, str], **kwargs):
		def _featurize(self, datapoint, **kwargs):
		"""
		Compute featurization for a molecular complex

		Parameters
		----------
		complex: Tuple[str, str]
		datapoint: Tuple[str, str]
		Filenames for molecule and protein.
		"""
		if 'complex' in kwargs:
		datapoint = kwargs.get("complex")
		raise DeprecationWarning(
		'Complex is being phased out as a parameter, please pass "datapoint" instead.'
		)

		try:
		fragments = load_complex(complex, add_hydrogens=False)
		fragments = load_complex(datapoint, add_hydrogens=False)

		except MoleculeLoadException:
		logger.warning("This molecule cannot be loaded by Rdkit. Returning None")
		@@ -236,17 +242,23 @@ class SplifVoxelizer(ComplexFeaturizer):
		self.voxel_width = voxel_width
		self.voxels_per_edge = int(self.box_width / self.voxel_width)

		def _featurize(self, complex: Tuple[str, str], **kwargs):
		def _featurize(self, datapoint, **kwargs):
		"""
		Compute featurization for a molecular complex

		Parameters
		----------
		complex: Tuple[str, str]
		datapoint: Tuple[str, str]
		Filenames for molecule and protein.
		"""
		if 'complex' in kwargs:
		datapoint = kwargs.get("complex")
		raise DeprecationWarning(
		'Complex is being phased out as a parameter, please pass "datapoint" instead.'
		)

		try:
		fragments = load_complex(complex, add_hydrogens=False)
		fragments = load_complex(datapoint, add_hydrogens=False)

		except MoleculeLoadException:
		logger.warning("This molecule cannot be loaded by Rdkit. Returning None")

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