Init commit on crystal featurizer (173ccbdb) · Commits · 钟慕尧 / deepchem

deepchem/feat/init.py

+1 −0

Original line number	Diff line number	Diff line
		@@ -3,6 +3,7 @@ Making it easy to import in classes.
		"""
		from deepchem.feat.base_classes import Featurizer
		from deepchem.feat.base_classes import MolecularFeaturizer
		from deepchem.feat.base_classes import CrystalFeaturizer
		from deepchem.feat.base_classes import ComplexFeaturizer
		from deepchem.feat.base_classes import UserDefinedFeaturizer
		from deepchem.feat.graph_features import ConvMolFeaturizer

deepchem/feat/base_classes.py

+89 −1

Original line number	Diff line number	Diff line
		@@ -5,6 +5,7 @@ import logging
		import types
		import numpy as np
		import multiprocessing
		from typing import Iterable, Union

		logger = logging.getLogger(__name__)

		@@ -165,7 +166,7 @@ class MolecularFeaturizer(Featurizer):
		molecules = [molecules]
		else:
		# Convert iterables to list
		molecutes = list(molecules)
		molecules = list(molecules)
		features = []
		for i, mol in enumerate(molecules):
		if i % log_every_n == 0:
		@@ -207,6 +208,93 @@ class MolecularFeaturizer(Featurizer):
		return self.featurize(molecules)


		class CrystalFeaturizer(Featurizer):
		"""
		Abstract class for calculating a set of features for a
		crystal structure.

		The defining feature of a `CrystalFeaturizer` is that it
		operates on 3D crystals with periodic boundary conditions. Inorganic
		crystal structures are represented by Pymatgen composition and structure
		objects. Featurizers for inorganic crystal structures that are subclasses of
		this class should plan to process input which comes as composition
		strings or pymatgen structure dictionaries.

		Child classes need to implement the _featurize method for
		calculating features for a single crystal.

		Notes
		-----
		Some subclasses of this class will require pymatgen and matminer to be
		installed.

		"""

		def featurize(self, crystals: Iterable, log_every_n: int = 1000) -> np.ndarray:
		"""Calculate features for crystals.

		Parameters
		----------
		crystals: Iterable
		Iterable sequence of composition strings, pymatgen structure
		dictionaries, or another crystal representation.
		log_every_n: int, default 1000
		Logging messages reported every `log_every_n` samples.

		Returns
		-------
		features: np.ndarray
		A numpy array containing a featurized representation of
		`crystals`.

		"""

		# Special case handling of single crystal
		if not isinstance(crystals, Iterable):
		crystals = [crystals]
		else:
		# Convert iterables to list
		crystals = list(crystals)

		features = []
		for idx, crystal in enumerate(crystals):
		if idx % log_every_n == 0:
		logger.info("Featurizing datapoint %i" % idx)
		try:
		features.append(self._featurize(crystal))
		except:
		logger.warning(
		"Failed to featurize datapoint %i. Appending empty array" % idx)
		features.append(np.array([]))

		features = np.asarray(features)
		return features

		def _featurize(self, crystal):
		"""Calculate features for a single crystal.

		Parameters
		----------
		crystal: crystal representation
		Crystal.

		"""

		raise NotImplementedError('Featurizer is not defined.')

		def __call__(self, crystals: Iterable):
		"""Calculate features for crystals.

		Parameters
		----------
		crystals: Iterable
		An iterable of crystal representations.

		"""

		return self.featurize(crystals)


		class UserDefinedFeaturizer(Featurizer):
		"""Directs usage of user-computed featurizations."""

deepchem/feat/materials_featurizers.py

+18 −9

Original line number	Diff line number	Diff line
		@@ -4,11 +4,11 @@ Featurizers for inorganic crystals.

		import numpy as np

		from deepchem.feat import Featurizer
		from deepchem.feat import CrystalFeaturizer
		from deepchem.utils import pad_array


		class ElementPropertyFingerprint(Featurizer):
		class ElementPropertyFingerprint(CrystalFeaturizer):
		"""
		Fingerprint of elemental properties from composition.

		@@ -67,8 +67,11 @@ class ElementPropertyFingerprint(Featurizer):

		"""

		try:
		from pymatgen import Composition
		from matminer.featurizers.composition import ElementProperty
		except ModuleNotFoundError:
		raise ValueError("This class requires pymatgen and matminer to be installed.")

		# Get pymatgen Composition object
		c = Composition(comp)
		@@ -83,7 +86,7 @@ class ElementPropertyFingerprint(Featurizer):
		return np.array(feats)


		class SineCoulombMatrix(Featurizer):
		class SineCoulombMatrix(CrystalFeaturizer):
		"""
		Calculate sine Coulomb matrix for crystals.

		@@ -144,8 +147,11 @@ class SineCoulombMatrix(Featurizer):

		"""

		try:
		from pymatgen import Structure
		from matminer.featurizers.structure import SineCoulombMatrix as SCM
		except ModuleNotFoundError:
		raise ValueError("This class requires pymatgen and matminer to be installed.")

		s = Structure.from_dict(struct)

		@@ -166,7 +172,7 @@ class SineCoulombMatrix(Featurizer):
		return features


		class StructureGraphFeaturizer(Featurizer):
		class StructureGraphFeaturizer(CrystalFeaturizer):
		"""
		Calculate structure graph features for crystals.

		@@ -224,7 +230,10 @@ class StructureGraphFeaturizer(Featurizer):

		"""

		try:
		from pymatgen import Structure
		except ModuleNotFoundError:
		raise ValueError("This class requires pymatgen to be installed.")

		# Get pymatgen structure object
		s = Structure.from_dict(struct)

docs/featurizers.rst

+12 −8

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		@@ -161,14 +161,18 @@ AtomConvFeaturizer
		.. autoclass:: deepchem.feat.NeighborListComplexAtomicCoordinates
		:members:

		MaterialsFeaturizers
		--------------------

		Materials Featurizers are those that work with datasets of inorganic crystals.
		These featurizers operate on chemical compositions (e.g. "MoS2"), or on a
		lattice and 3D coordinates that specify a periodic crystal structure. They
		should be applied on systems that have periodic boundary conditions. Materials
		featurizers are not designed to work with molecules.
		CrystalFeaturizer
		-----------------

		Crystal Featurizers are those that work with datasets of crystals with
		periodic boundary conditions. For inorganic crystal structures, these
		featurizers operate on chemical compositions (e.g. "MoS2"), or on a
		lattice and 3D coordinates that specify a periodic crystal structure.
		They should be applied on systems that have periodic boundary conditions.
		Crystal featurizers are not designed to work with molecules.

		.. autoclass:: deepchem.feat.CrystalFeaturizer
		:members:

		ElementPropertyFingerprint
		^^^^^^^^^^^^^^^^^^^^^^^^^^

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