changes (7ca8f488) · Commits · 钟慕尧 / deepchem

deepchem/feat/materials_featurizers.py

+2 −2

Original line number	Original line	Diff line number	Diff line
	@@ -50,7 +50,7 @@ class ElementPropertyFingerprint(CompositionFeaturizer):

	self.data_source = data_source		self.data_source = data_source

	def _featurize(self, composition: "pymatgen.Composition"):		def _featurize(self, composition):
	"""		"""
	Calculate chemical fingerprint from crystal composition.		Calculate chemical fingerprint from crystal composition.

	@@ -124,7 +124,7 @@ class SineCoulombMatrix(StructureFeaturizer):
	self.max_atoms = int(max_atoms)		self.max_atoms = int(max_atoms)
	self.flatten = flatten		self.flatten = flatten

	def _featurize(self, struct: "pymatgen.Structure"):		def _featurize(self, struct):
	"""		"""
	Calculate sine Coulomb matrix from pymatgen structure.		Calculate sine Coulomb matrix from pymatgen structure.

deepchem/utils/fragment_util.py

+17 −11

Original line number	Original line	Diff line number	Diff line
	"""A collection of utilities for dealing with Molecular Fragments"""		"""A collection of utilities for dealing with Molecular Fragments"""
	import itertools		import itertools
	import numpy as np		import numpy as np
			from typing import List, Optional, Any
	from deepchem.utils.geometry_utils import compute_pairwise_distances		from deepchem.utils.geometry_utils import compute_pairwise_distances
	from deepchem.utils.rdkit_util import compute_charges		from deepchem.utils.rdkit_util import compute_charges

	@@ -110,7 +111,8 @@ class AtomShim(object):
	the basic information in an AtomShim seems to avoid issues.		the basic information in an AtomShim seems to avoid issues.
	"""		"""

	def __init__(self, atomic_num, partial_charge, atom_coords):		def __init__(self, atomic_num: int, partial_charge: float,
			atom_coords: np.ndarray):
	"""Initialize this object		"""Initialize this object

	Parameters		Parameters
	@@ -126,16 +128,16 @@ class AtomShim(object):
	self.partial_charge = partial_charge		self.partial_charge = partial_charge
	self.coords = atom_coords		self.coords = atom_coords

	def GetAtomicNum(self):		def GetAtomicNum(self) -> int:
	"""Returns atomic number for this atom.		"""Returns atomic number for this atom.

	Returns		Returns
	-------		-------
	Atomic number fo this atom.		Atomic number for this atom.
	"""		"""
	return self.atomic_num		return self.atomic_num

	def GetPartialCharge(self):		def GetPartialCharge(self) -> float:
	"""Returns partial charge for this atom.		"""Returns partial charge for this atom.

	Returns		Returns
	@@ -144,7 +146,7 @@ class AtomShim(object):
	"""		"""
	return self.partial_charge		return self.partial_charge

	def GetCoords(self):		def GetCoords(self) -> np.ndarray:
	"""Returns 3D coordinates for this atom as numpy array.		"""Returns 3D coordinates for this atom as numpy array.

	Returns		Returns
	@@ -154,7 +156,8 @@ class AtomShim(object):
	return self.coords		return self.coords


	def merge_molecular_fragments(molecules):		def merge_molecular_fragments(
			molecules: List[MolecularFragment]) -> Optional[MolecularFragment]:
	"""Helper method to merge two molecular fragments.		"""Helper method to merge two molecular fragments.

	Parameters		Parameters
	@@ -180,7 +183,8 @@ def merge_molecular_fragments(molecules):
	return MolecularFragment(all_atoms, all_coords)		return MolecularFragment(all_atoms, all_coords)


	def get_mol_subset(coords, mol, atom_indices_to_keep):		def get_mol_subset(coords: np.ndarray, mol,
			atom_indices_to_keep: List[int]) -> MolecularFragment:
	"""Strip a subset of the atoms in this molecule		"""Strip a subset of the atoms in this molecule

	Parameters		Parameters
	@@ -219,7 +223,7 @@ def get_mol_subset(coords, mol, atom_indices_to_keep):
	return mol_frag		return mol_frag


	def strip_hydrogens(coords, mol):		def strip_hydrogens(coords: np.ndarray, mol) -> MolecularFragment:
	"""Strip the hydrogens from input molecule		"""Strip the hydrogens from input molecule

	Parameters		Parameters
	@@ -248,7 +252,8 @@ def strip_hydrogens(coords, mol):
	return get_mol_subset(coords, mol, atom_indices_to_keep)		return get_mol_subset(coords, mol, atom_indices_to_keep)


	def get_contact_atom_indices(fragments, cutoff=4.5):		def get_contact_atom_indices(fragments: List[Any],
			cutoff: float = 4.5) -> List[Any]:
	"""Compute that atoms close to contact region.		"""Compute that atoms close to contact region.

	Molecular complexes can get very large. This can make it unwieldy to		Molecular complexes can get very large. This can make it unwieldy to
	@@ -275,7 +280,7 @@ def get_contact_atom_indices(fragments, cutoff=4.5):
	sorted order.		sorted order.
	"""		"""
	# indices to atoms to keep		# indices to atoms to keep
	keep_inds = [set([]) for _ in fragments]		keep_inds: List[Any] = [set([]) for _ in fragments]
	for (ind1, ind2) in itertools.combinations(range(len(fragments)), 2):		for (ind1, ind2) in itertools.combinations(range(len(fragments)), 2):
	frag1, frag2 = fragments[ind1], fragments[ind2]		frag1, frag2 = fragments[ind1], fragments[ind2]
	pairwise_distances = compute_pairwise_distances(frag1[0], frag2[0])		pairwise_distances = compute_pairwise_distances(frag1[0], frag2[0])
	@@ -292,7 +297,8 @@ def get_contact_atom_indices(fragments, cutoff=4.5):
	return keep_inds		return keep_inds


	def reduce_molecular_complex_to_contacts(fragments, cutoff=4.5):		def reduce_molecular_complex_to_contacts(fragments: List,
			cutoff: float = 4.5) -> List:
	"""Reduce a molecular complex to only those atoms near a contact.		"""Reduce a molecular complex to only those atoms near a contact.

	Molecular complexes can get very large. This can make it unwieldy to		Molecular complexes can get very large. This can make it unwieldy to

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