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

deepchem/feat/materials_featurizers.py

+2 −2

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

		self.data_source = data_source

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

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

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

deepchem/utils/fragment_util.py

+17 −11

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

		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

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

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

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

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

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

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

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


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

		Parameters
		@@ -180,7 +183,8 @@ def merge_molecular_fragments(molecules):
		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

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


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

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

		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.
		"""
		# 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):
		frag1, frag2 = fragments[ind1], fragments[ind2]
		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


		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.

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

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