Merge pull request #2164 from nd-02110114/refactor-complex-feat (651df9f9) · Commits · 钟慕尧 / deepchem

deepchem/feat/init.py

+7 −3

Original line number	Diff line number	Diff line
		@@ -13,12 +13,10 @@ from deepchem.feat.base_classes import UserDefinedFeaturizer

		from deepchem.feat.graph_features import ConvMolFeaturizer
		from deepchem.feat.graph_features import WeaveFeaturizer
		from deepchem.feat.rdkit_grid_featurizer import RdkitGridFeaturizer
		from deepchem.feat.binding_pocket_features import BindingPocketFeaturizer
		from deepchem.feat.atomic_coordinates import AtomicCoordinates
		from deepchem.feat.atomic_coordinates import NeighborListComplexAtomicCoordinates

		# molecule featurizers
		from deepchem.feat.molecule_featurizers import AtomicCoordinates
		from deepchem.feat.molecule_featurizers import BPSymmetryFunctionInput
		from deepchem.feat.molecule_featurizers import CircularFingerprint
		from deepchem.feat.molecule_featurizers import CoulombMatrix
		@@ -32,6 +30,12 @@ from deepchem.feat.molecule_featurizers import RDKitDescriptors
		from deepchem.feat.molecule_featurizers import SmilesToImage
		from deepchem.feat.molecule_featurizers import SmilesToSeq, create_char_to_idx

		# complex featurizers
		from deepchem.feat.complex_featurizers import RdkitGridFeaturizer
		from deepchem.feat.complex_featurizers import NeighborListAtomicCoordinates
		from deepchem.feat.complex_featurizers import NeighborListComplexAtomicCoordinates
		from deepchem.feat.complex_featurizers import ComplexNeighborListFragmentAtomicCoordinates

		# material featurizers
		from deepchem.feat.material_featurizers import ElementPropertyFingerprint
		from deepchem.feat.material_featurizers import SineCoulombMatrix

deepchem/feat/complex_featurizers/init.py

0 → 100644

+8 −0

Original line number	Diff line number	Diff line
		"""
		Featurizers for complex.
		"""
		# flake8: noqa
		from deepchem.feat.complex_featurizers.rdkit_grid_featurizer import RdkitGridFeaturizer
		from deepchem.feat.complex_featurizers.complex_atomic_coordinates import NeighborListAtomicCoordinates
		from deepchem.feat.complex_featurizers.complex_atomic_coordinates import NeighborListComplexAtomicCoordinates
		from deepchem.feat.complex_featurizers.complex_atomic_coordinates import ComplexNeighborListFragmentAtomicCoordinates

deepchem/feat/atomic_coordinates.py→deepchem/feat/complex_featurizers/complex_atomic_coordinates.py

+8 −57

Original line number	Diff line number	Diff line
		@@ -2,50 +2,16 @@
		Atomic coordinate featurizer.
		"""
		import logging

		import numpy as np
		from deepchem.feat import Featurizer
		from deepchem.feat import ComplexFeaturizer

		from deepchem.feat.base_classes import Featurizer, ComplexFeaturizer
		from deepchem.feat.molecule_featurizers import AtomicCoordinates
		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


		class AtomicCoordinates(Featurizer):
		"""
		Nx3 matrix of Cartesian coordinates [Angstrom]
		"""
		name = ['atomic_coordinates']

		def _featurize(self, mol):
		"""
		Calculate atomic coodinates.

		Parameters
		----------
		mol : RDKit Mol
		Molecule.
		"""

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

		# RDKit stores atomic coordinates in Angstrom. Atomic unit of length is the
		# bohr (1 bohr = 0.529177 Angstrom). Converting units makes gradient calculation
		# consistent with most QM software packages.
		coords_in_bohr = [
		mol.GetConformer(0).GetAtomPosition(i).__idiv__(0.52917721092)
		for i in range(N)
		]

		for atom in range(N):
		coords[atom, 0] = coords_in_bohr[atom].x
		coords[atom, 1] = coords_in_bohr[atom].y
		coords[atom, 2] = coords_in_bohr[atom].z

		coords = [coords]
		return coords


		def compute_neighbor_list(coords, neighbor_cutoff, max_num_neighbors,
		periodic_box_size):
		"""Computes a neighbor list from atom coordinates."""
		@@ -76,21 +42,6 @@ def compute_neighbor_list(coords, neighbor_cutoff, max_num_neighbors,
		return neighbor_list


		def get_coords(mol):
		"""
		Gets coordinates in Angstrom for RDKit mol.
		"""
		N = mol.GetNumAtoms()
		coords = np.zeros((N, 3))

		coords_raw = [mol.GetConformer(0).GetAtomPosition(i) for i in range(N)]
		for atom in range(N):
		coords[atom, 0] = coords_raw[atom].x
		coords[atom, 1] = coords_raw[atom].y
		coords[atom, 2] = coords_raw[atom].z
		return coords


		class NeighborListAtomicCoordinates(Featurizer):
		"""
		Adjacency List of neighbors in 3-space
		@@ -122,7 +73,8 @@ class NeighborListAtomicCoordinates(Featurizer):
		self.periodic_box_size = periodic_box_size
		# Type of data created by this featurizer
		self.dtype = object
		self.coordinates_featurizer = AtomicCoordinates()
		self.bohr_coords_featurizer = AtomicCoordinates(use_bohr=True)
		self.coords_featurizer = AtomicCoordinates(use_bohr=False)

		def _featurize(self, mol):
		"""
		@@ -134,8 +86,8 @@ class NeighborListAtomicCoordinates(Featurizer):
		To be featurized.
		"""
		# TODO(rbharath): Should this return a list?
		bohr_coords = self.coordinates_featurizer._featurize(mol)[0]
		coords = get_coords(mol)
		bohr_coords = self.bohr_coords_featurizer._featurize(mol)
		coords = self.coords_featurizer._featurize(mol)
		neighbor_list = compute_neighbor_list(coords, self.neighbor_cutoff,
		self.max_num_neighbors,
		self.periodic_box_size)
		@@ -159,7 +111,6 @@ class NeighborListComplexAtomicCoordinates(ComplexFeaturizer):
		self.neighbor_cutoff = neighbor_cutoff
		# Type of data created by this featurizer
		self.dtype = object
		self.coordinates_featurizer = AtomicCoordinates()

		def _featurize(self, mol_pdb_file, protein_pdb_file):
		"""

deepchem/feat/rdkit_grid_featurizer.py→deepchem/feat/complex_featurizers/rdkit_grid_featurizer.py

+0 −0

File moved.

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deepchem/feat/graph_features.py

+1 −1

Original line number	Diff line number	Diff line
		@@ -3,7 +3,7 @@
		import numpy as np
		import deepchem as dc
		from deepchem.feat.base_classes import MolecularFeaturizer
		from deepchem.feat.atomic_coordinates import ComplexNeighborListFragmentAtomicCoordinates
		from deepchem.feat.complex_featurizers import ComplexNeighborListFragmentAtomicCoordinates
		from deepchem.feat.mol_graphs import ConvMol, WeaveMol
		from deepchem.data import DiskDataset
		import logging

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