Clean up fragment utils and continue docking cleanup (4b53c457) · Commits · 钟慕尧 / deepchem

deepchem/dock/pose_generation.py

+0 −2

Original line number	Diff line number	Diff line
		@@ -18,12 +18,10 @@ from deepchem.utils import download_url

		logger = logging.getLogger(__name__)

		DATA_DIR = deepchem.utils.get_data_dir()


		class PoseGenerator(object):
		"""A Pose Generator computes low energy conformations for molecular complexes.

		Many questions in structural biophysics reduce to that of computing
		the binding free energy of molecular complexes. A key step towards
		computing the binding free energy of two complexes is to find low

deepchem/feat/atomic_coordinates.py

+1 −1

Original line number	Diff line number	Diff line
		@@ -8,7 +8,7 @@ from deepchem.feat import MolecularFeaturizer
		from deepchem.feat import ComplexFeaturizer
		from deepchem.utils import rdkit_util, pad_array
		from deepchem.utils.rdkit_util import MoleculeLoadException
		from deepchem.utils.rdkit_util import reduce_molecular_complex_to_contacts
		from deepchem.utils.fragment_util import reduce_molecular_complex_to_contacts

		logger = logging.getLogger(__name__)

deepchem/feat/contact_fingerprints.py

+2 −2

Original line number	Diff line number	Diff line
		@@ -12,9 +12,9 @@ from deepchem.utils.voxel_utils import voxelize
		from deepchem.utils.voxel_utils import convert_atom_to_voxel
		from deepchem.utils.rdkit_util import compute_all_ecfp
		from deepchem.utils.rdkit_util import compute_contact_centroid
		from deepchem.utils.rdkit_util import subtract_centroid
		from deepchem.utils.rdkit_util import compute_pairwise_distances
		from deepchem.utils.rdkit_util import MoleculeLoadException
		from deepchem.utils.geometry_utils import compute_pairwise_distances
		from deepchem.utils.geometry_utils import subtract_centroid

		logger = logging.getLogger(__name__)

deepchem/feat/grid_featurizers.py

+8 −8

Original line number	Diff line number	Diff line
		@@ -5,21 +5,21 @@ import itertools
		import logging
		import numpy as np
		from deepchem.utils import rdkit_util
		from deepchem.utils.rdkit_util import get_partial_charge
		from deepchem.feat import ComplexFeaturizer
		from deepchem.utils.hash_utils import hash_ecfp_pair
		from deepchem.utils.voxel_utils import voxelize
		from deepchem.utils.rdkit_util import compute_salt_bridges
		from deepchem.utils.rdkit_util import compute_binding_pocket_cation_pi
		from deepchem.utils.voxel_utils import convert_atom_to_voxel
		from deepchem.utils.voxel_utils import convert_atom_pair_to_voxel
		from deepchem.utils.rdkit_util import compute_pairwise_distances
		from deepchem.utils.rdkit_util import compute_pi_stack
		from deepchem.utils.rdkit_util import compute_hydrogen_bonds
		from deepchem.utils.noncovalent_utils import compute_salt_bridges
		from deepchem.utils.noncovalent_utils import compute_binding_pocket_cation_pi
		from deepchem.utils.noncovalent_utils import compute_pi_stack
		from deepchem.utils.noncovalent_utils import compute_hydrogen_bonds
		from deepchem.utils.rdkit_util import MoleculeLoadException
		from deepchem.utils.rdkit_util import compute_contact_centroid
		from deepchem.utils.rdkit_util import subtract_centroid
		from deepchem.utils.rdkit_util import reduce_molecular_complex_to_contacts
		from deepchem.utils.geometry_utils import compute_pairwise_distances
		from deepchem.utils.geometry_utils import subtract_centroid
		from deepchem.utils.fragment_util import get_partial_charge
		from deepchem.utils.fragment_util import reduce_molecular_complex_to_contacts

		logger = logging.getLogger(__name__)

deepchem/feat/rdkit_grid_featurizer.py

+3 −3

Original line number	Diff line number	Diff line
		@@ -24,11 +24,11 @@ from deepchem.feat.grid_featurizers import PiStackVoxelizer
		from deepchem.feat.grid_featurizers import HydrogenBondCounter
		from deepchem.feat.grid_featurizers import HydrogenBondVoxelizer
		from deepchem.utils.rdkit_util import load_molecule
		from deepchem.utils.rdkit_util import compute_centroid
		from deepchem.utils.rdkit_util import subtract_centroid
		from deepchem.utils.geometry_utils import compute_centroid
		from deepchem.utils.geometry_utils import subtract_centroid
		from deepchem.utils.geometry_utils import compute_pairwise_distances
		from deepchem.utils.rdkit_util import compute_ring_center
		from deepchem.utils.rdkit_util import rotate_molecules
		from deepchem.utils.rdkit_util import compute_pairwise_distances
		from deepchem.utils.rdkit_util import MoleculeLoadException
		from deepchem.feat import ComplexFeaturizer

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