Cleaning up docking module (025301bf) · Commits · 钟慕尧 / deepchem

deepchem/dock/binding_pocket.py

+1 −9

Original line number	Diff line number	Diff line
		@@ -14,7 +14,6 @@ from deepchem.utils.fragment_util import get_contact_atom_indices

		logger = logging.getLogger(__name__)


		def extract_active_site(protein_file, ligand_file, cutoff=4):
		"""Extracts a box for the active site.

		@@ -83,25 +82,18 @@ class ConvexHullPocketFinder(BindingPocketFinder):
		Based on https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4112621/pdf/1472-6807-14-18.pdf
		"""

		def __init__(self, scoring_model=None, pocket_featurizer=None, ligand_featurizer=None, pad=5):
		def __init__(self, scoring_model=None, pad=5):
		"""Initialize the pocket finder.

		Parameters
		----------
		scoring_model: `dc.models.Model`, optional
		If specified, use this model to prune pockets.
		pocket_featurizer: `dc.feat.BindingPocketFeaturizer`, optional
		If `scoring_model` is specified, `pocket_featurizer` must be as
		well. This featurizer is used to featurize binding pockets.
		ligand_featurizer: `dc.feat.MolecularFeaturizer`, optional
		Featurizer used to featurize the ligand.
		pad: float, optional
		The number of angstroms to pad around a binding pocket's atoms
		to get a binding pocket box.
		"""
		self.scoring_model = scoring_model
		self.pocket_featurizer = pocket_featurizer
		self.ligand_featurizer = ligand_featurizer
		self.pad = pad

		def find_all_pockets(self, protein_file):

+0 −1

Original line number	Diff line number	Diff line
		@@ -81,7 +81,6 @@ class BindingPocketFeaturizer(Featurizer):
		-------
		A numpy array of shale `(len(pockets), n_residues)`
		"""
		if len(
		import mdtraj
		protein_coords = rdkit_util.load_molecule(
		protein_file, add_hydrogens=False, calc_charges=False)[0]