Loading deepchem/dock/binding_pocket.py +8 −1 Original line number Diff line number Diff line Loading @@ -83,18 +83,25 @@ 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, pad=5): def __init__(self, scoring_model=None, pocket_featurizer=None, ligand_featurizer=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): Loading deepchem/utils/rdkit_util.py +5 −0 Original line number Diff line number Diff line Loading @@ -16,6 +16,7 @@ from copy import deepcopy from collections import Counter from deepchem.utils.pdbqt_utils import pdbqt_to_pdb from scipy.spatial.distance import cdist from deepchem.utils import pdbqt_utils from deepchem.utils.pdbqt_utils import convert_mol_to_pdbqt from deepchem.utils.pdbqt_utils import convert_protein_to_pdbqt from deepchem.utils.geometry_utils import angle_between Loading Loading @@ -141,6 +142,10 @@ def apply_pdbfixer(mol, add_missing=True, hydrogenate=True, pH=7.4, Returns ------- Rdkit Mol Note ---- This function requires RDKit and PDBFixer to be installed. """ molecule_file = None try: Loading Loading
deepchem/dock/binding_pocket.py +8 −1 Original line number Diff line number Diff line Loading @@ -83,18 +83,25 @@ 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, pad=5): def __init__(self, scoring_model=None, pocket_featurizer=None, ligand_featurizer=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): Loading
deepchem/utils/rdkit_util.py +5 −0 Original line number Diff line number Diff line Loading @@ -16,6 +16,7 @@ from copy import deepcopy from collections import Counter from deepchem.utils.pdbqt_utils import pdbqt_to_pdb from scipy.spatial.distance import cdist from deepchem.utils import pdbqt_utils from deepchem.utils.pdbqt_utils import convert_mol_to_pdbqt from deepchem.utils.pdbqt_utils import convert_protein_to_pdbqt from deepchem.utils.geometry_utils import angle_between Loading Loading @@ -141,6 +142,10 @@ def apply_pdbfixer(mol, add_missing=True, hydrogenate=True, pH=7.4, Returns ------- Rdkit Mol Note ---- This function requires RDKit and PDBFixer to be installed. """ molecule_file = None try: Loading
