bapred.data package¶

Submodules¶

bapred.data.atom_feature module¶

bapred.data.atom_feature.atom_feature(atom)[source]¶

bapred.data.atom_feature.bond_feature(bond)[source]¶

bapred.data.atom_feature.get_atom_feature(mol)[source]¶

bapred.data.atom_feature.get_bond_feature(mol)[source]¶

bapred.data.atom_feature.get_distance_feature(distance)[source]¶

bapred.data.atom_feature.get_indices(mol, smarts)[source]¶

bapred.data.atom_feature.get_indices_sparse(sparse, indices)[source]¶

bapred.data.atom_feature.get_interact_feature(pmol, lmol, protein_node_idx, ligand_node_idx)[source]¶

bapred.data.atom_feature.get_mol_coordinate(mol)[source]¶

bapred.data.atom_feature.get_smarts_feature(mol, smarts, index)[source]¶

bapred.data.data module¶

class bapred.data.data.BAPredDataset(protein_pdb, ligand_file, train=True)[source]¶

Bases: DGLDataset

comp_dummy_graph(num_nodes)[source]¶

complex_to_graph(pmol, lmol)[source]¶

get_pocket_with_ligand_in_protein(prot_atom_line, prot_atom_coord, lig_mol)[source]¶

get_protein_info(prot_pdb)[source]¶

lig_dummy_graph(num_nodes)[source]¶

mol_to_graph(mol)[source]¶

prot_dummy_graph(num_nodes)[source]¶

bapred.data.data.load_ligands(file_path)[source]¶

bapred.data.data.process_ligand_file(file_path)[source]¶

bapred.data.utils module¶

bapred.data.utils.calculate_pair_distance(arr1, arr2)[source]¶

bapred.data.utils.is_one(x, allowable_set)[source]¶

bapred.data.utils.load_obj(name)[source]¶

bapred.data.utils.one_hot(x, allowable_set)[source]¶

bapred.data.utils.save_obj(data, name)[source]¶

Module contents¶