bindingrmsd.data package

Submodules

bindingrmsd.data.data module

class bindingrmsd.data.data.PoseSelectionDataset(protein_pdb, ligand_file)

Bases: DGLDataset

lig_dummy_graph(num_nodes)

bindingrmsd.data.data.load_ligands(file_path)

Loads ligands from a file or a list of files.

bindingrmsd.data.data.process_ligand_file(file_path)

Processes a single ligand file (.dlg, .pdbqt, .sdf, .mol2).

bindingrmsd.data.data_bck module

class bindingrmsd.data.data_bck.PoseSelectionDataset(protein_pdb, ligand_file)

Bases: DGLDataset

lig_dummy_graph(num_nodes)

bindingrmsd.data.data_bck.load_ligands(file_path)

bindingrmsd.data.data_bck.process_dlg(file_path, only_cluster=False)

bindingrmsd.data.data_bck.process_ligand_file(file_path)

bindingrmsd.data.ligand_atom_feature module

bindingrmsd.data.ligand_atom_feature.atom_feature(atom)

bindingrmsd.data.ligand_atom_feature.bond_feature(bond)

bindingrmsd.data.ligand_atom_feature.calculate_pair_distance(arr1, arr2)

bindingrmsd.data.ligand_atom_feature.get_atom_feature(mol)

bindingrmsd.data.ligand_atom_feature.get_bond_feature(mol)

bindingrmsd.data.ligand_atom_feature.get_distance_feature(distance)

bindingrmsd.data.ligand_atom_feature.get_indices(mol, smarts)

bindingrmsd.data.ligand_atom_feature.get_indices_sparse(sparse, indices)

bindingrmsd.data.ligand_atom_feature.get_interact_feature(pmol, lmol, protein_node_idx, ligand_node_idx)

bindingrmsd.data.ligand_atom_feature.get_mol_coordinate(mol)

bindingrmsd.data.ligand_atom_feature.get_smarts_feature(mol, smarts, index)

bindingrmsd.data.ligand_atom_feature.is_one(x, allowable_set)

bindingrmsd.data.ligand_atom_feature.load_obj(name)

bindingrmsd.data.ligand_atom_feature.mol_to_graph(mol)

bindingrmsd.data.ligand_atom_feature.one_hot(x, allowable_set)

bindingrmsd.data.ligand_atom_feature.save_obj(data, name)

bindingrmsd.data.protein_atom_feature module

bindingrmsd.data.protein_atom_feature.get_all_graph(gp, gl, cutoff=10)

bindingrmsd.data.protein_atom_feature.pl_to_c_graph(gp, gl, cutoff=5)

bindingrmsd.data.protein_atom_feature.prot_to_graph(pdb)

bindingrmsd.data.protein_atom_feature.scaler(distance)

bindingrmsd.data.utils module

bindingrmsd.data.utils.is_one(x, allowable_set)

bindingrmsd.data.utils.load_obj(name)

bindingrmsd.data.utils.one_hot(x, allowable_set)

bindingrmsd.data.utils.save_obj(data, name)

Module contents