def test_merge_molecules_xyz(self): current_dir = os.path.dirname(os.path.realpath(__file__)) ligand_file = os.path.join(current_dir, "../../dock/tests/1jld_ligand.sdf") xyz, mol = rdkit_util.load_molecule( ligand_file, calc_charges=False, add_hydrogens=False) merged = rdkit_util.merge_molecules_xyz(xyz, xyz) for i in range(len(xyz)): first_atom_equal = np.all(xyz[i] == merged[i]) second_atom_equal = np.all(xyz[i] == merged[i + len(xyz)]) assert_true(first_atom_equal) assert_true(second_atom_equal)
def test_merge_molecules_xyz(self): current_dir = os.path.dirname(os.path.realpath(__file__)) ligand_file = os.path.join(current_dir, "../../dock/tests/1jld_ligand.sdf") xyz, mol = rdkit_util.load_molecule(ligand_file, calc_charges=False, add_hydrogens=False) merged = rdkit_util.merge_molecules_xyz([xyz, xyz]) for i in range(len(xyz)): first_atom_equal = np.all(xyz[i] == merged[i]) second_atom_equal = np.all(xyz[i] == merged[i + len(xyz)]) assert first_atom_equal assert second_atom_equal
def _featurize_complex(self, mol_pdb_file, protein_pdb_file): """ Compute neighbor list for complex. Parameters ---------- mol_pdb: list Should be a list of lines of the PDB file. complex_pdb: list Should be a list of lines of the PDB file. """ mol_coords, ob_mol = rdkit_util.load_molecule(mol_pdb_file) protein_coords, protein_mol = rdkit_util.load_molecule(protein_pdb_file) system_coords = rdkit_util.merge_molecules_xyz(mol_coords, protein_coords) system_neighbor_list = compute_neighbor_list( system_coords, self.neighbor_cutoff, self.max_num_neighbors, None) return (system_coords, system_neighbor_list)
def _featurize_complex(self, mol_pdb_file, protein_pdb_file): """ Compute neighbor list for complex. Parameters ---------- mol_pdb_file: Str Filename for ligand pdb file. protein_pdb_file: Str Filename for protein pdb file. """ mol_coords, ob_mol = rdkit_util.load_molecule(mol_pdb_file) protein_coords, protein_mol = rdkit_util.load_molecule(protein_pdb_file) system_coords = rdkit_util.merge_molecules_xyz([mol_coords, protein_coords]) system_neighbor_list = compute_neighbor_list( system_coords, self.neighbor_cutoff, self.max_num_neighbors, None) return (system_coords, system_neighbor_list)
def _featurize_complex(self, mol_pdb_file, protein_pdb_file): """ Compute neighbor list for complex. Parameters ---------- mol_pdb: list Should be a list of lines of the PDB file. complex_pdb: list Should be a list of lines of the PDB file. """ mol_coords, ob_mol = rdkit_util.load_molecule(mol_pdb_file) protein_coords, protein_mol = rdkit_util.load_molecule(protein_pdb_file) system_coords = rdkit_util.merge_molecules_xyz(mol_coords, protein_coords) system_neighbor_list = compute_neighbor_list( system_coords, self.neighbor_cutoff, self.max_num_neighbors, None) return (system_coords, system_neighbor_list)