def calculate_anm(structure, num_nmodes, file_name): """Calculates ANM for representative structure""" modes = calculate_nmodes(structure.structure_file_names[structure.representative_id], num_nmodes, structure) structure.n_modes = modes write_nmodes(modes, file_name) log.info("%d normal modes calculated" % num_nmodes)
def test_calculate_anm_dna(self): pdb_file = self.golden_data_path / 'nm_dna' / '1DIZ_lig.pdb.H' _, _, chains = parse_complex_from_file(pdb_file) molecule = Complex(chains) nmodes = calculate_nmodes(pdb_file, n_modes=10, molecule=molecule) expected_nmodes = read_nmodes(self.golden_data_path / 'nm_dna' / 'lightdock_lig.nm.npy') assert np.allclose(expected_nmodes, nmodes)
def test_calculate_anm_protein_2(self): pdb_file = self.golden_data_path / 'nm_prot' / '2UUY_rec.pdb' _, _, chains = parse_complex_from_file(pdb_file) molecule = Complex(chains) nmodes = calculate_nmodes(pdb_file, n_modes=10, molecule=molecule) expected_nmodes = read_nmodes(self.golden_data_path / 'nm_prot' / 'lightdock_rec.nm.npy') assert np.allclose(expected_nmodes, nmodes)
def calculate_anm(structure, num_nmodes, file_name): """Calculates ANM for representative structure""" original_file_name = structure.structure_file_names[ structure.representative_id] # We have to use the parsed structure by LightDock parsed_lightdock_structure = Path(original_file_name).parent / \ Path(DEFAULT_LIGHTDOCK_PREFIX % Path(original_file_name).name) modes = calculate_nmodes(parsed_lightdock_structure, num_nmodes, structure) structure.n_modes = modes write_nmodes(modes, file_name) log.info(f"{num_nmodes} normal modes calculated")
def calculate_anm(structure, num_nmodes, file_name): """Calculates ANM for representative structure""" original_file_name = structure.structure_file_names[ structure.representative_id] # We have to use the parsed structure by LightDock parsed_lightdock_structure = os.path.join( os.path.dirname(original_file_name), DEFAULT_LIGHTDOCK_PREFIX % os.path.basename(original_file_name)) modes = calculate_nmodes(parsed_lightdock_structure, num_nmodes, structure) structure.n_modes = modes write_nmodes(modes, file_name) log.info("%d normal modes calculated" % num_nmodes)
def test_calculate_anm_dna(self): pdb_file = os.path.join(self.golden_data_path, 'nm_dna', '1DIZ_lig.pdb.H') atoms, residues, chains = parse_complex_from_file(pdb_file) molecule = Complex(chains) nmodes = calculate_nmodes(pdb_file, n_modes=10, molecule=molecule) expected_nmodes = read_nmodes( os.path.join(self.golden_data_path, 'nm_dna', 'lightdock_lig.nm.npy')) assert np.allclose(expected_nmodes, nmodes)