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)
