def test_calculate_initial_poses(self):
file_name = self.golden_data_path / '3p0g' / 'receptor_membrane.pdb'
_, _, chains = parse_complex_from_file(file_name)
receptor = Complex(chains, structure_file_name=file_name)
file_name = self.golden_data_path / '3p0g' / 'ligand.pdb'
_, _, chains = parse_complex_from_file(file_name)
ligand = Complex(chains, structure_file_name=file_name)
rec_translation = receptor.move_to_origin()
lig_translation = ligand.move_to_origin()
num_swarms = 100
num_glowworms = 10
surface_density = 50.
restraints = parse_restraints_file(self.golden_data_path / '3p0g' / 'restraints.list')
receptor_restraints = get_restraints(receptor, restraints['receptor'])
ligand_restraints = get_restraints(ligand, restraints['ligand'])
rec_restraints = receptor_restraints['active'] + receptor_restraints['passive']
lig_restraints = ligand_restraints['active'] + ligand_restraints['passive']
positions_files = calculate_initial_poses(receptor, ligand, num_swarms, num_glowworms,
STARTING_POINTS_SEED, rec_restraints, lig_restraints,
rec_translation, lig_translation, surface_density,
dest_folder=self.test_path, is_membrane=True)
assert filecmp.cmp(positions_files[0], self.golden_data_path / '3p0g' / 'init' / 'initial_positions_0.dat')
assert filecmp.cmp(positions_files[1], self.golden_data_path / '3p0g' / 'init' / 'initial_positions_1.dat')
def test_blocked_restraints_file(self):
input_file = os.path.join(self.golden_data_path, 'rst_4.lst')
restraints = parse_restraints_file(input_file)
expected = {'receptor': {'active': ['A.ALA.1'], 'passive': [], 'blocked':['A.LYS.2']},
'ligand': {'active': [], 'passive': ['B.TYR.1'], 'blocked':['B.TRP.2']}}
assert restraints == expected
def test_empty_restraints_file(self):
input_file = os.path.join(self.golden_data_path, 'rst_3.lst')
restraints = parse_restraints_file(input_file)
expected = {'receptor': {'active': [], 'passive': [], 'blocked':[]},
'ligand': {'active': [], 'passive': [], 'blocked':[]}}
assert restraints == expected
def test_restraints_file_with_duplicate(self):
input_file = os.path.join(self.golden_data_path, 'rst_2.lst')
restraints = parse_restraints_file(input_file)
expected = {
'receptor': {
'active': ['A.ALA.1'],
'passive': []
},
'ligand': {
'active': [],
'passive': ['B.TYR.1']
}
}
assert restraints == expected
def test_calculate_initial_poses(self):
atoms, residues, chains = parse_complex_from_file(
os.path.join(self.golden_data_path, '3p0g',
'receptor_membrane.pdb'))
receptor = Complex(chains)
atoms, residues, chains = parse_complex_from_file(
os.path.join(self.golden_data_path, '3p0g', 'ligand.pdb'))
ligand = Complex(chains)
rec_translation = receptor.move_to_origin()
lig_translation = ligand.move_to_origin()
num_swarms = 10
num_glowworms = 10
seed = 324324
restraints = parse_restraints_file(
os.path.join(self.golden_data_path, '3p0g', 'restraints.list'))
receptor_restraints = get_restraints(receptor, restraints['receptor'])
ligand_restraints = get_restraints(ligand, restraints['ligand'])
rec_restraints = receptor_restraints['active'] + receptor_restraints[
'passive']
lig_restraints = ligand_restraints['active'] + ligand_restraints[
'passive']
positions_files = calculate_initial_poses(receptor,
ligand,
num_swarms,
num_glowworms,
seed,
rec_restraints,
lig_restraints,
rec_translation,
lig_translation,
dest_folder=self.test_path,
is_membrane=True)
assert filecmp.cmp(
positions_files[0],
os.path.join(self.golden_data_path, '3p0g', 'init',
'initial_positions_0.dat'))
assert filecmp.cmp(
positions_files[1],
os.path.join(self.golden_data_path, '3p0g', 'init',
'initial_positions_1.dat'))
def test_simple_restraints_file(self):
input_file = self.golden_data_path / 'rst_1.lst'
restraints = parse_restraints_file(input_file)
expected = {
'receptor': {
'active': ['A.ALA.1'],
'passive': [],
'blocked': []
},
'ligand': {
'active': [],
'passive': ['B.TYR.1'],
'blocked': []
}
}
assert restraints == expected
save_lightdock_structure(ligand)
# Calculate and save ANM if required
if args.use_anm:
if args.anm_rec > 0:
log.info("Calculating ANM for receptor molecule...")
calculate_anm(receptor, args.anm_rec, DEFAULT_REC_NM_FILE)
if args.anm_lig > 0:
log.info("Calculating ANM for ligand molecule...")
calculate_anm(ligand, args.anm_lig, DEFAULT_LIG_NM_FILE)
# Parse restraints if any:
receptor_restraints = ligand_restraints = None
if args.restraints:
log.info("Reading restraints from %s" % args.restraints)
restraints = parse_restraints_file(args.restraints)
# Calculate number of restraints in order to check them
num_rec_active = len(restraints['receptor']['active'])
num_rec_passive = len(restraints['receptor']['passive'])
num_lig_active = len(restraints['ligand']['active'])
num_lig_passive = len(restraints['ligand']['passive'])
# Check if restraints have been defined for the ligand, but not to the receptor
if not num_rec_active and not num_rec_passive and (
num_lig_active or num_lig_passive):
raise LightDockError(
"Restraints defined for ligand, but not receptor. Try switching structures."
)
if not num_rec_active and not num_rec_passive and not num_lig_active and not num_lig_passive:
save_lightdock_structure(ligand)
# Calculate and save ANM if required
if args.use_anm:
if args.anm_rec > 0:
log.info("Calculating ANM for receptor molecule...")
calculate_anm(receptor, args.anm_rec, DEFAULT_REC_NM_FILE)
if args.anm_lig > 0:
log.info("Calculating ANM for ligand molecule...")
calculate_anm(ligand, args.anm_lig, DEFAULT_LIG_NM_FILE)
# Parse restraints if any:
receptor_restraints = ligand_restraints = None
if args.restraints:
log.info("Reading restraints from %s" % args.restraints)
restraints = parse_restraints_file(args.restraints)
# Calculate number of restraints in order to check them
num_rec_active = len(restraints['receptor']['active'])
num_rec_passive = len(restraints['receptor']['passive'])
num_lig_active = len(restraints['ligand']['active'])
num_lig_passive = len(restraints['ligand']['passive'])
# Check if restraints have been defined for the ligand, but not to the receptor
if not num_rec_active and not num_rec_passive and (num_lig_active or num_lig_passive):
raise LightDockError("Restraints defined for ligand, but not receptor. Try switching structures.")
if not num_rec_active and not num_rec_passive and not num_lig_active and not num_lig_passive:
raise LightDockError("Restraints file specified, but not a single restraint found")
# Check if restraints correspond with real residues
