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_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_get_restraints_with_error(self):
input_file = os.path.join(self.golden_data_path, '2UUY_lig.pdb')
atoms, residues, chains = parse_complex_from_file(input_file)
structure = Complex(chains)
restraints = {'active':['B.VAL.21'], 'passive':['B.GLY.75'], 'blocked':[]}
residues = get_restraints(structure, restraints)
assert False
def test_get_restraints(self):
input_file = os.path.join(self.golden_data_path, '2UUY_lig.pdb')
atoms, residues, chains = parse_complex_from_file(input_file)
structure = Complex(chains)
restraints = {'active':['B.ALA.21'], 'passive':['B.GLY.75'], 'blocked':[]}
residues = get_restraints(structure, restraints)
assert len(residues['active']) == 1 and len(residues['passive']) == 1
assert residues['active'][0].name == 'ALA' and residues['active'][0].number == 21
assert residues['passive'][0].name == 'GLY' and residues['passive'][0].number == 75
def test_get_restraints_with_error(self):
input_file = self.golden_data_path / '2UUY_lig.pdb'
_, _, chains = parse_complex_from_file(input_file)
structure = Complex(chains)
restraints = {
'active': ['B.VAL.21'],
'passive': ['B.GLY.75'],
'blocked': []
}
residues = get_restraints(structure, restraints)
assert residues is not None
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
receptor_restraints = get_restraints(receptor,
restraints['receptor'])
args.receptor_restraints = restraints['receptor']
ligand_restraints = get_restraints(ligand, restraints['ligand'])
args.ligand_restraints = restraints['ligand']
log.info(
"Number of receptor restraints is: %d (active), %d (passive)" %
(num_rec_active, num_rec_passive))
log.info(
"Number of ligand restraints is: %d (active), %d (passive)" %
(num_lig_active, num_lig_passive))
rec_restraints = None
try:
rec_restraints = receptor_restraints[
'active'] + receptor_restraints['passive']
# 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
receptor_restraints = get_restraints(receptor, restraints['receptor'])
args.receptor_restraints = restraints['receptor']
ligand_restraints = get_restraints(ligand, restraints['ligand'])
args.ligand_restraints = restraints['ligand']
log.info("Number of receptor restraints is: %d (active), %d (passive)" % (num_rec_active, num_rec_passive))
log.info("Number of ligand restraints is: %d (active), %d (passive)" % (num_lig_active, num_lig_passive))
rec_restraints = None
try:
rec_restraints = receptor_restraints['active'] + receptor_restraints['passive']
except:
pass
lig_restraints = None
try: