def test_create_setup_file(self):
shutil.copyfile(os.path.join(self.golden_data_path, '2UUY_rec.pdb'),
os.path.join(self.test_path, '2UUY_rec.pdb'))
shutil.copyfile(os.path.join(self.golden_data_path, '2UUY_lig.pdb'),
os.path.join(self.test_path, '2UUY_lig.pdb'))
os.chdir(self.test_path)
parser = SetupCommandLineParser(['2UUY_rec.pdb', '2UUY_lig.pdb', '5', '10', '-anm', '--noxt'])
create_setup_file(parser.args)
assert filecmp.cmp(os.path.join(self.test_path, 'setup.json'),
os.path.join(self.golden_data_path, 'setup.json'))
get_restraints
from lightdock.constants import DEFAULT_LIGHTDOCK_PREFIX, DEFAULT_ELLIPSOID_DATA_EXTENSION, \
DEFAULT_NMODES_REC, DEFAULT_REC_NM_FILE, DEFAULT_NMODES_LIG, DEFAULT_LIG_NM_FILE, DEFAULT_OUTPATH
from lightdock.mathutil.ellipsoid import MinimumVolumeEllipsoid
from lightdock.util.logger import LoggingManager
from lightdock.error.lightdock_errors import LightDockError
log = LoggingManager.get_logger('lightdock_setup')
if __name__ == "__main__":
try:
parser = SetupCommandLineParser()
args = parser.args
create_setup_file(args)
# Read input structures
receptor = read_input_structure(args.receptor_pdb, args.noxt, args.noh,
args.verbose_parser)
ligand = read_input_structure(args.ligand_pdb, args.noxt, args.noh,
args.verbose_parser)
# Move structures to origin
rec_translation = receptor.move_to_origin()
lig_translation = ligand.move_to_origin()
# Calculate reference points for receptor
log.info("Calculating reference points for receptor %s..." %
args.receptor_pdb)
rec_ellipsoid = MinimumVolumeEllipsoid(
lig_restraints = None
try:
lig_restraints = ligand_restraints['active'] + ligand_restraints['passive']
except:
pass
# Calculate surface points (swarm centers) over receptor structure
starting_points_files = calculate_starting_positions(receptor, ligand,
args.swarms, args.glowworms,
args.starting_points_seed,
rec_restraints, lig_restraints,
rec_translation, lig_translation,
args.ftdock_file, args.use_anm, args.anm_seed,
args.anm_rec, args.anm_lig, args.membrane)
if len(starting_points_files) != args.swarms:
args.swarms = len(starting_points_files)
log.info('Number of swarms is %d after applying restraints' % args.swarms)
# Create simulation folders
prepare_results_environment(args.swarms)
# Dump to a setup file the actual configuration
create_setup_file(args)
log.info("LightDock setup OK")
except LightDockError, error:
log.error("LightDock setup failed. Please see:")
log.error(error)