try:
rec_restraints = receptor_restraints['active'] + receptor_restraints['passive']
except:
pass
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")
rec_restraints = receptor_restraints[
'active'] + receptor_restraints['passive']
except:
pass
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")
)
log.info(
f"Number of ligand restraints is: {num_lig_active} (active), {num_lig_passive} (passive)"
)
try:
lig_restraints = ligand_restraints['active'] + ligand_restraints[
'passive']
except (KeyError, TypeError):
lig_restraints = None
# Calculate surface points (swarm centers) over receptor structure
starting_points_files = calculate_starting_positions(
receptor, ligand, args.swarms, args.glowworms,
args.starting_points_seed, receptor_restraints, lig_restraints,
rec_translation, lig_translation, args.surface_density,
args.use_anm, args.anm_seed, args.anm_rec, args.anm_lig,
args.membrane, args.transmembrane, args.write_starting_positions,
args.swarm_radius)
if len(starting_points_files) != args.swarms:
args.swarms = len(starting_points_files)
log.info(f"Number of calculated swarms is {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")