dest="lnuc",
action='store_true',
default=False)
return parser.parse_args()
if __name__ == '__main__':
# Parse command line
args = parse_command_line()
log.info("Calculating interface at {:3.1f}A".format(args.cutoff))
# Get ranking
ranking = read_ranking_file(args.ranking_file)
# Get all the PDB structures in a given directory
base_path = os.path.abspath(os.path.dirname(args.ranking_file))
structures = get_structures(ranking, base_path)
restraints_receptor, restraints_ligand = get_restraints(
args.restraints_file)
# Total number of restraints to be satisfied
total = float(len(restraints_receptor) + len(restraints_ligand))
if os.path.exists(filtered_folder):
raise SystemExit("Folder {} already exists".format(filtered_folder))
else:
os.makedirs(filtered_folder)
r31 = 2 * (q.x * q.z) + 2 * (q.w * q.y)
r32 = 2 * (q.y * q.z) - 2 * (q.w * q.x)
r33 = 1 - 2 * x2 - 2 * y2
return r11, r12, r13, r21, r22, r23, r31, r32, r33
def create_rot_file(file_name, results):
t = open(file_name, 'w')
for i, result in enumerate(results):
q = Quaternion(result.pose[3], result.pose[4], result.pose[5], result.pose[6])
r11, r12, r13, r21, r22, r23, r31, r32, r33 = quaternion_to_matrix(q)
t1 = result.pose[0]
t2 = result.pose[1]
t3 = result.pose[2]
t.write('%8.3f %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f %6d\n' %
(r11, r12, r13, r21, r22, r23, r31, r32, r33, t1, t2, t3, i + 1))
t.close()
if __name__ == "__main__":
try:
# Parse command line
args = parse_command_line()
results = read_ranking_file(args.ranking_file)
log.info('%d results read from %s' % (len(results), args.ranking_file))
create_rot_file(args.rotation_file, results)
log.info("Done.")
except (KeyboardInterrupt):
log.info("Caught interrupt...")
log.info("bye.")
return r11, r12, r13, r21, r22, r23, r31, r32, r33
def create_rot_file(file_name, results):
t = open(file_name, 'w')
for i, result in enumerate(results):
q = Quaternion(result.pose[3], result.pose[4], result.pose[5],
result.pose[6])
r11, r12, r13, r21, r22, r23, r31, r32, r33 = quaternion_to_matrix(q)
t1 = result.pose[0]
t2 = result.pose[1]
t3 = result.pose[2]
t.write(
'%8.3f %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f %6d\n'
% (r11, r12, r13, r21, r22, r23, r31, r32, r33, t1, t2, t3, i + 1))
t.close()
if __name__ == "__main__":
try:
# Parse command line
args = parse_command_line()
results = read_ranking_file(args.ranking_file)
log.info('%d results read from %s' % (len(results), args.ranking_file))
create_rot_file(args.rotation_file, results)
log.info("Done.")
except (KeyboardInterrupt):
log.info("Caught interrupt...")
log.info("bye.")
# Ligand
structures = []
for structure in get_lightdock_structures(args.ligand_structures):
log.info("Reading %s ligand PDB file..." % structure)
atoms, residues, chains = parse_complex_from_file(structure)
structures.append({
'atoms': atoms,
'residues': residues,
'chains': chains,
'file_name': structure
})
log.info("%s atoms, %s residues read." % (len(atoms), len(residues)))
ligand = Complex.from_structures(structures)
# Read ranking file
predictions = read_ranking_file(args.lightdock_ranking_file)
# Destination path is the same as the lightdock output
destination_path = os.path.dirname(args.lightdock_ranking_file)
# If normal modes used, need to read them
nmodes_rec = nmodes_lig = None
nm_path = os.path.abspath(os.path.dirname(args.receptor_structures))
# Check NM file for receptor
nm_rec_file = os.path.join(nm_path, DEFAULT_REC_NM_FILE + '.npy')
if os.path.exists(nm_rec_file):
nmodes_rec = read_nmodes(nm_rec_file)
# Check NM file for ligand
nm_lig_file = os.path.join(nm_path, DEFAULT_LIG_NM_FILE + '.npy')
if os.path.exists(nm_lig_file):
nmodes_lig = read_nmodes(nm_lig_file)
parser.add_argument("ligand_chains", help="Chains on the receptor partner", metavar="ligand_chains")
parser.add_argument("--cutoff", "-cutoff", "-c", help="Interaction cutoff",
dest="cutoff", type=float, default=1.0)
return parser.parse_args()
if __name__ == '__main__':
# Parse command line
args = parse_command_line()
log.info("Cutoff for membrane is {:3.1f}A".format(args.cutoff))
# Get ranking
ranking = read_ranking_file(args.ranking_file)
# Get all the PDB structures in a given directory
base_path = os.path.abspath(os.path.dirname(args.ranking_file))
structures = get_structures(ranking, base_path)
restraints_receptor, restraints_ligand = get_restraints(args.restraints_file)
membrane_height_z = calculate_membrane_height(args.parsed_receptor_file, restraints_receptor)
if os.path.exists(filtered_folder):
raise SystemExit("Folder {} already exists".format(filtered_folder))
else:
os.makedirs(filtered_folder)
filter_passed = {}