ensemble_list = []
rmsd_cutoff = 2.0
for replica_index in range(len(replica_positions)):
trajectory = md.load(str("replica_" + str(replica_index + 1) + ".pdb"))
rmsds = md.rmsd(trajectory, native_structure)
rmsd_to_helical[replica_index] = rmsds
for rmsd_index in range(len(rmsd_to_helical[replica_index])):
if rmsd_to_helical[replica_index][rmsd_index] < rmsd_cutoff:
rmsd_list.append(rmsd_to_helical[replica_index][rmsd_index])
ensemble_list.append(replica_positions[replica_index][rmsd_index])
random.shuffle(ensemble_list)
file_index = 1
for pose in ensemble_list:
if file_index <= 100:
file_name = str("pose_" + str(file_index) + ".pdb")
cgmodel.positions = pose
write_pdbfile_without_topology(cgmodel, file_name)
target_traj = md.load(file_name)
aligned_target_traj = target_traj.superpose(native_structure)
cgmodel.positions = unit.Quantity(aligned_target_traj.xyz[0],
cgmodel.positions.unit)
write_pdbfile_without_topology(cgmodel, file_name)
file_index = file_index + 1
else:
exit()
if os.path.exists(nonnative_ensemble_directory):
nonnative_ensemble, nonnative_ensemble_energies = get_ensemble_data(
cgmodel, nonnative_ensemble_directory)
if len(nonnative_ensemble) != nonnative_ensemble_size:
print("ERROR: " + str(len(nonnative_ensemble_energies)) +
" nonnative poses were found in existing output folders, but " +
str(nonnative_ensemble_size) + " poses were requested.")
print(
"This probably means that the requested ensemble size changed since the script was last run."
)
exit()
else:
os.mkdir(nonnative_ensemble_directory)
for pose in nonnative_ensemble:
cgmodel.positions = pose
write_ensemble_pdb(cgmodel,
ensemble_directory=nonnative_ensemble_directory)
if os.path.exists(native_ensemble_directory):
native_ensemble, native_ensemble_energies = get_ensemble_data(
cgmodel, native_ensemble_directory)
if len(native_ensemble_energies) != native_ensemble_size:
print("ERROR: " + str(len(native_ensemble_energies)) +
" native poses were found in existing output folders, but " +
str(native_ensemble_size) + " poses were requested.")
print(
"This probably means that the requested ensemble size changed since the script was last run."
)
exit()
else: