def test_process_pdb(file_name, group_solvent, num_atom, num_res):
base_location = os.path.dirname(os.path.realpath(__file__))
pdb_path = os.path.join(base_location, '..', '..', 'test', 'pytest_data', file_name)
residues = util.process_pdb(pdb_path, group_solvent=group_solvent)[0]
assert len(residues) == num_atom
assert residues[-1] == num_res
mdi.MDI_Init(args.mdi, mpi_world)
if use_mpi4py:
mpi_world = mdi.MDI_Get_Intra_Code_MPI_Comm()
world_rank = mpi_world.Get_rank()
snapshot_filename = args.snap
probes = [int(x) for x in args.probes.split()]
if args.byres and args.bymol:
parser.error(
"--byres and --bymol cannot be used together. Please only use one."
)
if args.byres:
residues = process_pdb(args.byres)[0]
engine_comm = mdi_checks(mdi, nengines)
# Print the probe atoms
print(F"Probes: {probes}")
elapsed = time.time() - start
print(F'Setup:\t {elapsed}')
###########################################################################
#
# Get Information from Tinker
#
###########################################################################