def test_index_fragments():
ipoles = list(range(1, 11))
fragments = [1, 1, 1, 2, 2, 3, 3, 4, 4, 4]
pole_index_by_fragment = util.index_fragments(fragments, ipoles)[0]
print(pole_index_by_fragment)
print(len(pole_index_by_fragment))
expected_index = np.array([
np.array([1, 2, 3]),
np.array([4, 5]),
np.array([6, 7]),
np.array([8, 9, 10])],
dtype=object)
assert len(expected_index) == len(pole_index_by_fragment)
for i in range(len(expected_index)):
assert np.array_equal(pole_index_by_fragment[i], expected_index[i])
print(F'Probe pole indices {probe_pole_indices}')
# Get the atom and pole numbers for the molecules/residues of interest.
atoms_pole_numbers = []
if args.bymol:
by_type = 'molecule'
fragment_list = molecules
elif args.byres:
by_type = 'residue'
fragment_list = residues
else:
by_type = 'atom'
# We are interested in all of the atoms.
fragment_list = list(range(1, natoms_engine + 1))
atoms_pole_numbers, from_fragment = index_fragments(fragment_list, ipoles)
elapsed = time.time() - start
print(F'Bookkeeping:\t {elapsed}')
###########################################################################
#
# Send Probe Information to Tinker
#
###########################################################################
start = time.time()
# Inform Tinker of the probe atoms
for comm in engine_comm:
mdi.MDI_Send_Command(">NPROBES", comm)
mdi.MDI_Send(len(probes), 1, mdi.MDI_INT, comm)
mdi.MDI_Send_Command(">PROBES", comm)