def test_parse_summary_line_options_rejected(self):
options_rejected_converter = StupidOneWayTPSConverter(
storage=None,
initial_file="file0.data",
mover=self.shoot,
network=self.network,
options=oink.TPSConverterOptions(trim=False,
auto_reverse=False,
full_trajectory=True),
options_rejected=oink.TPSConverterOptions(trim=False,
auto_reverse=True,
full_trajectory=False))
self._standard_summary_line_check(
summary_file="summary_full_accepted.txt",
converter=options_rejected_converter)
def test_parse_summary_line_extras(self):
extras_converter = StupidOneWayTPSConverter(
storage=None,
initial_file="file0_extra.data",
mover=self.shoot,
network=self.network,
options=oink.TPSConverterOptions(trim=True,
auto_reverse=True,
includes_shooting_point=True))
self._standard_summary_line_check(summary_file="summary_extra.txt",
converter=extras_converter)
def test_parse_summary_line_retrim_shooting_full_accepted(self):
retrim_shooting_converter = StupidOneWayTPSConverter(
storage=None,
initial_file="file0_extra.data",
mover=self.shoot,
network=self.network,
options=oink.TPSConverterOptions(trim=True,
retrim_shooting=True,
auto_reverse=False,
full_trajectory=True))
self._standard_summary_line_check(
summary_file="summary_full_retrim.txt",
converter=retrim_shooting_converter)
def setUp(self):
from openpathsampling.engines.openmm.tools import ops_load_trajectory
if not HAS_MDTRAJ:
raise SkipTest("Missing MDTraj")
test_dir = "gromacs_1way"
self.data_filename = lambda f : \
data_filename(os.path.join(test_dir, f))
topology_file = self.data_filename("dna.gro")
initial_file = self.data_filename("initial.xtc")
init_traj = ops_load_trajectory(initial_file, top=topology_file)
self.network = self._wc_hg_TPS_network(init_traj.topology)
acc_options = oink.TPSConverterOptions(trim=True,
retrim_shooting=True,
auto_reverse=False,
includes_shooting_point=True,
full_trajectory=True)
rej_options = oink.TPSConverterOptions(trim=True,
retrim_shooting=True,
auto_reverse=True,
includes_shooting_point=True,
full_trajectory=False)
storage = paths.Storage(self.data_filename("gromacs.nc"), 'w')
# initialization includes smoke test of load_trajectory
self.converter = oink.GromacsOneWayTPSConverter(
storage=storage,
network=self.network,
initial_file=initial_file,
topology_file=topology_file,
options=acc_options,
options_rejected=rej_options
)
self.converter.report_progress = sys.stdout
self.converter.n_trajs_per_block = 1
def setup(self):
test_dir = "one_way_tps_examples"
self.data_filename = lambda f : \
data_filename(os.path.join(test_dir, f))
old_store = paths.Storage(data_filename("tps_setup.nc"), "r")
self.network = old_store.networks[0]
tps_ensemble = self.network.sampling_ensembles[0]
self.shoot = oink.ShootingStub(tps_ensemble, pre_joined=False)
self.converter = StupidOneWayTPSConverter(
storage=paths.Storage(self.data_filename("output.nc"), "w"),
initial_file="file0.data",
mover=self.shoot,
network=self.network,
options=oink.TPSConverterOptions(includes_shooting_point=False,
trim=False))
old_store.close()
def test_run_with_negative_shooting_point(self):
shoot = oink.ShootingStub(self.network.sampling_ensembles[0],
pre_joined=False)
converter = StupidOneWayTPSConverter(
storage=paths.Storage(self.data_filename("neg_sp.nc"), "w"),
initial_file="file0.data",
mover=shoot,
network=self.network,
options=oink.TPSConverterOptions(includes_shooting_point=False,
trim=False))
converter.run(self.data_filename("summary_neg_sp.txt"))
converter.storage.close()
analysis = paths.AnalysisStorage(self.data_filename("neg_sp.nc"))
self._standard_analysis_checks(analysis)
analysis.close()
if os.path.isfile(self.data_filename("neg_sp.nc")):
os.remove(self.data_filename("neg_sp.nc"))
def test_run_with_neg_sp_retrim(self):
storage_file = self.data_filename("retrim_negsp.nc")
storage = paths.Storage(storage_file, 'w')
converter = StupidOneWayTPSConverter(storage=storage,
initial_file="file0_extra.data",
mover=self.shoot,
network=self.network,
options=oink.TPSConverterOptions(
trim=True,
retrim_shooting=True,
auto_reverse=False,
full_trajectory=True))
converter.run(self.data_filename("summary_full_retrim_negsp.txt"))
storage.close()
analysis = paths.AnalysisStorage(storage_file)
step4 = analysis.steps[4]
self._standard_analysis_checks(analysis)
analysis.close()
if os.path.isfile(storage_file):
os.remove(storage_file)
