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)