def setUp(self):
self.mdtraj = md.load(data_filename("ala_small_traj.pdb"))
self.traj = paths.tools.trajectory_from_mdtraj(self.mdtraj)
self.filename = data_filename("storage_test.nc")
self.filename_clone = data_filename("storage_test_clone.nc")
self.simplifier = ObjectJSON()
self.template_snapshot = self.traj[0]
self.solute_indices = range(22)
class testStorage(object):
def setUp(self):
self.mdtraj = md.load(data_filename("ala_small_traj.pdb"))
self.traj = paths.tools.trajectory_from_mdtraj(self.mdtraj)
self.filename = data_filename("storage_test.nc")
self.filename_clone = data_filename("storage_test_clone.nc")
self.simplifier = ObjectJSON()
self.template_snapshot = self.traj[0]
self.solute_indices = range(22)
def teardown(self):
if os.path.isfile(self.filename):
os.remove(self.filename)
if os.path.isfile(self.filename_clone):
os.remove(self.filename_clone)
def test_create_template(self):
store = Storage(filename=self.filename, template=self.template_snapshot, mode='w')
assert(os.path.isfile(data_filename("storage_test.nc")))
store.close()
def test_stored_topology(self):
store = Storage(filename=self.filename, template=self.template_snapshot, mode='w')
assert(os.path.isfile(self.filename))
store.close()
store = Storage(filename=self.filename, mode='a')
loaded_topology = store.template.topology
# check if poth topologies have the same JSON string (this also tests the simplifier for topologies
assert_equal(
self.simplifier.to_json(self.template_snapshot.topology),
self.simplifier.to_json(loaded_topology)
)
store.close()
def test_stored_template(self):
store = Storage(filename=self.filename, template=self.template_snapshot, mode='w')
assert(os.path.isfile(self.filename))
store.close()
store = Storage(filename=self.filename, mode='a')
loaded_template = store.template
compare_snapshot(loaded_template, self.template_snapshot)
store.close()
def test_load_save(self):
store = Storage(filename=self.filename, template=self.template_snapshot, mode='w')
assert(os.path.isfile(self.filename))
copy = self.template_snapshot.copy()
store.save(copy)
store.close()
store = Storage(filename=self.filename, mode='a')
loaded_template = store.template
compare_snapshot(loaded_template, self.template_snapshot)
loaded_copy = store.load(Snapshot, 1)
compare_snapshot(loaded_template, loaded_copy)
store.close()
def test_clone(self):
store = Storage(filename=self.filename, template=self.template_snapshot, mode='w')
assert(os.path.isfile(self.filename))
copy = self.template_snapshot.copy()
store.save(copy)
store.save(self.traj)
store.clone(filename=self.filename_clone, subset = self.solute_indices)
# clone the storage and reduce the number of atoms to only solute
store2 = Storage(filename=self.filename_clone, mode='a')
# do some tests, if this is still the same data
compare_snapshot(
store2.snapshots.load(0),
store.snapshots.load(0).subset(self.solute_indices)
)
compare_snapshot(
store2.snapshots.load(1),
store.snapshots.load(1).subset(self.solute_indices)
)
store.close()
store2.close()
pass
def test_clone_empty(self):
store = Storage(filename=self.filename, template=self.template_snapshot, mode='w')
assert(os.path.isfile(self.filename))
copy = self.template_snapshot.copy()
store.save(copy)
store.save(self.traj)
store.clone_empty(filename=self.filename_clone)
# clone the storage and reduce the number of atoms to only solute
store2 = Storage(filename=self.filename_clone, mode='a')
# do some tests, if this is still the same data
compare_snapshot(
store2.snapshots.load(0),
store.snapshots.load(0)
)
# check if the reversed copy also works
compare_snapshot(
store2.snapshots.load(1),
store.snapshots.load(1)
)
assert_equal(len(store2.snapshots), 2)
assert_equal(len(store2.trajectories), 0)
store.close()
store2.close()
pass
