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
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
def test_load_save_uuid(self):
store = Storage(filename=self.filename, mode='w')
assert (os.path.isfile(self.filename))
store.save(self.template_snapshot)
store.close()
store = Storage(filename=self.filename, mode='a')
loaded_template = store.snapshots[self.template_snapshot.__uuid__]
loaded_r = store.snapshots[self.template_snapshot.reversed.__uuid__]
compare_snapshot(loaded_template, self.template_snapshot, True)
compare_snapshot(loaded_template.reversed,
self.template_snapshot.reversed, True)
compare_snapshot(loaded_r, self.template_snapshot.reversed)
store.close()
def test_load_save_toy(self):
store = Storage(filename=self.filename, mode='w')
assert (os.path.isfile(self.filename))
store.save(self.toy_template)
store.close()
store = Storage(filename=self.filename, mode='a')
loaded_template = store.snapshots[0]
loaded_r = store.snapshots[1]
compare_snapshot(loaded_template, self.toy_template, True)
compare_snapshot(loaded_template.reversed, self.toy_template.reversed,
True)
compare_snapshot(loaded_r, self.toy_template.reversed)
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_load_save_uuid(self):
store = Storage(filename=self.filename, mode='w')
assert(os.path.isfile(self.filename))
store.save(self.template_snapshot)
store.close()
store = Storage(filename=self.filename, mode='a')
loaded_template = store.snapshots[self.template_snapshot.__uuid__]
loaded_r = store.snapshots[self.template_snapshot.reversed.__uuid__]
compare_snapshot(loaded_template, self.template_snapshot, True)
compare_snapshot(
loaded_template.reversed,
self.template_snapshot.reversed, True)
compare_snapshot(loaded_r, self.template_snapshot.reversed)
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_load_save_toy(self):
store = Storage(filename=self.filename, mode='w', use_uuid=False)
assert(os.path.isfile(self.filename))
store.save(self.toy_template)
store.close()
store = Storage(filename=self.filename, mode='a')
loaded_template = store.snapshots[0]
loaded_r = store.snapshots[1]
compare_snapshot(loaded_template, self.toy_template, True)
compare_snapshot(
loaded_template.reversed,
self.toy_template.reversed, True)
compare_snapshot(loaded_r, self.toy_template.reversed)
store.close()
def test_load_save(self):
for use_uuid in [True, False]:
store = Storage(filename=self.filename, mode='w', use_uuid=use_uuid)
assert(os.path.isfile(self.filename))
store.save(self.template_snapshot)
store.close()
store = Storage(filename=self.filename, mode='a')
loaded_template = store.snapshots[0]
loaded_r = store.snapshots[1]
compare_snapshot(loaded_template, self.template_snapshot, True)
compare_snapshot(
loaded_template.reversed,
self.template_snapshot.reversed, True)
compare_snapshot(loaded_r, self.template_snapshot.reversed)
store.close()
def test_proxy(self):
for use_uuid in [True, False]:
store = Storage(filename=self.filename,
mode='w',
use_uuid=use_uuid)
assert (os.path.isfile(self.filename))
tm = self.template_snapshot
store.save(tm)
px = store.snapshots.proxy(0)
# make sure that the proxy and
assert (hash(px) == hash(tm))
assert (px == tm)
store.snapshots.cache.clear()
s0 = store.snapshots[0]
assert (hash(px) == hash(s0))
assert (px == s0)
compare_snapshot(px, tm)
compare_snapshot(s0, tm)
px = store.snapshots.proxy(0)
# make sure that after reloading it still works
assert (hash(px) == hash(tm))
assert (px == tm)
store.close()
store = Storage(filename=self.filename, mode='a')
s1 = store.snapshots[0]
store.close()
# when loading only for uuid based storages you get the same id
assert ((hash(px) == hash(s1)) is use_uuid)
assert ((px == s1) is use_uuid)
def test_load_save(self):
for use_uuid in [True, False]:
store = Storage(filename=self.filename,
mode='w',
use_uuid=use_uuid)
assert (os.path.isfile(self.filename))
store.save(self.template_snapshot)
store.close()
store = Storage(filename=self.filename, mode='a')
loaded_template = store.snapshots[0]
loaded_r = store.snapshots[1]
compare_snapshot(loaded_template, self.template_snapshot, True)
compare_snapshot(loaded_template.reversed,
self.template_snapshot.reversed, True)
compare_snapshot(loaded_r, self.template_snapshot.reversed)
store.close()
def test_proxy(self):
for use_uuid in [True, False]:
store = Storage(filename=self.filename, mode='w', use_uuid=use_uuid)
assert(os.path.isfile(self.filename))
tm = self.template_snapshot
store.save(tm)
px = store.snapshots.proxy(0)
# make sure that the proxy and
assert(hash(px) == hash(tm))
assert(px == tm)
store.snapshots.cache.clear()
s0 = store.snapshots[0]
assert(hash(px) == hash(s0))
assert(px == s0)
compare_snapshot(px, tm)
compare_snapshot(s0, tm)
px = store.snapshots.proxy(0)
# make sure that after reloading it still works
assert(hash(px) == hash(tm))
assert(px == tm)
store.close()
store = Storage(filename=self.filename, mode='a')
s1 = store.snapshots[0]
store.close()
# when loading only for uuid based storages you get the same id
assert((hash(px) == hash(s1)) is use_uuid)
assert((px == s1) is use_uuid)
