def setup_package():
# this should generate the trajectory.nc file which we'll use for
# everything else
mdtrajectory = md.load(data_filename("ala_small_traj.pdb"))
snapshot = peng.snapshot_from_pdb(data_filename("ala_small_traj.pdb"))
storage = Storage(filename=data_filename("ala_small_traj.nc"),
template=snapshot,
mode='w')
mytraj = peng.trajectory_from_mdtraj(mdtrajectory, simple_topology=True)
storage.trajectories.save(mytraj)
storage.close()
def setup_package():
# this should generate the trajectory.nc file which we'll use for
# everything else
mdtrajectory = md.load(data_filename("ala_small_traj.pdb"))
snapshot = peng.snapshot_from_pdb(data_filename("ala_small_traj.pdb"))
storage = Storage(
filename=data_filename("ala_small_traj.nc"),
template=snapshot,
mode='w'
)
mytraj = peng.trajectory_from_mdtraj(mdtrajectory, simple_topology=True)
storage.trajectories.save(mytraj)
storage.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_reverse_bug(self):
store = Storage(filename=self.filename, mode='w')
assert (os.path.isfile(self.filename))
store.snapshots.save(self.template_snapshot)
rev = self.template_snapshot.reversed
# save the reversed one
store.snapshots.save(rev)
# check that the reversed one has index 1 and not 3!
assert (store.idx(rev) == 1)
# and we have exactly one snapshot
assert (len(store.snapshots) == 2)
assert (len(store.dimensions['snapshots']) == 1)
store.close()
def test_reverse_bug(self):
store = Storage(filename=self.filename,
mode='w', use_uuid=False)
assert(os.path.isfile(self.filename))
store.snapshots.save(self.template_snapshot)
rev = self.template_snapshot.reversed
# save the reversed one
store.snapshots.save(rev)
# check that the reversed one has index 1 and not 3!
assert(store.idx(rev) == 1)
# and we have exactly one snapshot
assert(len(store.snapshots) == 2)
assert(len(store.dimensions['snapshots']) == 1)
store.close()
def setup_package():
if not md:
return
# this should generate the ala_small_traj.nc file which we'll use for
# everything else
# NOTE: tests using this must be skipped if there's no mdtraj!
mdtrajectory = md.load(data_filename("ala_small_traj.pdb"))
snapshot = peng.snapshot_from_pdb(data_filename("ala_small_traj.pdb"))
storage = Storage(filename=data_filename("ala_small_traj.nc"),
template=snapshot,
mode='w')
mytraj = peng.trajectory_from_mdtraj(mdtrajectory, simple_topology=True)
storage.trajectories.save(mytraj)
storage.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_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 setup_package():
# this should generate the trajectory.nc file which we'll use for
# everything else
mdtrajectory = md.load(data_filename("ala_small_traj.pdb"))
snapshot = paths.snapshot_from_pdb(data_filename("ala_small_traj.pdb"))
# once we have a template configuration (coordinates to not really matter)
# we can create a storage. We might move this logic out of the dynamics engine
# and keep sotrage and engine generation completely separate!
storage = Storage(filename=data_filename("ala_small_traj.nc"),
template=snapshot,
mode='w')
mytraj = paths.tools.trajectory_from_mdtraj(mdtrajectory)
storage.trajectories.save(mytraj)
storage.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 setup_package():
# this should generate the trajectory.nc file which we'll use for
# everything else
mdtrajectory = md.load(data_filename("ala_small_traj.pdb"))
snapshot = paths.snapshot_from_pdb(data_filename("ala_small_traj.pdb"))
# once we have a template configuration (coordinates to not really matter)
# we can create a storage. We might move this logic out of the dynamics engine
# and keep sotrage and engine generation completely separate!
storage = Storage(
filename=data_filename("ala_small_traj.nc"),
template=snapshot,
mode='w'
)
mytraj = paths.Trajectory.from_mdtraj(mdtrajectory)
storage.trajectories.save(mytraj)
storage.close()
def test_stored_topology(self):
raise SkipTest
store = Storage(filename=self.filename, 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_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_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):
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_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_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_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_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(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_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_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_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_version(self):
store = Storage(filename=self.filename, mode='w')
assert (os.path.isfile(self.filename))
assert (store.storage_version == paths.version.version)
"""
This is an example file of how to remove water from a netCDF file.
@author: Jan-Hendrik Prinz
"""
from openpathsampling.storage import Storage
if __name__=="__main__":
storage = Storage(
filename="trajectory.nc",
mode='a'
)
solute = range(22)
storage.clone('test_solute.nc', subset=None)
storage.close()
storage2 = Storage('test_solute.nc')
storage2.clone('test_solute2.nc', subset=solute)
const=True,
default=False,
help='shows collectivevariables in degree and not plain')
args = parser.parse_args()
rejected = args.rejected
file = args.file
degrees = 180 / 3.14159 # psi reports in radians; I think in degrees
if not os.path.isfile(file):
print file, 'does not exist ! ENDING!'
exit()
storage = Storage(filename=file, mode='a')
if args.show == 'snapshot':
show_op = storage.snapshots.op_idx
elif args.show == 'configuration':
show_op = storage.snapshots.op_configuration_idx
elif args.show == 'momentum':
show_op = storage.snapshots.op_momentum_idx
elif args.show == '':
def show_id(s):
return ''
show_op = show_id
else:
show_op = storage.cvs.load(args.show)
def test_create_storage(self):
store = Storage(filename=self.filename, mode='w')
assert (os.path.isfile(data_filename("storage_test.nc")))
store.close()
from openpathsampling.storage import Storage
if __name__ == '__main__':
parser = argparse.ArgumentParser(description='Analyze a file.')
parser.add_argument('file', metavar='file.nc', help='an integer for the accumulator')
args = parser.parse_args()
file = args.file
if not os.path.isfile(file):
print file, 'does not exist ! ENDING!'
exit()
storage = Storage(
filename = file,
mode = 'a'
)
storage.samples.cache_all()
storage.samplesets.cache_all()
storage.pathmovechanges.cache_all()
class ReadableObjectJSON(paths.todict.ObjectJSON):
def __init__(self, unit_system = None):
super(ReadableObjectJSON, self).__init__(unit_system)
self.excluded_keys = ['name', 'idx', 'json', 'identifier']
self.storage = storage
def build(self,obj):
if type(obj) is dict:
if '_cls' in obj and '_idx' in obj:
