def setup(self):
self.mdtraj = md.load(data_filename("ala_small_traj.pdb"))
self.traj_topology = peng.trajectory_from_mdtraj(self.mdtraj)
self.traj_simple = peng.trajectory_from_mdtraj(self.mdtraj,
simple_topology=True)
self.topology = self.traj_topology[0].engine.topology
if os.path.isfile("myfile.nc"):
os.remove("myfile.nc")
def setup(self):
self.mdtraj = md.load(data_filename("ala_small_traj.pdb"))
self.traj_topology = peng.trajectory_from_mdtraj(self.mdtraj)
self.traj_simple = peng.trajectory_from_mdtraj(
self.mdtraj,
simple_topology=True)
self.topology = self.traj_topology[0].engine.topology
if os.path.isfile("myfile.nc"):
os.remove("myfile.nc")
def setup(self):
if not md:
raise SkipTest("mdtraj not installed")
self.mdtraj = md.load(data_filename("ala_small_traj.pdb"))
_ = pytest.importorskip('simtk.unit')
self.traj_topology = peng.trajectory_from_mdtraj(self.mdtraj)
self.traj_simple = peng.trajectory_from_mdtraj(self.mdtraj,
simple_topology=True)
self.topology = self.traj_topology[0].engine.topology
if os.path.isfile("myfile.nc"):
os.remove("myfile.nc")
def setUp(self):
self.mdtraj = md.load(data_filename("ala_small_traj.pdb"))
self.traj = peng.trajectory_from_mdtraj(
self.mdtraj, simple_topology=True)
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)
self.toy_topology = toys.Topology(
n_spatial=2,
masses=[1.0, 1.0],
pes=None
)
self.engine = toys.Engine({}, self.toy_topology)
self.toy_template = toys.Snapshot(
coordinates=np.array([[-0.5, -0.5]]),
velocities=np.array([[0.0,0.0]]),
engine=self.engine
)
def setup(self):
self.mdtraj = md.load(data_filename("ala_small_traj.pdb"))
self.traj = peng.trajectory_from_mdtraj(
self.mdtraj, simple_topology=True)
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 = list(range(22))
self.toy_topology = toys.Topology(
n_spatial=2,
masses=[1.0, 1.0],
pes=None
)
self.engine = toys.Engine({}, self.toy_topology)
self.toy_template = toys.Snapshot(
coordinates=np.array([[-0.5, -0.5]]),
velocities=np.array([[0.0,0.0]]),
engine=self.engine
)
def setup(self):
if not HAS_PLUMED:
pytest.skip("PLUMED module not installed.")
if not HAS_OPENMM:
pytest.skip("OpenMM module not installed.")
if not HAS_MDTRAJ:
pytest.skip("MDTraj module not installed.")
self.topology = peng_omm.tools.topology_from_pdb(
data_filename("plumed_wrapper/" + "AD_initial_frame" + ".pdb"))
self.trajectory = peng_omm.trajectory_from_mdtraj(
md.load(data_filename("ala_small_traj" + ".pdb")))
if os.path.isfile("test.nc"):
os.remove("test.nc")
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 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 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"))
# print snapshot.__dict__
# print snapshot.engine.__dict__
# 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 = 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"))
# print snapshot.__dict__
# print snapshot.engine.__dict__
# 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 = peng.trajectory_from_mdtraj(mdtrajectory, simple_topology=True)
storage.trajectories.save(mytraj)
storage.close()