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()