def test_reference(self): traj = pt.iterload(fn("tz2.ortho.nc"), fn("tz2.ortho.parm7")) # store reference dslist = CpptrajDatasetList() ref = dslist.add('reference') ref.top = traj.top ref.append(traj[3]) fi = pt.pipe(traj, ['autoimage', 'rms refindex 0 @CA'], dslist=dslist) xyz = np.array([frame.xyz.copy() for frame in fi]) t0 = (traj[:].autoimage().superpose(ref=traj[3], mask='@CA')) aa_eq(xyz, t0.xyz) t1 = traj[:].autoimage() aa_eq(pt.rmsd(t1, ref=traj[3], mask='@CA'), dslist[-1].values)
def test_modify_frame_use_Pipeline(self): traj = pt.iterload("data/tz2.ortho.nc", "data/tz2.ortho.parm7") dslist = CpptrajDatasetList() dslist.add_new('topology', name='mytop') # add a new topology dslist[0].data = pt.strip(traj.top, ':WAT') commands = ['autoimage', 'strip :WAT', 'createcrd mycrd', ] actlist = Pipeline(commands, top=traj.top, dslist=dslist) for frame in traj: actlist.compute(frame) aa_eq(dslist['mycrd'].xyz, pt.get_coordinates(traj, mask='!:WAT', autoimage=True))
def test_modify_frame_use_Pipeline(self): traj = pt.iterload(fn("tz2.ortho.nc"), fn("tz2.ortho.parm7")) dslist = CpptrajDatasetList() dslist.add('topology', name='mytop') # add a new topology dslist[0].data = pt.strip(traj.top, ':WAT') commands = [ 'autoimage', 'strip :WAT', 'createcrd mycrd', ] actlist = Pipeline(commands, top=traj.top, dslist=dslist) for frame in traj: actlist.compute(frame) aa_eq(dslist['mycrd'].xyz, pt.get_coordinates(traj, mask='!:WAT', autoimage=True))
def test_rmsd(input_traj): from pytraj.analysis.c_action.c_action import Action_Rmsd from pytraj.datasets import DatasetList dslist = DatasetList() act = Action_Rmsd() act.read_input('first @CA', top=input_traj.top, dslist=dslist) act.setup(input_traj.top) for frame in input_traj: act.compute(frame) return (dslist.values)
def test_reference(self): traj = pt.iterload("data/tz2.ortho.nc", "data/tz2.ortho.parm7") # store reference dslist = CpptrajDatasetList() ref = dslist.add_new('reference') ref.top = traj.top ref.append(traj[3]) fi = pt.pipe(traj, ['autoimage', 'rms refindex 0 @CA'], dslist=dslist) xyz = np.array([frame.xyz.copy() for frame in fi]) t0 = (traj[:] .autoimage() .superpose(ref=traj[3], mask='@CA')) print('ok') aa_eq(xyz, t0.xyz) t1 = traj[:].autoimage() aa_eq(pt.rmsd(t1, ref=traj[3], mask='@CA'), dslist[-1].values)
def test_constructor_from_command_list_TrajectoryIterator(self): traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top") commands = [ 'rmsd @CA', 'distance :3 :7', 'distance :3 :7', 'vector :2 :3' ] dslist = CpptrajDatasetList() actlist = ActionList(commands, traj.top, dslist=dslist) d0 = dslist.add('ref_frame', 'my_ref') d0.add_frame(traj[3]) for frame in traj: actlist.compute(frame) aa_eq(pt.rmsd(traj, mask='@CA'), dslist[0]) aa_eq(pt.distance(traj, ':3 :7'), dslist[1]) aa_eq(pt.distance(traj, ':3 :7'), dslist[2]) aa_eq(pt.vector.vector_mask(traj(rmsfit=(0, '@CA')), ':2 :3'), dslist[3].values)
def test_rmsd_actlist(input_traj): from pytraj.analysis.c_action.c_action import Action_Rmsd from pytraj import ActionList from pytraj.datasets import DatasetList alist = ActionList() dslist = DatasetList() act = Action_Rmsd() alist.add(act, 'first @CA', top=input_traj.top, dslist=dslist) for frame in input_traj: alist.compute(frame) return (dslist.values)
def test_constructor_from_command_list_TrajectoryIterator(self): traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top") commands = ['rmsd @CA', 'distance :3 :7', 'distance :3 :7', 'vector :2 :3'] dslist = CpptrajDatasetList() actlist = ActionList(commands, traj.top, dslist=dslist) d0 = dslist.add('ref_frame', 'my_ref') d0.add_frame(traj[3]) for frame in traj: actlist.compute(frame) aa_eq(pt.rmsd(traj, mask='@CA'), dslist[0]) aa_eq(pt.distance(traj, ':3 :7'), dslist[1]) aa_eq(pt.distance(traj, ':3 :7'), dslist[2]) aa_eq( pt.vector.vector_mask( traj(rmsfit=(0, '@CA')), ':2 :3'), dslist[3].values)