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("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_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_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)