def test_frame(self): traj = pt.iterload("data/Tc5b.x", "data/Tc5b.top") frame = traj[0] pt.to_pickle(frame, 'output/frame.pk') frame0 = pt.read_pickle('output/frame.pk') aa_eq(frame0.xyz, frame.xyz) # test list of frames fname = 'output/flist.pk' pt.to_pickle([traj[0], traj[1]], fname) f01 = pt.read_pickle(fname) aa_eq(np.array([f.xyz for f in f01]), traj[[0, 1]].xyz)
def test_frame(self): traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top')) frame = traj[0] pt.to_pickle(frame, 'frame.pk') frame0 = pt.read_pickle('frame.pk') aa_eq(frame0.xyz, frame.xyz) # test list of frames fname = 'flist.pk' pt.to_pickle([traj[0], traj[1]], fname) f01 = pt.read_pickle(fname) aa_eq(np.array([f.xyz for f in f01]), traj[[0, 1]].xyz)
def test_frame(self): traj = pt.iterload("data/Tc5b.x", "data/Tc5b.top") frame = traj[0] pt.to_pickle(frame, 'output/frame.pk') frame0 = pt.read_pickle('output/frame.pk') aa_eq(frame0.xyz, frame.xyz) # test list of frames fname = 'output/flist.pk' pt.to_pickle([traj[0], traj[1]], fname) f01 = pt.read_pickle(fname) aa_eq(np.array([f.xyz for f in f01]), traj[[0, 1]].xyz)
def test_trajiter_with_actionlist(self): traj = pt.iterload(fn('tz2.ortho.nc'), fn('tz2.ortho.parm7')) traj.autoimage().center('origin').superpose('@CA') pk_fn = 'test.pk' pt.to_pickle(traj, pk_fn) traj2 = pt.read_pickle(pk_fn) print(traj2._transform_commands) aa_eq(traj.xyz, traj2.xyz)
def test_pickle_frame(self): traj = pt.iterload(fn('tz2.nc'), fn('tz2.parm7')) f0 = traj[0] print(f0.mass) fn = 'f.pk' pt.to_pickle(f0, fn) f1 = pt.read_pickle(fn) print(f1.mass)
def test_pickle_frame(self): traj = pt.iterload("./data/tz2.nc", "./data/tz2.parm7") f0 = traj[0] print(f0.mass) fn = 'output/f.pk' pt.to_pickle(f0, fn) f1 = pt.read_pickle(fn) print(f1.mass)
def test_pickle_frame(self): traj = pt.iterload("./data/tz2.nc", "./data/tz2.parm7") f0 = traj[0] print(f0.mass) fn = 'output/f.pk' pt.to_pickle(f0, fn) f1 = pt.read_pickle(fn) print(f1.mass)
def test_nupars(self): pdb_fn = fn('Test_NAstruct/adh026.3.pdb') traj = pt.iterload(pdb_fn, pdb_fn) data = pt.nastruct(traj) # default text = ''' parm {} trajin {} nastruct groovecalc 3dna '''.format(fn('Test_NAstruct/adh026.3.pdb'), fn('Test_NAstruct/adh026.3.pdb')) state = pt.load_cpptraj_state(text) state.run() for key in ['major', 'minor', 'twist']: cpp_data = np.array( [x.values for x in state.data if x.aspect == key]) # need to transpose to get shape=(n_frames, n_pairs) cpp_data = cpp_data.T aa_eq(data[key][1], cpp_data) # TODO: assert data._summary(np.mean, indices=None) data._summary(np.mean, indices=[ 1, ]) data._summary(np.mean, keys=['major', 'twist'], indices=[ 1, ]) data._summary(np.mean, keys='major', indices=[ 1, ]) data._summary(np.std, indices=[ 1, ]) data._summary([np.std, np.mean], indices=[ 1, ]) data._explain() dir(data) # pickle pt.to_pickle(data, 'na.pk') na2 = pt.read_pickle('na.pk') for key in data.keys(): aa_eq(data[key][1], na2[key][1]) # raise self.assertRaises(ValueError, lambda: pt.nastruct(traj, dtype='ndarray'))
def test_pickle_progress_bar(): traj = pt.datafiles.load_tz2() with tempfolder(): t2 = ProgressBarTrajectory(traj) pt.to_pickle(t2, 'test.pk') t3 = pt.read_pickle('test.pk') data0 = pt.rmsd(traj) data1 = pt.rmsd(t2) data2 = pt.rmsd(t3) aa_eq(data0, data1) aa_eq(data0, data2)
def test_nupars(self): fn = "./data/Test_NAstruct/adh026.3.pdb" traj = pt.iterload(fn, fn) data = pt.nastruct(traj) # default text = ''' parm "./data/Test_NAstruct/adh026.3.pdb" trajin "./data/Test_NAstruct/adh026.3.pdb" nastruct groovecalc 3dna ''' state = pt.load_cpptraj_state(text) state.run() for key in ['major', 'minor', 'twist']: cpp_data = np.array([x.values for x in state.data if x.aspect == key]) # need to transpose to get shape=(n_frames, n_pairs) cpp_data = cpp_data.T aa_eq(data[key][1], cpp_data) # TODO: assert data._summary(np.mean, indices=None) data._summary(np.mean, indices=[1, ]) data._summary(np.mean, keys=['major', 'twist'], indices=[1, ]) data._summary(np.mean, keys='major', indices=[1, ]) data._summary(np.std, indices=[1, ]) data._summary([np.std, np.mean], indices=[1, ]) data._explain() dir(data) # pickle pt.to_pickle(data, 'data/na.pk') na2 = pt.read_pickle('data/na.pk') for key in data.keys(): aa_eq(data[key][1], na2[key][1]) # raise self.assertRaises(ValueError, lambda: pt.nastruct(traj, dtype='ndarray'))
def test_picle(self): '''test_picle ''' pt.to_pickle(self.traj.top, 'new_top.pk') new_top = pt.read_pickle('new_top.pk') assert_equal_topology(self.traj.top, new_top, self.traj)
def test_pickle_datasetlist(self): traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top')) dslist = pt.multidihedral(traj) pt.to_pickle(dslist, 'ds.pk') dslist2 = pt.read_pickle('ds.pk') aa_eq(dslist.values, dslist2.values)
def test_picle(self): '''test_picle ''' pt.to_pickle(self.traj.top, 'output/new_top.pk') new_top = pt.read_pickle('output/new_top.pk') assert_equal_topology(self.traj.top, new_top, self.traj)
def test_pickle_datasetlist(self): traj = pt.iterload("data/Tc5b.x", "data/Tc5b.top") dslist = pt.multidihedral(traj) pt.to_pickle(dslist, 'output/ds.pk') dslist2 = pt.read_pickle('output/ds.pk') aa_eq(dslist.values, dslist2.values)
def test_pickle_datasetlist(self): traj = pt.iterload("data/Tc5b.x", "data/Tc5b.top") dslist = pt.multidihedral(traj) pt.to_pickle(dslist, 'output/ds.pk') dslist2 = pt.read_pickle('output/ds.pk') aa_eq(dslist.values, dslist2.values)