def test_0(self): if os.path.exists(amberhome): from pytraj.amber_wrapper import minimize traj = pt.iterload("./data/Ala3/Ala3.crd", "./data/Ala3/Ala3.top") t0 = traj[:1] if has_("sander"): print('egb: ', pt.energy_decomposition(t0, igb=8)['gb']) minimize(t0) self.assertRaises(ValueError, lambda: minimize(traj)) if has_("sander"): print('egb: ', pt.energy_decomposition(t0, igb=8)['gb']) # load saved file saved_coords = pt.load("./data/Ala3/min/min.r", traj.top).xyz aa_eq(t0.xyz, saved_coords, decimal=5)
def test_0(self): if os.path.exists(amberhome): from pytraj.amber_wrapper import minimize traj = pt.iterload("./data/Ala3/Ala3.crd", "./data/Ala3/Ala3.top") t0 = traj[:1] if has_("sander"): print('egb: ', pt.energy_decomposition(t0, igb=8)['gb']) minimize(t0) self.assertRaises(ValueError, lambda: minimize(traj)) if has_("sander"): print('egb: ', pt.energy_decomposition(t0, igb=8)['gb']) # load saved file saved_coords = pt.load("./data/Ala3/min/min.r", traj.top).xyz aa_eq(t0.xyz, saved_coords, decimal=5)
def test_0(self): traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top") if has_("numpy"): import numpy as np from numpy.testing import assert_almost_equal arr0 = traj.xyz aa_eq(arr0, traj[:, :, :].xyz) # create Trajectory farray = traj[:] aa_eq(arr0, farray[:, :, :].xyz) else: pass
def test_0(self): traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top") if has_("numpy"): import numpy as np from numpy.testing import assert_almost_equal arr0 = traj.xyz aa_eq(arr0, traj[:, :, :].xyz) # create Trajectory farray = traj[:] aa_eq(arr0, farray[:, :, :].xyz) else: pass
class TestSimpleRMSD(unittest.TestCase): def setUp(self): self.traj = pt.iterload(tc5b_trajin, tc5b_top) def test_fit_and_then_nofit(self): traj = pt.iterload(tc5b_trajin, tc5b_top) t0 = traj[:] pt.superpose(t0, ref=traj[3], mask='@CA') rmsd_0 = pt.rmsd_nofit(traj, ref=traj[3], mask='@CB') rmsd_1 = pt.rmsd(traj, ref=traj[3], mask='@CB', nofit=True) aa_eq(rmsd_1, rmsd_0) def test_rmsd_with_mask(self): TRAJ = pt.iterload(filename=tc5b_trajin, top=tc5b_top) cpptraj_rmsd = np.loadtxt(fn("rmsd_to_firstFrame_CA_allres.Tc5b.dat"), skiprows=1).transpose()[1] f0 = TRAJ[0] arr0 = np.zeros(TRAJ.n_frames) arr1 = np.zeros(TRAJ.n_frames) mask = "@CA" atm = AtomMask(mask) TRAJ.top._set_integer_mask(atm) for i, frame in enumerate(TRAJ): arr0[i] = frame.rmsd(f0, mask=mask, top=TRAJ.top) arr1[i] = frame.rmsd(f0, atommask=atm) arr2 = pt.rmsd(TRAJ, mask=mask, ref=f0) arr3 = pt.rmsd(TRAJ, mask=mask, ref=0) aa_eq(arr0, cpptraj_rmsd, decimal=3) aa_eq(arr1, cpptraj_rmsd, decimal=3) aa_eq(arr2, cpptraj_rmsd, decimal=3) aa_eq(arr3, cpptraj_rmsd, decimal=3) def testsuperpose_alias(self): '''testsuperpose_alias''' t0 = self.traj[:] t1 = self.traj[:] pt.transform(t0, ['superpose']) pt.transform(t1, ['rms']) aa_eq(t0.xyz, t1.xyz) def test_reference_with_different_topology_basic(self): traj1 = pt.iterload(filename=tc5b_trajin, top=tc5b_top) traj2 = pt.iterload(fn('tz2.nc'), fn('tz2.parm7')) # re-establish ActionList dslist = CpptrajDatasetList() dslist.add('reference', name='myref') dslist[0].top = traj2.top dslist[0].add_frame(traj2[0]) actlist = pt.ActionList(['rmsd @1-11 @CB ref myref'], top=traj1.top, dslist=dslist) for frame in traj1: actlist.compute(frame) # raise if ref_mask is given but not mask self.assertRaises(ValueError, lambda: pt.rmsd(traj1, ref=3, ref_mask='@CB')) self.assertRaises( ValueError, lambda: pt.rmsd(traj1, ref=traj2[:1], ref_mask='@CB')) # assert to cpptraj tc5b_traj = traj1[:] tz2_traj = traj2[:1] cm = ''' parm {} [tc5b] trajin {} parm {} [tz2] reference {} parm [tz2] 1 [myref] rms myrmsd ref [myref] @1-10 @11-20 '''.format(tc5b_top, tc5b_trajin, tz2_top, tz2_trajin) print(cm) state = pt.load_cpptraj_state(cm) with tempfolder(): state.run() expected_rmsd = state.data[-1].values rmsd_data = pt.rmsd(tc5b_traj, mask='@1-10', ref=tz2_traj, ref_mask='@11-20') aa_eq(expected_rmsd, rmsd_data) @unittest.skipIf(not has_('mdtraj'), 'does not have mdtraj') def test_ComparetoMDtraj(self): import mdtraj as md traj = pt.load(filename=tc5b_trajin, top=tc5b_top) m_top = md.load_prmtop(tc5b_top) m_traj = md.load_mdcrd(tc5b_trajin, m_top) m_traj.xyz = m_traj.xyz * 10 # convert `nm` to `Angstrom` unit arr0 = pt.rmsd(traj, ref=0) arr1 = pt.rmsd(traj, ref=0) arr2 = pt.rmsd(traj, ) a_md0 = md.rmsd(m_traj, m_traj, 0) aa_eq(arr0, arr1) aa_eq(arr0, arr2) aa_eq(arr0, a_md0) arr0 = pt.rmsd(traj, ref=-1) arr1 = pt.rmsd(traj, ref=-1) a_md = md.rmsd(m_traj, m_traj, -1) aa_eq(arr0, arr1) aa_eq(arr0, a_md) mask = ":3-18@CA,C" atm = traj.top(mask) arr0 = pt.rmsd(traj, ref=-1, mask=mask) arr1 = pt.rmsd(traj, mask=atm.indices, ref=-1) arr2 = pt.rmsd(traj, mask=list(atm.indices), ref=-1) arr3 = pt.rmsd(traj, mask=tuple(atm.indices), ref=-1) a_md = md.rmsd(m_traj, m_traj, -1, atm.indices) aa_eq(arr0, a_md) aa_eq(arr1, a_md) aa_eq(arr2, a_md) aa_eq(arr3, a_md) fa = Trajectory(traj) arr0 = pt.rmsd(fa, ref=-1, mask=mask) arr1 = pt.rmsd(fa, mask=atm.indices, ref=-1) arr2 = pt.rmsd(fa, mask=list(atm.indices), ref=-1) arr3 = pt.rmsd(fa, mask=tuple(atm.indices), ref=-1) a_md = md.rmsd(m_traj, m_traj, -1, atm.indices) aa_eq(arr0, a_md) aa_eq(arr1, a_md) aa_eq(arr2, a_md) aa_eq(arr3, a_md) fa = Trajectory(traj) mask = "!@H=" atm = fa.top(mask) arr0 = pt.rmsd(fa, ref=4, mask=mask) a_md = md.rmsd(m_traj, m_traj, 4, atm.indices) # exclude 0-th frame for ref aa_eq(arr0, a_md) def test_list_of_masks(self): traj = self.traj.copy() mask = ['@CA', '@CB', ':3-18@CA,C'] arr = pt.rmsd(traj, mask=mask) for idx, m in enumerate(mask): aa_eq(arr[idx], pt.rmsd(traj, mask=m)) aa_eq(arr[idx], pt.rmsd(traj, mask=traj.top.select(m))) mask = ['@CA', '@CB', ':3-18@CA,C', [0, 3, 5]] self.assertRaises(ValueError, lambda: pt.rmsd(traj, mask=mask)) mask_2 = [[0, 3, 6], range(50)] aa_eq(pt.rmsd(traj, mask=mask_2)[0], pt.rmsd(traj, mask=mask_2[0])) aa_eq(pt.rmsd(traj, mask=mask_2)[1], pt.rmsd(traj, mask=mask_2[1])) ca = pt.select('@CA', traj.top) cb = pt.select('@CB', traj.top) aa_eq(pt.rmsd(traj, mask=ca), pt.rmsd(traj, mask=[ca, cb])[0]) aa_eq(pt.rmsd(traj, mask=cb), pt.rmsd(traj, mask=[ca, cb])[1]) def test_raise_savematrices_if_not_dataset(self): traj = self.traj.copy() self.assertRaises( ValueError, lambda: pt.rmsd(traj, mask='@CA savematrices', dtype='ndarray')) def test_not_update_coordinates(self): traj = self.traj[:] data = pt.rmsd(traj, ref=3, update_coordinate=False) # make sure coordinates are not updated aa_eq(traj.xyz, self.traj.xyz) # make sure give the same rmsd values aa_eq(pt.rmsd(traj, ref=3), data) def test_combine_nofit_mass_nomod(self): cm = ''' parm {} trajin {} rms @CA nofit mass nomod '''.format(fn('tz2.parm7'), fn('tz2.nc')) state = pt.load_cpptraj_state(cm) state.run() unmut_traj = pt.iterload(fn('tz2.nc'), fn('tz2.parm7')) mut_traj = unmut_traj[:] data = pt.rmsd(mut_traj, mask='@CA', mass=True, nofit=True, update_coordinate=False) aa_eq(data, state.data[-1])