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])