def test_2(self):
traj = pt.iterload(fn('Tc5b.nat.crd'), fn('Tc5b.top'))
t0 = traj[:1]
pt.set_dihedral(t0, resid='4', dihedral_type='phi', deg=120)
dih = pt.calc_phi(t0, resrange='4').values[0]
assert abs(dih - 120) < 1E-3
t0.save('test.pdb', options='model', overwrite=True)
def test_2(self):
traj = pt.iterload("./data/Tc5b.nat.crd", "./data/Tc5b.top")
t0 = traj[:1]
pt.set_dihedral(t0, resid='4', dihedral_type='phi', deg=120)
dih = pt.calc_phi(t0, resrange='4').values[0]
assert abs(dih - 120) < 1E-3
t0.save('test.pdb', options='model', overwrite=True)
def test_1(self):
dslist0 = pt.calc_phi(traj)
dslist1 = pt.calc_psi(traj)
dslist2 = pt.search_hbonds(traj)
self.assertRaises(KeyError, lambda: stack((dslist0, dslist1)))
self.assertRaises(TypeError, lambda: stack((dslist0, dslist2)))
stack((dslist0 for _ in range(3)))
def test_1(self):
dslist0 = pt.calc_phi(traj)
dslist1 = pt.calc_psi(traj)
dslist2 = pt.search_hbonds(traj)
self.assertRaises(KeyError, lambda: stack((dslist0, dslist1)))
self.assertRaises(TypeError, lambda: stack((dslist0, dslist2)))
stack((dslist0 for _ in range(3)))
def test_1(self):
dslist0 = pt.calc_phi(traj)
dslist1 = pt.calc_psi(traj)
dslist2 = pt.search_hbonds(traj)
with pytest.raises(KeyError):
stack((dslist0, dslist1))
with pytest.raises(TypeError):
stack((dslist0, dslist2))
stack((dslist0 for _ in range(3)))
def test_0(self):
traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top")
# convert to mutable traj
t0 = traj[:1]
for deg in range(-170, 170, 10):
pt.rotate_dihedral(t0, "custom:3:phi:" + str(deg))
_deg = pt.calc_phi(t0, '3', dtype='ndarray')[0]
dih = pt.dihedral(t0, ':2@C :3@N :3@CA :3@C')[0]
aa_eq(deg, _deg)
aa_eq(deg, dih)
aa_eq(pt.calc_psi(traj[:1]).values, pt.calc_psi(t0).values)
def test_0(self):
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
# convert to mutable traj
t0 = traj[:1]
for deg in range(-170, 170, 10):
pt.rotate_dihedral(t0, "custom:3:phi:" + str(deg))
_deg = pt.calc_phi(t0, '3', dtype='ndarray')[0]
dih = pt.dihedral(t0, ':2@C :3@N :3@CA :3@C')[0]
aa_eq(deg, _deg)
aa_eq(deg, dih)
aa_eq(pt.calc_psi(traj[:1]).values, pt.calc_psi(t0).values)
def test_1(self):
# different from test_0 a bit in `mask`
traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top")
# convert to mutable traj
t0 = traj[:1]
for deg in range(-170, 170, 10):
pt.rotate_dihedral(t0, "3:phi:" + str(deg))
_deg = pt.calc_phi(t0, '3', dtype='ndarray')[0]
dih = pt.dihedral(t0, ':2@C :3@N :3@CA :3@C')[0]
aa_eq(deg, _deg)
aa_eq(deg, dih)
aa_eq(pt.calc_psi(traj[:1]).values, pt.calc_psi(t0).values)
def test_autoimage_rotatedihedral(self):
traj = pt.iterload(fn('tz2.ortho.nc'), fn('tz2.ortho.parm7'))
farray = traj[:]
t0trajectory = pt.Trajectory(traj)
aa_eq(farray.unitcells, t0trajectory.unitcells)
# autoimage
farray.autoimage()
t0trajectory.autoimage()
aa_eq(farray.xyz, t0trajectory.xyz)
# rotate_dihedral
pt.rotate_dihedral(t0trajectory, '3:phi:120')
pt.rotate_dihedral(farray, '3:phi:120')
aa_eq(farray.xyz, t0trajectory.xyz)
aa_eq(
pt.calc_phi(t0trajectory, '3').values,
[120 for _ in range(t0trajectory.n_frames)])
def test_autoimage_rotatedihedral(self):
traj = pt.iterload("./data/tz2.ortho.nc", "./data/tz2.ortho.parm7")
farray = traj[:]
t0trajectory = pt.Trajectory(traj)
aa_eq(farray.unitcells, t0trajectory.unitcells)
# autoimage
farray.autoimage()
t0trajectory.autoimage()
aa_eq(farray.xyz, t0trajectory.xyz)
# rotate_dihedral
pt.rotate_dihedral(t0trajectory, '3:phi:120')
pt.rotate_dihedral(farray, '3:phi:120')
aa_eq(farray.xyz, t0trajectory.xyz)
aa_eq(
pt.calc_phi(t0trajectory, '3').values,
[120 for _ in range(t0trajectory.n_frames)])
import pytraj as pt
# use iterload for memory saving
traj = pt.iterload("../tests/data/Tc5b.x", "../tests/data/Tc5b.top")
# calculate phi residue 3
dset = pt.calc_phi(traj, resrange='3-7')
# calcuate autocorrelation function for 1st dataset
af = pt.acorr(dset[0])
print(af)