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##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2017 Stanford University and the Authors
#
# Authors: Christoph Klein
# Contributors: Tim Moore
#
# MDTraj is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 2.1
# of the License, or (at your option) any later version.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with MDTraj. If not, see <http://www.gnu.org/licenses/>.
##############################################################################
import numpy as np
import pytest
import mdtraj as md
from mdtraj.geometry import order
from mdtraj.testing import eq
"""The trajectories `2lines.pdb` and `3lines.pdb` contain several frames of,
respectively, 2 and 3 "residues" each consisting of two atoms in different
orientations relative to one another.
`2lines.pdb`
Frame 0: || in x - S2 should be 1.0
Frame 1: || in y - S2 should be 1.0
Frame 2: || in z - S2 should be 1.0
Frame 3: |- in x/y - S2 should be 0.25
Frame 4: |- in y/z - S2 should be 0.25
`3lines.pdb`
Frame 0: ||| in x - S2 should be 1.0
Frame 1: ||| in y - S2 should be 1.0
Frame 2: ||| in z - S2 should be 1.0
Frame 3: at right angles - S2 should be 0.0
"""
# TRAJ1 = md.load(get_fn('1line.pdb'))
# TRAJ2 = md.load(get_fn('2lines.pdb'))
# TRAJ2_LINE1 = TRAJ2.atom_slice((0, 1))
# TRAJ2_LINE2 = TRAJ2.atom_slice((2, 3))
# TRAJ3 = md.load(get_fn('3lines.pdb'))
@pytest.fixture()
def traj1(get_fn):
return md.load(get_fn("1line.pdb"))
@pytest.fixture()
def traj2(get_fn):
return md.load(get_fn("2lines.pdb"))
@pytest.fixture()
def traj3(get_fn):
return md.load(get_fn("3lines.pdb"))
def test_nematic_order(traj2, traj3):
assert eq(
np.array([1.0, 1.0, 1.0, 0.25, 0.25]),
order.compute_nematic_order(traj2),
)
assert eq(
np.array([1.0, 1.0, 1.0, 0.0]),
order.compute_nematic_order(traj3),
)
def test_director(traj2):
traj2_line1 = traj2.atom_slice((0, 1))
traj2_line2 = traj2.atom_slice((2, 3))
directors = order._compute_director(traj2_line1)
assert eq(
directors,
np.array(
[
[1, 0, 0], # Frame 0
[0, 1, 0], # Frame 1
[0, 0, 1], # Frame 2
[1, 0, 0], # Frame 3
[1, 0, 0], # Frame 4
],
),
)
directors = order._compute_director(traj2_line2)
assert eq(
directors,
np.array(
[
[1, 0, 0], # Frame 0
[0, 1, 0], # Frame 1
[0, 0, 1], # Frame 2
[0, 1, 0], # Frame 3
[0, 0, 1], # Frame 4
],
),
)
def test_inertia(traj1, traj2, traj3):
assert eq(
order.compute_inertia_tensor(traj1),
order._compute_inertia_tensor_slow(traj1),
)
assert eq(
order.compute_inertia_tensor(traj2),
order._compute_inertia_tensor_slow(traj2),
)
assert eq(
order.compute_inertia_tensor(traj3),
order._compute_inertia_tensor_slow(traj3),
)
def test_nematic_order_args(traj2):
with pytest.raises(ValueError):
order.compute_nematic_order(traj2, indices="dog")
with pytest.raises(ValueError):
order.compute_nematic_order(traj2, indices="O")
with pytest.raises(ValueError):
order.compute_nematic_order(traj2, indices=1)
# Input indices with wrong "shapes".
with pytest.raises(ValueError):
order.compute_nematic_order(traj2, indices=[[1, [2]], [2]])
with pytest.raises(ValueError):
order.compute_nematic_order(traj2, indices=[1, 2, 3])
def test_order_from_traj(get_fn):
"""Made a perfectly aligned monolayer, should have S2 = 1"""
traj = md.load(get_fn("alkane-monolayer.pdb"))
indices = [list(range(1900 + x, 1900 + x + 36)) for x in range(0, 64 * 36, 36)]
s2 = md.compute_nematic_order(traj, indices=indices)
np.testing.assert_allclose(1.0, s2)
def test_directors_angle_from_traj(get_fn):
"""All chains in example system aligned along z axis"""
traj = md.load(get_fn("alkane-monolayer.pdb"))
# only use the carbons for this calculation since they are excactly aligned
# with the z-axis, and the hydrogens can throw things off just a bit
indices = [list(range(1900 + x, 1900 + x + 30, 3)) for x in range(0, 64 * 36, 36)]
directors = md.compute_directors(traj, indices=indices)
for axis, target_angle in zip(np.eye(3), [90.0, 90.0, 0.0]):
dotproducts = np.tensordot(directors, axis, axes=1)
angles = np.degrees(np.arccos(dotproducts))
angles = np.minimum(angles, 180 - angles) # make vector point in positive z
np.testing.assert_allclose(target_angle, angles, atol=1e-6)
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