def make_contact_frequency(self, trajectory):
"""Convenience for making a ContactFrequency object.
"""
return ContactFrequency(trajectory=trajectory_to_mdtraj(trajectory),
query=self.query,
haystack=self.haystack,
cutoff=self.cutoff)
def _eval(self, items):
trajectory = paths.Trajectory(items)
# create an mdtraj trajectory out of it
ptraj = trajectory_to_mdtraj(trajectory, self.topology.mdtraj)
# run the featurizer
return self._instance.partial_transform(ptraj)
def _eval(self, items):
trajectory = peng.Trajectory(items)
# create an mdtraj trajectory out of it
ptraj = trajectory_to_mdtraj(trajectory, self.topology.mdtraj)
# run the featurizer
return self._instance.partial_transform(ptraj)
def test_trajectory_mdtraj_round_trip(self):
# first test that the ops trajectory works
nptest.assert_allclose(self.ops_trajectory.xyz, self.md_trajectory.xyz)
nptest.assert_allclose(self.ops_trajectory.box_vectors, self.md_trajectory.unitcell_vectors)
# switch back to mdtraj
md_trajectory_2 = trajectory_to_mdtraj(self.ops_trajectory, self.md_topology)
nptest.assert_allclose(self.md_trajectory.xyz, md_trajectory_2.xyz)
nptest.assert_allclose(self.md_trajectory.unitcell_vectors, md_trajectory_2.unitcell_vectors)
def test_trajectory_mdtraj_round_trip(self):
# first test that the ops trajectory works
nptest.assert_allclose(self.ops_trajectory.xyz, self.md_trajectory.xyz)
nptest.assert_allclose(self.ops_trajectory.box_vectors,
self.md_trajectory.unitcell_vectors)
# switch back to mdtraj
md_trajectory_2 = trajectory_to_mdtraj(self.ops_trajectory,
self.md_topology)
nptest.assert_allclose(self.md_trajectory.xyz, md_trajectory_2.xyz)
nptest.assert_allclose(self.md_trajectory.unitcell_vectors,
md_trajectory_2.unitcell_vectors)
def _check_one_side(self, trajectory, direction, cache=None):
if len(trajectory) < self.n_frames:
return False
traj = trajectory_to_mdtraj(trajectory=trajectory,
md_topology=self.md_topology)
if not cache:
subtraj = self.subtraj_for_direction(trajectory, direction)
contacts = self.make_contact_frequency(subtraj)
else:
contacts = cache.updated_contact_frequency(trajectory, direction)
most_common = \
contacts.residue_contacts.most_common()[:self.n_contacts]
return (len(most_common) >= self.n_contacts
and most_common[-1][1] >= self.frequency)
def _eval(self, items):
trajectory = paths.Trajectory(items)
t = trajectory_to_mdtraj(trajectory, self.topology.mdtraj)
return self._instance.transform(t)
def _eval(self, items):
trajectory = paths.Trajectory(items)
t = trajectory_to_mdtraj(trajectory, self.topology.mdtraj)
return self.cv_callable(t, **self.kwargs)
def _eval(self, items):
trajectory = peng.Trajectory(items)
t = trajectory_to_mdtraj(trajectory, self.topology.mdtraj)
return self._instance.transform(t)
def _eval(self, items):
trajectory = peng.Trajectory(items)
t = trajectory_to_mdtraj(trajectory, self.topology.mdtraj)
return self.cv_callable(t, **self.kwargs)
def test_trajectory_to_mdtraj_other_input(self):
snap = self.ops_trajectory[0]
md1 = trajectory_to_mdtraj(snap)
md2 = trajectory_to_mdtraj([snap])
assert_equal(md1, md2)
def test_trajectory_to_mdtraj_other_input(self):
snap = self.ops_trajectory[0]
md1 = trajectory_to_mdtraj(snap)
md2 = trajectory_to_mdtraj([snap])
assert_equal(md1, md2)