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)