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 _eval(self, trajectory): trajectory = peng.Trajectory(trajectory) return self.cv_callable(self, trajectory)
def all(self): return peng.Trajectory(map(self.proxy, range(len(self))))
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 _eval(self, items): trajectory = peng.Trajectory(items) return [self._instance(snap) for snap in trajectory]
def all(self): return peng.Trajectory(map(self.proxy, self.index.list))
def all(self): if self.reference_by_uuid: return peng.Trajectory(map(self.proxy, self.vars['uuid'][:])) else: return peng.Trajectory(map(self.proxy, range(len(self))))
def all(self): return peng.Trajectory(map(self.proxy, self.vars['uuid'][:]))