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'][:]))
