def __iter__(self):
from pytraj.analysis.c_action import c_action
# do not import c_action in the top to avoid circular importing
if self.autoimage:
image_act = c_action.Action_AutoImage()
image_act.read_input("", top=self.original_top)
image_act.setup(self.original_top)
if self.rmsfit is not None:
ref, mask_for_rmsfit = self.rmsfit
need_align = True
if self.autoimage:
# need to do autoimage for ref too
# make a copy to avoid changing ref
ref = ref.copy()
image_act.compute(ref)
rmsd_act = c_action.Action_Rmsd()
rmsd_act.read_input(mask_for_rmsfit, top=self.original_top)
rmsd_act.setup(self.original_top)
# creat first frame to trick cpptraj to align to this.
rmsd_act.compute(ref)
else:
need_align = False
ref, mask_for_rmsfit = None, None
if self.mask is not None:
mask = self.mask
atm = self.original_top(mask)
for frame0 in self.frame_iter:
if self.copy:
# use copy for TrajectoryIterator
# so [f for f in traj()] will return a list of different
# frames
frame = frame0.copy()
else:
frame = frame0
if self.autoimage:
# from pytraj.c_action.c_action import Action_AutoImage
# Action_AutoImage()("", frame, self.top)
image_act.compute(frame)
if need_align:
# trick cpptraj to fit to 1st frame (=ref)
rmsd_act.compute(frame)
if self.mask is not None:
frame2 = Frame(frame, atm)
yield frame2
else:
yield frame
def autoimage(self, command=''):
'''perform autoimage
Returns
-------
self
Examples
--------
>>> import pytraj as pt; from pytraj.testing import get_fn
>>> t0 = pt.load(*get_fn('tz2'))
>>> t0.top.has_box()
True
>>> t0 = t0.autoimage()
'''
from pytraj.analysis.c_action import c_action
act = c_action.Action_AutoImage()
act(command, self, top=self.top)
return self