def get_traj(self, file_input):
""" Read and store the trajectory
:param file_input: binary file read by Konrad Hinsen's package
GromacsTrajectory
"""
traj = XTCTrajectory(file_input)
while traj.readStep():
f = Frame()
f.create_frame(traj.coordinates,
traj.frame_counter,
traj.natoms,
traj.step,
traj.time)
self.frame.append(f)
from GromacsTrajectory import XTCTrajectory
t = XTCTrajectory("trajectory.xtc")
while t.readStep():
print "Frame number ", t.frame_counter
print "Simulation step ", t.step
print "Time %f ps" % t.time
print "Box vectors (nm):"
print t.box
print "Coordinates of the first five atoms (nm):"
print t.coordinates[:5]
print
