def main_user_coordinates(filename,delta_t,arguments):
#arguments will be a nested list with the desired coordinates.
workfile = tools.readfile(filename)
geoms = tools.trajectory_extractor(filename)
internals = [ check_internal(geoms,argument) for argument in arguments ]
coordinates = zip(*internals)
times_all = tools.times(workfile ,delta_t)[0]
times_hop = tools.times(workfile ,delta_t)[1]
time_internals = zip(times_all,coordinates)
inds = [times_all.index(i) for i in times_hop]
time_internals_hop = [time_internals[j] for j in inds]
return (time_internals , time_internals_hop)
def getgeoms(filename):
g = tools.trajectory_extractor(filename)
return g
