def center_frac_coords(frac_crds, parm, s, e):
coords = frac_crds[s:e, :]
masses = parm.parm_data['MASS'][s:e]
com = raf.COM(coords, masses)
shift = array([0.5, 0.5, 0.5]) - com
cntred_frac_crds = frac_crds + shift
return cntred_frac_crds
def get_origin_translation(asu_prmtop_file_name, asu_rst7_file_name):
rst7 = raf.rst7(asu_rst7_file_name)
coords = rst7.Get_Coords()
UCbox = rst7.Get_Box()
u, invu = raf.CompXfrm(UCbox)
masses = raf.prmtop(asu_prmtop_file_name).Get_Masses()
com = raf.COM(coords, masses)
frac_com = dot(u, com)
origin_translation = array([0.5, 0.5, 0.5]) - frac_com
return u, origin_translation
