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