Two new methods of computer simulation of synchrotron radiation nanofocusing with planar compound refractive lenses (PCRLs) are presented. The methods are based on the results of analytical theory. In contrast to previous works, the new methods take into account the PCRL aperture. It is especially important at high photon energies, when absorption is low and the calculations based on analytical theory, i.e. without taking into account the aperture, give incorrect results. A computer program was created and specific results were obtained for a silicon PCRL having an aperture of 50 µm, element length of 102 µm and minimum thickness of 2 µm. For an energy of 50 keV and number of elements 300, it focuses the beam to 31 nm size at a distance of one and a half times its length. Analysis of the calculation accuracy for the proposed methods is performed, as well as a demonstration of the capabilities of the computer program.