schrodinger.application.bioluminate.patch_utils.msurfext module

schrodinger.application.bioluminate.patch_utils.msurfext.erf_then_divide(x, constant)

smoothing function based on error function.


charge smoothing routine. By default, we allow the charge to be visible over 10 Angstroms. Other distances may require some adjustments of the constants being used.

schrodinger.application.bioluminate.patch_utils.msurfext.lipo_smoothing(distances, rcut=5.0)

calculates the lipophilicity field along an exponential function on the basis of a distance cutoff

schrodinger.application.bioluminate.patch_utils.msurfext.smooth_grid_values(vertex_positions, atom_positions, atom_values, smooth_func='ele', rcutoff=10.0, verbose=False)

core function to smooth the surface grid values according to partial charge (‘ele’) or hydrophobicity (‘lipo’).

  • vertex_positions (np.array) – vertex positions (x,y,z) for each input value

  • atom_positions (tuple) – atom positions, same format

  • atom_values (tuple) – atom values

  • smooth_func – smoothing function (valid entries are ‘lipo’, ‘ele’)

  • rcutoff – distance cutoff for smooth_func