schrodinger.application.bioluminate.epitope.utils.esc_utils module

schrodinger.application.bioluminate.epitope.utils.esc_utils.safe_mkdir(dir, overwrite=False)

schrodinger.application.bioluminate.epitope.utils.esc_utils.gen_file_list(dir)

schrodinger.application.bioluminate.epitope.utils.esc_utils.gen_names(dir)

schrodinger.application.bioluminate.epitope.utils.esc_utils.gen_faux_epitopes(fab_dir, faux_epi_dir, overwrite=False)

Wrapper function for step 1 - Generate faux epitope

schrodinger.application.bioluminate.epitope.utils.esc_utils.extract_binding_sites(fab_dir, faux_epi_dir, if_dir, overwrite=False)

Wrapper function for step 2 - Generate MIFs

schrodinger.application.bioluminate.epitope.utils.esc_utils.gen_sim_mat(SCHRODINGER, fab_dir, if_dir)

Compute the pairwise similarity matrix between binding sites using Phase Shape approach. Compare all i,j pairs of MIFs in the if_dir.

schrodinger.application.bioluminate.epitope.utils.esc_utils.plot_sim_mat(data, IDs, plot_title, cmap, plot_width, plot_height, dpi)

schrodinger.application.bioluminate.epitope.utils.esc_utils.save_sym_mat_csv(mat, IDs, name)

schrodinger.application.bioluminate.epitope.utils.esc_utils.sim2dist(S)

Convert the simularity matrix S in to a symmetric distance matrix D

schrodinger.application.bioluminate.epitope.utils.esc_utils.cond_1d_dist_mat(D, triag)

Convert the fully symmetric distance matrix into a condensed 1D distance matrix triag = ‘upper’ or ‘lower’, specifying whether the upper or lower triangle to use to compute the