select specific sites for masif_seed_search

[slieped]

I was trying to find an option to select a specific site (not residueID) to run the masif_seach docking algorithm.
I was checking the code at masif_seed_search_nn.py and realized that the conditional block at line 103 is coded to return the specific topN instead of a specific site.

if 'selected_site_ixs' in params:
    site_ixs = params['selected_site_ixs']
    site_vixs = [vix for ix,vix in enumerate(target_vertices) if ix in site_ixs]

Is this the expected outcome? Should the variable params["selected_site_ixs"] in params_peptide.py allow selecting a specific site?
If thats the case, a simple edit in the code as follows should solve it!

site_ixs = [ix for ix,vix in enumerate(params['selected_site_ixs'])]
site_vixs = [vix for vix in params['selected_site_ixs'] if vix in target_vertices]

This will return the desired site, if and only if its part of the TOP_N vertices

Thanks for this amazing tool!
Victor

[viviyanran]

Hello! There are some specific residues in my target protein and I want to match descriptors near these residues. How can I do that? Many thanks!