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Update to prepare data using RNA graphs generated by RNAglib #5
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Thank you for this @jgcarvajalp ! Would you be able to include a small step by step guide with this PR for what steps should be taken now to prepare the data? |
if __name__ == "__main__":
pdb_path = os.path.join("../data/cif_files") # path to cif files
process_all(pdb_path, "../data/lig_dict.p")
if __name__ == "__main__":
d = pickle.load(open('../data/lig_dict.p', 'rb'))
c = 10
conc = .6
ligs = get_valids(d, c, conc, min_size=4)
pickle.dump(ligs, open("../data/lig_dict_filter.p", "wb"))
if __name__ == "__main__":
get_binding_site_graphs_all('../data/lig_dict_filter.p', '../data/pockets_nx', non_binding=False)
annotate_all(parallel=False, graph_path="../data/pockets_nx", dump_path="../data/annotated/pockets_nx_annotated",
ablate=False, mode='fp') |
@jgcarvajalp i am assuming here that the user should run RNAglib separately in order to create the folder that stores the graphs? see: "Line 194: update the path to the folder that contains the RNA graphs" |
@cgoliver Yes. The user should generate the graphs separately. |
Hello, thank you for concluding this data preparation pipeline. But when I follow this pipeline, it seems I had some issues. First, in the second step of getting the lig_dict.p, it only contains the mg ions as the ligand, so I reversed the conditional statement at line 150 in I am wondering if you have encountered similar issues, please let me know if I have done anything wrong during the process. Thank you very much for any advice and help! Best, |
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