npxxy_residues = convert_list_to_resobject_list([("P", r) for r in range(255,260)]) #dry_network_residues = convert_list_to_resobject_list([("P", r) for r in [165, 279, 252]]) #triad_residues = convert_list_to_resobject_list([("P", r) for r in [289, 244, 155]]) #tm6_tm3_residues_new = convert_list_to_resobject_list([("P", 277), ("P", 339)]) tm6_packing_residues = convert_list_to_resobject_list([("P", r) for r in range(206, 216)]) tm3_packing_residues = convert_list_to_resobject_list([("P", r) for r in range(95, 106)]) tm7_packing_residues = convert_list_to_resobject_list([("P", r) for r in range(250, 260)]) tm5_packing_residues = convert_list_to_resobject_list([("P", r) for r in range(181, 193)]) cutoff = .66 feature_name = "all_residues_5f8u_hom_under_cutoff%dA" %(int(10*cutoff)) #eature_name = "protein_ligand_atom_contacts" feature_name_residues_dict = {} feature_name_residues_dict["rmsd_npxxy_inactive"] = npxxy_residues feature_name_residues_dict["rmsd_npxxy_active"] = npxxy_residues feature_name_residues_dict["tm6_tm3_packing"] = [tm3_packing_residues, tm6_packing_residues] feature_name_residues_dict["tm6_tm7_packing"] = [tm7_packing_residues, tm6_packing_residues] feature_name_residues_dict["tm6_tm5_packing"] = [tm5_packing_residues, tm6_packing_residues] common_residues_pkl = get_common_residues_pkl(base) contact_residues = find_common_residues([inactive_dir, active_dir, simulation_structure], common_residues_pkl) #ligand_residue = Residue(resSeq = 900, chain_id = "L", res_name = "LIG") #contact_residues += [ligand_residue]
#CHOOSE RESIDUES: all_residues = list(range(29, 340)) bp_residues = convert_list_to_resobject_list([("A", r) for r in bp_residues]) tm6_tm3_residues = convert_list_to_resobject_list([("A", 279), ("A", 165)]) print("tm6_tm3_residues") print(tm6_tm3_residues) npxxy_residues = convert_list_to_resobject_list([("A", r) for r in range(332, 337)]) npxxy_edf3_residues = list(range(332, 337)) + [285, 252, 158] npxxy_edf3 = convert_list_to_resobject_list([("A", r) for r in npxxy_edf3_residues]) connector_residues = convert_list_to_resobject_list([("A", 165), ("A", 252)]) triad_residues = convert_list_to_resobject_list([("A", 289), ("A", 244), ("A", 155)]) feature_name = "all_residues_4dkl_5c1m_under_cutoff%dnm" % (int(cutoff)) feature_name_residues_dict = {} feature_name_residues_dict["tm6_tm3_dist"] = tm6_tm3_residues feature_name_residues_dict["rmsd_npxxy_active"] = npxxy_residues feature_name_residues_dict["rmsd_npxxy_inactive"] = npxxy_residues contact_residues = find_common_residues( [inactive_dir, active_dir, mor_active_apo_crystalwaters_protein], get_common_residues_pkl(base))