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))