def exercise(): lysozyme = """KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL""" homologs = rcsb_web_services.sequence_search(lysozyme, d_max=2.0) assert (len(homologs) > 500) atp_binding = rcsb_web_services.chemical_id_search("ATP", protein_only=True) assert (len(atp_binding) > 650) report = rcsb_web_services.get_high_resolution_for_structures(atp_binding) assert (len(report) == len(atp_binding)) and (len(report[0]) == 2) # print (report) report = rcsb_web_services.get_high_resolution_and_residue_count_for_structures( atp_binding) assert (len(report) == len(atp_binding)) and (len(report[0]) == 3) # print (report) ligand_info = rcsb_web_services.get_ligand_info_for_structures(['1mru']) # print (ligand_info) assert ligand_info == [ ['1MRU', 'A', 'MG', 24.305, 'Mg', 'MAGNESIUM ION', '[Mg++]'], ['1MRU', 'B', 'MG', 24.305, 'Mg', 'MAGNESIUM ION', '[Mg++]'], [ '1MRU', 'A', 'AGS', 523.247, 'C10 H16 N5 O12 P3 S', 'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER', 'Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[CH](O)[CH]3O' ], [ '1MRU', 'B', 'AGS', 523.247, 'C10 H16 N5 O12 P3 S', 'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER', 'Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[CH](O)[CH]3O' ] ]
def exercise () : from mmtbx.wwpdb import rcsb_web_services lysozyme = """KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL""" homologs = rcsb_web_services.sequence_search(lysozyme, d_max=2.0) assert (len(homologs) > 500) atp_binding = rcsb_web_services.chemical_id_search("ATP", protein_only=True) assert (len(atp_binding) > 650) report = rcsb_web_services.get_high_resolution_for_structures(atp_binding) assert (len(report) == len(atp_binding)) and (len(report[0]) == 2) ligand_info = rcsb_web_services.get_ligand_info_for_structures(['1mru']) assert (len(ligand_info) == 4) print "OK"
def exercise () : from mmtbx.wwpdb import rcsb_web_services lysozyme = """KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL""" homologs = rcsb_web_services.sequence_search(lysozyme, d_max=2.0) assert (len(homologs) > 500) atp_binding = rcsb_web_services.chemical_id_search("ATP", protein_only=True) assert (len(atp_binding) > 650) report = rcsb_web_services.get_high_resolution_for_structures(atp_binding) assert (len(report) == len(atp_binding)) and (len(report[0]) == 2) ligand_info = rcsb_web_services.get_ligand_info_for_structures(['1mru']) assert (len(ligand_info) == 4) assert (ligand_info[1][-1] == u'[Mg+2]') print "OK"