af_analysis

• af_analysis package
  • Submodules
  • af_analysis.data module
    • Data
      • Data.add_fasta()
      • Data.add_json()
      • Data.add_pdb()
      • Data.count_msa_seq()
      • Data.export_csv()
      • Data.extract_data()
      • Data.extract_fields()
      • Data.get_plddt()
      • Data.import_csv()
      • Data.keep_last_recycle()
      • Data.plot_maxscore_as_col()
      • Data.plot_msa()
      • Data.plot_pae()
      • Data.plot_plddt()
      • Data.read_directory()
      • Data.set_chain_length()
      • Data.show_3d()
      • Data.show_plot_info()
    • concat_data()
    • read_multiple_alphapulldown()
  • af_analysis.plot module
    • plot_msa_v2()
    • show_info()
  • af_analysis.sequence module
    • convert_aa_msa()
    • parse_a3m()
  • af_analysis.docking module
    • LIS_pep()
    • cLIS_lig()
    • iLIS_lig()
    • ipSAE_lig()
    • ipTM_between_chains()
    • ipTM_d0_interface_lig()
    • ipTM_d0_lig()
    • pae_contact_pep()
    • pae_pep()
    • pdockq2_lig()
    • plddt_contact_pep()
    • plddt_pep()
  • af_analysis.analysis module
    • LIS_matrix()
    • PAE_matrix()
    • cLIS_matrix()
    • chain_plddt()
    • compute_LIS_matrix()
    • compute_cLIS_matrix()
    • compute_dockq()
    • compute_ftdmp()
    • compute_ipSAE_matrix()
    • compute_iptm_d0_interface_values()
    • compute_iptm_d0_values()
    • compute_pdockQ()
    • compute_pdockQ2()
    • extract_fields_file()
    • extract_ftdmp()
    • extract_pae_json()
    • extract_pae_npy()
    • extract_pae_npz()
    • extract_pae_pkl()
    • get_pae()
    • inter_chain_pae()
    • ipSAE()
    • ipTM_d0()
    • ipTM_d0_interface()
    • iplddt()
    • mpdockq()
    • pdockq()
    • pdockq2()
    • read_ftdmp_raw_score()
  • af_analysis.format module
    • af_analysis.format package
      • af_analysis.format.af3_webserver module
      • af_analysis.format.afpulldown module
      • af_analysis.format.colabfold_1_5 module
      • af_analysis.format.default module