Index

A

add_fasta() (af_analysis.data.Data method) (in module af_analysis.format.colabfold_1_5) add_json() (af_analysis.data.Data method) (in module af_analysis.format.colabfold_1_5) (in module af_analysis.format.default) add_pdb() (af_analysis.data.Data method) (in module af_analysis.format.colabfold_1_5) af_analysis.analysis module af_analysis.data module af_analysis.docking module

af_analysis.format.af3_webserver module af_analysis.format.afpulldown module af_analysis.format.colabfold_1_5 module af_analysis.format.default module af_analysis.plot module af_analysis.sequence module af_analysis_gui module

C

chain_plddt() (in module af_analysis.analysis) cLIS_lig() (in module af_analysis.docking) cLIS_matrix() (in module af_analysis.analysis) compute_cLIS_matrix() (in module af_analysis.analysis) compute_dockq() (in module af_analysis.analysis) compute_ftdmp() (in module af_analysis.analysis) compute_ipSAE_matrix() (in module af_analysis.analysis)

compute_iptm_d0_interface_values() (in module af_analysis.analysis) compute_iptm_d0_values() (in module af_analysis.analysis) compute_LIS_matrix() (in module af_analysis.analysis) compute_pdockQ() (in module af_analysis.analysis) compute_pdockQ2() (in module af_analysis.analysis) concat_data() (in module af_analysis.data) convert_aa_msa() (in module af_analysis.sequence) count_msa_seq() (af_analysis.data.Data method)

D

Data (class in af_analysis.data)

E

export_csv() (af_analysis.data.Data method) extract_data() (af_analysis.data.Data method) extract_fields() (af_analysis.data.Data method) extract_fields_file() (in module af_analysis.analysis)

extract_ftdmp() (in module af_analysis.analysis) extract_pae_json() (in module af_analysis.analysis) extract_pae_npy() (in module af_analysis.analysis) extract_pae_npz() (in module af_analysis.analysis) extract_pae_pkl() (in module af_analysis.analysis)

G

get_pae() (in module af_analysis.analysis)

get_plddt() (af_analysis.data.Data method)

I

iLIS_lig() (in module af_analysis.docking) import_csv() (af_analysis.data.Data method) inter_chain_pae() (in module af_analysis.analysis) iplddt() (in module af_analysis.analysis) ipSAE() (in module af_analysis.analysis)

ipSAE_lig() (in module af_analysis.docking) ipTM_between_chains() (in module af_analysis.docking) ipTM_d0() (in module af_analysis.analysis) ipTM_d0_interface() (in module af_analysis.analysis) ipTM_d0_interface_lig() (in module af_analysis.docking) ipTM_d0_lig() (in module af_analysis.docking)

K

keep_last_recycle() (af_analysis.data.Data method)

L

LIS_matrix() (in module af_analysis.analysis)

LIS_pep() (in module af_analysis.docking)

M

module af_analysis.analysis af_analysis.data af_analysis.docking af_analysis.format.af3_webserver af_analysis.format.afpulldown af_analysis.format.colabfold_1_5 af_analysis.format.default af_analysis.plot af_analysis.sequence af_analysis_gui

mpdockq() (in module af_analysis.analysis)

P

pae_contact_pep() (in module af_analysis.docking) PAE_matrix() (in module af_analysis.analysis) pae_pep() (in module af_analysis.docking) parse_a3m() (in module af_analysis.sequence) pdockq() (in module af_analysis.analysis) pdockq2() (in module af_analysis.analysis) pdockq2_lig() (in module af_analysis.docking)

plddt_contact_pep() (in module af_analysis.docking) plddt_pep() (in module af_analysis.docking) plot_maxscore_as_col() (af_analysis.data.Data method) plot_msa() (af_analysis.data.Data method) plot_msa_v2() (in module af_analysis.plot) plot_pae() (af_analysis.data.Data method) plot_plddt() (af_analysis.data.Data method)

R

read_dir() (in module af_analysis.format.af3_webserver) (in module af_analysis.format.afpulldown) (in module af_analysis.format.default) read_directory() (af_analysis.data.Data method)

read_ftdmp_raw_score() (in module af_analysis.analysis) read_full_dir() (in module af_analysis.format.afpulldown) read_log() (in module af_analysis.format.colabfold_1_5) read_multiple_alphapulldown() (in module af_analysis.data)

S

set_chain_length() (af_analysis.data.Data method) show_3d() (af_analysis.data.Data method)

show_info() (in module af_analysis.plot) show_plot_info() (af_analysis.data.Data method)