AlphaFold Analysis
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User Guide
User Guide
Basic Example
Graphical User Interface (GUI)
Development
Contributing to AF-Analysis
Github Repository
API Reference
af_analysis
AlphaFold Analysis
Index
Index
A
|
C
|
D
|
E
|
G
|
I
|
K
|
L
|
M
|
P
|
R
|
S
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)