Welcome to AlphaFold Analysis’s documentation!

af_analysis is a python library designed to facilitate analysis of AlphaFold results.

Getting Started

• About
  • About Alphafold Analysis
    • Statement of Need
    • Main features
    • Installation
      • Optional GUI (Flask)
    • Conda environment
    • Documentation
    • Usage
      • Importing data
      • Analysis
      • Docking Analysis
      • Plots
    • GUI
    • Dependencies
    • Contributing
    • Authors
    • Release a new package version - Only for maintainers
    • Citing this work
    • License
  • References
    • TODO
• Installation Quick Start
  • Through Pypi
  • Get sources from the GithubRepo
  • Install af_analysis
  • Test the installation

User Guide

• User Guide
  • Importing Alphafold Data
    • Supported formats
    • Importing procedure
    • Merge Data objects
  • Scores
    • pDockq
    • pDockq2
    • LIS Score
    • actifpTM and chain ipTM
  • Protein-Protein and Protein-Peptide Docking
  • Plots
    • Interactive Visualization
    • MSA Plot
    • pLDDT Plot
    • PAE Plot
  • 3D Structure Visualization
  • Clustering
  • Custom Analysis functions
  • FTDMP Scores
  • Citing this work
  • References
• Basic Example
  • Importing packages
  • Importing Alphafold Data
  • Analysing scores
    • Plots
    • show 3D structure
  • Computing scores
  • Clustering
  • Multidimensional scaling representation
• Graphical User Interface (GUI)
  • Overview
  • Main Interface
  • Typical Workflow
  • Supported Inputs
  • GUI Features
    • Dataset table
    • Structure viewer
    • Plots
    • Computed metrics
    • Clustering
  • Command-Line Usage
  • HTTP API
  • API Reference
    • af_analysis_gui package
    • CLI entry point
    • Flask application entry point

Development

• Contributing to AF-Analysis
  • Table of Contents
  • Code of Conduct
  • Getting Started
  • How Can I Contribute?
  • Style Guide
  • Pull Requests
  • Issue Tracking
  • Any questions?
• Github Repository

API Reference

• af_analysis
  • af_analysis package
    • Submodules
    • af_analysis.data module
      • Data
      • 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

Indices and tables

• Index

• Module Index

• Search Page