Welcome to the official documentation for AlphaFragment, a Python package designed to optimally fragment proteins and streamline the preparation of protein data for structure prediction.

• Introduction
  • AlphaFragment: Protein Fragmentation and Pair Generation for AlphaFold and AlphaPulldown
  • Features
  • Getting Started
• Installation
  • Requirements
  • Installation from Source
  • Verifying Installation
  • Troubleshooting
• Usage Guide
  • Workflow

Detailed function documentation

• Custom classes
  • Domain
  • Protein
  • ProteinSubsection
• Handling protein objects and domains in a csv file
  • domains_from_manual_pae()
  • find_user_specified_domains()
  • fragments_from_csv()
  • initialize_proteins_from_csv()
  • reinitialize_proteins_from_csv()
  • update_csv_with_fragments()
• Identifying protein domains using AlphaFoldDB
  • find_domain_by_res()
  • find_domains_from_pae()
  • read_afdb_json()
• Handling data from UniProt
  • fetch_uniprot_info()
  • find_uniprot_domains()
• Compiling domains from various sources
  • compile_domains()
• Utility functions for protein fragmentation
  • break_in_half()
  • check_valid_cutpoint()
  • find_next_start()
  • merge_overlapping_domains()
  • recursive_fragmentation()
  • validate_fragmentation_parameters()
• Dealing with long domains
  • handle_long_domains()
• Protein fragmentation
  • fragment_protein()
• Plotting fragmentation output
  • calculate_tick_freq()
  • draw_label()
  • plot_domain()
  • plot_fragment()
  • plot_fragmentation_output()
• Creating input files for AlphaFold or AlphaPulldown
  • get_protein_combinations()
  • output_fastas()
  • output_pulldown()

Indices and Tables

• Index

• Module Index

• Search Page