CoDIAC

Contents:

• Examples
  • Demo of the CoDIAC package - the full pipeline
  • Adjacency file generation
  • Contact mapping
• Dependencies (Examples)
• Installation
  • Pip
  • Tarball
  • Git

Indices and tables

• Index

• Module Index

• Search Page

Overview

An overview of the key aspects of CoDIAC. The modules and pipeline for setting up the reference files. The structure analysis modules that fetch all structure files (whether PDB of AlphaFold) from the reference file, convert to adjacency files of contacts, and allow for region of interest contact analysis between domains (intraprotein) or between a protein and a ligand (interprotein). Additional layers, such as other annotations of proteins and domains PTM and Mutations allow fetching on the reference file of PTMs and mutations within the regions of interest and the Jalview tools allow for the integration of any feature types and calculation of annotation tracks for visualization.

Reference Setup

• UniProt
  • makeRefFile()
  • print_domain_fasta_file()
  • translate_fasta_back()
  • translate_fasta_to_new_headers()
• PDB
  • generateStructureRefFile_fromUniprotFile()
• AlphaFold
  • makeRefFile()
• InterPro
  • appendRefFile()
  • fetch_uniprotids()
• Integrate the Structure and Reference files
  • add_reference_info_to_struct_file()
  • filter_structure_file()

Structure Analysis

• contactMap
  • print_fasta_feature_files()
  • return_interChain_adj()
  • translate_chainMap_to_RefSeq()
• AdjacencyFiles
  • BinaryFeatures()
  • ProcessArpeggio()

Annotation tools

• Mutations
  • OMIM_mutations()
  • PDB_mutations()
  • gnomAD_mutations()
• PTM
  • write_PTM_features()

Jalview and Feature tools

• Jalview Tools
  • combine_feature_files()
  • print_ann_file()
• translateFeatures
  • return_translated_features()