SCOPe/CATH domain creation pipeline

This pipeline processes SCOPe and CATH domain files, extracts relevant domain, chain and residue information, downloads associated PDB files, and generates PDB files by domain.

Features

1. Domain File Processing:

   • Extracts information from SCOPe or CATH domain files.
   • Creates TSV files containing details of domains, chains, and residues.

2. Automated PDB File Downloading:

   • Identifies the necessary PDB files.
   • Parallel downloading of PDB files from the PDB database.

3. PDB File Generation by Domain:

   • Extracts specific chains and residues for each domain.
   • Creates PDB files for each identified domain.

Prerequisites

• Python 3.8 or higher
• Standard Python modules (re, logging, sys, os, csv, multiprocessing)
• aria2c download tool for downloading PDB files

Installation

Clone the repository and navigate to the project folder:

git clone https://your-repo.git
cd your-repo

Usage

The main script to run the entire pipeline is allPipeline.sh. It manages all steps, from initial domain file processing to generating PDB files by domain.

Basic Command

bash allPipeline.sh <domainFile> <SCOPEorCATH> <outputDir> <nbCPUs>

Arguments

• <domainFile>: Path to the SCOPe or CATH domain file to be processed.
• <SCOPEorCATH>: Specify "SCOPE" to process a SCOPe file or "CATH" to process a CATH file.
• <outputDir>: Output directory where all generated files will be stored.
• <nbCPUs>: Number of CPU cores to use for parallel processing.

Usage Example

See runTest.sh and the test folder.

Domains not processed

Certain domains may not be processed due to the following reasons:

• The corresponding PDB file is available only as a CIF file, not a PDB file.
• The PDB ID is obsolete and no longer available in the PDB database.
• The positions extracted from the domain files (SCOPe or CATH) are unusual or do not match expected formats.
• The specified positions or chains do not exist within the PDB file.

Domains affected by the first two reasons will be logged in pdb_notDownloaded.log, while those affected by the latter two reasons will be logged in unprocessed_domains.log located in the output directory. This allows for easy identification and further investigation of any issues encountered during processing.