Overview

This script serves as a controller to automate the mutation and analysis of a protein structure using multiple supporting Python scripts:

• mutintro.py - Introduces mutations into the provided PDB file.
• contacts.py - Analyzes residue contacts in the mutated PDB structure.
• foldxana.py - Evaluates the energetic effects of mutations using FoldX.

The script reads user-provided input through command-line arguments, processes the mutation data, and orchestrates the execution of the analysis pipeline.

Usage

python main_script.py --pdb_file path/to/input.pdb --output_dir path/to/output --mutations path/to/mutations.csv --mode single

Arguments

• --pdb_file (required): Path to the input PDB file that the mutations will be introduced into.
• --output_dir (required): Path to the directory where the variant PDB systems will be saved.
• --mutations (required): Path to a CSV file containing a list of mutations.
• --mode (optional): Mutation introduction mode.
  • single (default): Introduces mutations one at a time.
  • multiple: Introduces multiple mutations at once.

Workflow

1. The script captures the current working directory with os.getcwd().
2. Command-line arguments are parsed using argparse.
3. The script calls three external Python scripts sequentially using os.system():
   1. mutintro.py: Introduces mutations.
   2. contacts.py: Analyzes contacts between residues post-mutation.
   3. foldxana.py: Performs energetic evaluation of the mutated structures.

Example

To run the script in single mutation mode:

python main_script.py --pdb_file 1abc.pdb --output_dir ./output --mutations mutations.csv

To run in multiple mutation mode:

python main_script.py --pdb_file 1abc.pdb --output_dir ./output --mutations mutations.csv --mode multiple

Dependencies

• Python 3.x
• argparse
• os (standard library)
• External scripts: mutintro.py, contacts.py, foldxana.py

Notes

• Ensure that the supporting scripts are in the same directory or accessible via PATH.
• The mutation CSV file should follow the expected format required by mutintro.py.
• Consider replacing os.system() with subprocess.run() for better error handling and security. For example:

  import subprocess
      subprocess.run(["python", "mutintro.py", "--arg1", "value1"], check=True)

Prerequisites

• Ensure Python 3.x is installed and added to your system PATH.
• Install any required Python libraries using pip install.
• Verify that the external scripts (mutintro.py, contacts.py, foldxana.py) are present in the working directory.

Error Handling

To improve error handling, consider implementing logging and exception handling in your script. For example:

import logging

    logging.basicConfig(level=logging.INFO, format='%(asctime)s - %(levelname)s - %(message)s')

    try:
        subprocess.run(["python", "mutintro.py", "--arg1", "value1"], check=True)
    except subprocess.CalledProcessError as e:
        logging.error(f"Error occurred: {e}")
        exit(1)