PDB Structure Cleaning and Preprocessing Script

This Python script provides a simple automated approach for cleaning and preprocessing PDB files using Biopython. It allows users to remove water molecules, specific heteroatoms, and non-standard residues, ensuring that the resulting structures are clean and standardized for downstream computational analyses like molecular dynamics (MD) simulations, docking, or structural analysis.

Features

• Remove Water Molecules: Option to remove all water molecules (HOH, WAT) from the PDB structure.
• Selective Heteroatom Removal: Remove specified heteroatoms (e.g., PO4, SO4) by providing their residue names.
• Keep Only Protein Residues: Retains only standard amino acids and common protonation variants, removing all non-protein residues.
• Flexible Usage: Users can apply different cleaning operations based on their specific requirements.

Here’s a refined version with improved wording and clarity:

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Using Docker: How to Use the Docker Image

Build the Docker Image

Clone this repository and navigate to the directory containing the Dockerfile. Build the Docker image with the following command:

docker build -t pdb_cleaner .

Run the Docker Container

Navigate to the directory containing your input PDB files. Use the following command to run the script:

docker run --rm -v "$(pwd):/data" -t pdb_cleaner -i /data/input.pdb -o /data/output.pdb

• Replace input.pdb and output.pdb with the names of your input and output PDB files, respectively.
• The --rm flag ensures the container is removed after execution.
• The -v "$(pwd):/data" mounts the current directory to /data inside the container.

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Using Python: How to Use the Script

Requirements

• Python 3.6 or newer
• Biopython

Installing Biopython

Install Biopython using one of the following methods:

• Using pip:

  pip install biopython

• Using conda:

  conda install -c conda-forge biopython

Running the Script

Run the script directly with Python:

python pdb_processor.py -i <input_pdb_file> -o <output_pdb_file> [options]

• Replace <input_pdb_file> and <output_pdb_file> with the names of your input and output PDB files, respectively.

Command-line Arguments

Argument	Description
-i, --input	Path to the input PDB file (required).
-o, --output	Path to save the cleaned PDB file (required).
-r, --hetatm	List of heteroatoms to remove (e.g., PO4, SO4).
-p, --keep-protein-only	Remove all non-protein residues, keeping only protein residues (cannot be used with --hetatm).
-w, --remove-water	Remove all water molecules from the structure.

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Example Usages

1. Remove water and keep only protein residues:

   python pdb_processor.py -i input.pdb -o output_cleaned.pdb -p
   

2. Remove specific heteroatoms (e.g., PO4) and water molecules:

   python pdb_processor.py -i input.pdb -o output_no_hetatm.pdb -r PO4 -w
   

3. Error Example: The following command will raise an error because --hetatm and --keep-protein-only are incompatible:

   python pdb_processor.py -i input.pdb -o output_error.pdb -r PO4 -p
   

Error Handling: Ensures incompatible options are not used together (e.g., --hetatm and --keep-protein-only).

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Issues and Contributions

If you encounter any issues, discover any bugs, or would like to contribute to the project, feel free to:

1. Report an Issue: Open an issue describing the problem in detail, including error messages, input files, and the command used.
2. Request a Feature: If you have a feature in mind that would enhance the script, you can create a feature request.
3. Contribute: Fork the repository, make your changes, and submit a pull request. Contributions are always welcome, and your support will help improve the project!

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Aaryesh Deshpande Email: aaryeshad@gmail.com

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