Molecular Batch Converter

Introduction

Are you frequently faced with the challenge of performing batch conversions for various molecular file formats, such as Structure Data Files (SDF) to Protein Data Bank (PDB) or converting SMILES representations to AutoDock PDBQT format? If you've encountered this dilemma in your scientific or computational endeavors, worry not – this repository is designed to simplify and streamline your molecular data conversion needs.

Say goodbye to tedious, manual conversions!

Features

1. SDF to PDB Conversion

Easily convert Structure Data Files (SDF) to Protein Data Bank (PDB) format. This feature is particularly useful when dealing with large datasets of molecular structures.

2. SMILES to PDBQT Conversion

Effortlessly convert SMILES representations stored in an Excel sheet to AutoDock PDBQT format. This feature enables seamless integration with AutoDock for molecular docking studies.

3. Batch Processing

Perform conversions on hundreds or even thousands of molecular files simultaneously. The batch processing capability ensures efficiency and saves valuable time.

4. Interactive Jupyter Notebooks

Leverage the power of Jupyter Notebooks for a customizable and interactive conversion environment. The provided notebooks offer a user-friendly interface for performing and customizing conversions.

Getting Started

1. Clone the Repository:

   git clone https://github.com/your-username/molecular-batch-converter.git

2. Requirements:

   • This project requires Python, and the necessary libraries include:
     • RDKit
     • Pandas
     • Open Babel

3. Install Dependencies:

   pip install rdkit pandas openbabel

4. Explore Jupyter Notebooks:

   • Navigate to the notebooks directory and open the provided notebooks.

5. Run Your Conversions:

   • Customize the notebook to suit your specific conversion needs.
   • Execute the notebook cells to perform batch operations seamlessly.

Notebooks Overview

- SDF to PDB Conversion.ipynb

Convert SDF files to PDB format. Ideal for scenarios where structural data needs to be processed and visualized in PDB format.

- SMILES to PDBQT Conversion.ipynb

Convert SMILES representations stored in an Excel sheet to PDBQT format. Perfect for preparing molecular structures for AutoDock docking studies.

- Custom Conversion.ipynb

Tailor the conversion process based on your specific requirements. This notebook provides a versatile framework for creating custom conversion scripts.

Contributions

Contributions are highly encouraged! If you have additional conversion scripts, improvements, or bug fixes, feel free to submit a pull request.

License

This project is licensed under the MIT License. You are free to use, modify, and distribute it according to the license terms.

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Effortless Batch Conversions for Molecular Data! 🧪✨