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https://github.com/rohanv01/molecule_format_converter
This jupyter notebook let's you convert sdf to pdb or SMILES to pdbqt file formats for a batch of compounds to perform cheminformatics and drug discovery projects
https://github.com/rohanv01/molecule_format_converter
cheminformatics drug-design drug-discovery molecule problem-solving smiles
Last synced: 27 days ago
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This jupyter notebook let's you convert sdf to pdb or SMILES to pdbqt file formats for a batch of compounds to perform cheminformatics and drug discovery projects
- Host: GitHub
- URL: https://github.com/rohanv01/molecule_format_converter
- Owner: RohanV01
- Created: 2023-09-25T16:42:52.000Z (about 1 year ago)
- Default Branch: main
- Last Pushed: 2023-11-22T05:20:31.000Z (12 months ago)
- Last Synced: 2024-10-09T22:05:48.706Z (27 days ago)
- Topics: cheminformatics, drug-design, drug-discovery, molecule, problem-solving, smiles
- Language: Jupyter Notebook
- Homepage:
- Size: 4.88 KB
- Stars: 6
- Watchers: 1
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# 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:**
```bash
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:**
```bash
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](LICENSE). You are free to use, modify, and distribute it according to the license terms.
---
**Effortless Batch Conversions for Molecular Data!** 🧪✨