README.md

metadata

title: CDK_library
app_file: app.py
sdk: gradio
sdk_version: 4.36.1

Molecular Descriptor Analysis and Chemical Reaction Visualization

This repository provides a web-based interface using Gradio for performing various molecular descriptor calculations, geometric analyses, substructure checks, similarity calculations, and chemical reaction visualizations. It integrates functionalities from RDKit and CDK libraries, enabling users to interactively analyze chemical data without needing extensive programming knowledge.

Features

• Calculate Descriptors: Input SMILES strings and optionally include 3D coordinates to generate MolFile outputs and download descriptors as Excel.
• Geometric Values: Compute molecular weight, centroid, mean distance to centroid, and max distance to centroid for a given molecule and display its structure.
• Check Substructure: Check if a specified substructure is present within a molecule and visualize both structures.
• Calculate Similarity: Compute Tanimoto similarity coefficient between two molecules based on their SMILES strings.
• Chemical Reaction: Define chemical reactions using SMARTS notation, input reactant SMILES strings, and visualize the resulting reaction products interactively.

Usage

1. Setup Environment:

   • Ensure Python 3.7+ is installed.
   • Install required packages using pip install -r requirements.txt.

2. Run the Application:

   • Execute python app.py to start the Gradio interface locally.
   • Access the interface at http://localhost:7860.

3. Interface Navigation:

   • Use the tabs provided to input SMILES strings and parameters for the desired chemical analysis or reaction.
   • Click buttons to perform calculations or reactions and view results interactively.

4. Contribute:

   • Fork the repository, make your changes, and submit a pull request.
   • Report any issues or suggest improvements through GitHub issues.

Dependencies

• RDKit: Open-source cheminformatics software.
• CDK: Chemistry Development Kit for molecular descriptor calculation.
• Gradio: User-friendly Python library for creating UIs around ML models.

License

This project is licensed under the MIT License - see the LICENSE file for details.