RDKit Isomer Generator

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This Python script is designed to generate and visualize isomers of a given molecule in Simplified Molecular Input Line Entry System (SMILES) format using the RDKit library. It also generates IUPAC-like names for each isomer and stores the results in a JSON file.

Prerequisites
Installation
Usage
Generated Output
- JSON Data
- Isomer Images
License

Prerequisites

Before using this script, ensure you have the following prerequisites installed:

RDKit: The RDKit library must be installed. You can follow the installation guide provided on their website.

Installation

Clone this repository to your local machine using the following command:

git clone https://github.com/yourusername/rdkit-isomer-generator.git

Navigate to the project directory:

cd rdkit-isomer-generator

Install the required Python packages (assuming you have Python installed):

pip install rdkit-pypi

Usage

Edit the input_smiles variable in the script to specify the SMILES notation of the molecule for which you want to generate isomers. For example:

input_smiles = "CCC(Cl)C(Cl)C"

Run the script using the following command:

python isomer_generator.py

After running the script, you will get the following output:

A JSON file named isomer_data.json containing information about the generated isomers and their IUPAC-like names.
PNG image files for each isomer, e.g., Isomer_1.png, Isomer_2.png, etc., showing the visual representation of each isomer.

Generated Output

The script generates two types of output:

JSON Data

The JSON file isomer_data.json contains a dictionary with information about each generated isomer, including its SMILES notation and an IUPAC-like name.

{
  "Isomer_1": {
    "SMILES": "CCC(Cl)C(Cl)C",
    "IUPAC_Like_Name": "CCC(Cl)[C@H](C)Cl"
  },
  "Isomer_2": {
    "SMILES": "CCC(Cl)[C@H](C)Cl",
    "IUPAC_Like_Name": "CCC(Cl)[C@@H](C)Cl"
  },
  ...
}

Isomer Images

PNG images are generated for each isomer, showing their structural representation. These images are saved as Isomer_1.png, Isomer_2.png, etc.

![Isomer_1.png]

![Isomer_2.png]

...

biohacker0 / Isomer_generator