https://github.com/biohacker0/isomer_generator
generate stereoisomers using rdkit library with pics
https://github.com/biohacker0/isomer_generator
Last synced: over 1 year ago
JSON representation
generate stereoisomers using rdkit library with pics
- Host: GitHub
- URL: https://github.com/biohacker0/isomer_generator
- Owner: biohacker0
- Created: 2023-09-28T19:57:45.000Z (almost 3 years ago)
- Default Branch: main
- Last Pushed: 2023-09-28T20:07:03.000Z (almost 3 years ago)
- Last Synced: 2025-02-07T16:43:20.959Z (over 1 year ago)
- Language: Python
- Size: 13.7 KB
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# RDKit Isomer Generator
# [Blog]( https://corvus-ikshana.hashnode.dev/isomer-generations-using-rdkit-library-for-mass-molecular-docking-tests-part-1)
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.
## Table of Contents
- [Prerequisites](#prerequisites)
- [Installation](#installation)
- [Usage](#usage)
- [Generated Output](#generated-output)
- [JSON Data](#json-data)
- [Isomer Images](#isomer-images)
- [License](#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:
```shell
git clone https://github.com/yourusername/rdkit-isomer-generator.git
```
Navigate to the project directory:
```shell
cd rdkit-isomer-generator
```
Install the required Python packages (assuming you have Python installed):
```shell
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:
```python
input_smiles = "CCC(Cl)C(Cl)C"
```
Run the script using the following command:
```shell
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.
```json
{
"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]
...