{"id":22957379,"url":"https://github.com/biohacker0/isomer_generator","last_synced_at":"2025-04-02T01:42:08.929Z","repository":{"id":197073062,"uuid":"697945950","full_name":"biohacker0/Isomer_generator","owner":"biohacker0","description":"generate stereoisomers using rdkit library with pics","archived":false,"fork":false,"pushed_at":"2023-09-28T20:07:03.000Z","size":14,"stargazers_count":1,"open_issues_count":1,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-02-07T16:43:20.959Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/biohacker0.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2023-09-28T19:57:45.000Z","updated_at":"2023-10-18T20:03:18.000Z","dependencies_parsed_at":null,"dependency_job_id":"3b103827-dd7d-4cfa-968b-1f2e53a876d2","html_url":"https://github.com/biohacker0/Isomer_generator","commit_stats":null,"previous_names":["biohacker0/isomer_generator"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biohacker0%2FIsomer_generator","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biohacker0%2FIsomer_generator/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biohacker0%2FIsomer_generator/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biohacker0%2FIsomer_generator/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/biohacker0","download_url":"https://codeload.github.com/biohacker0/Isomer_generator/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":246741186,"owners_count":20826063,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-12-14T17:16:22.119Z","updated_at":"2025-04-02T01:42:08.902Z","avatar_url":"https://github.com/biohacker0.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# RDKit Isomer Generator\n\n # [Blog]( https://corvus-ikshana.hashnode.dev/isomer-generations-using-rdkit-library-for-mass-molecular-docking-tests-part-1)\n\nThis 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.\n\n## Table of Contents\n- [Prerequisites](#prerequisites)\n- [Installation](#installation)\n- [Usage](#usage)\n- [Generated Output](#generated-output)\n  - [JSON Data](#json-data)\n  - [Isomer Images](#isomer-images)\n- [License](#license)\n\n## Prerequisites\nBefore using this script, ensure you have the following prerequisites installed:\n\n- RDKit: The RDKit library must be installed. You can follow the installation guide provided on their website.\n\n## Installation\nClone this repository to your local machine using the following command:\n\n```shell\ngit clone https://github.com/yourusername/rdkit-isomer-generator.git\n```\n\nNavigate to the project directory:\n\n```shell\ncd rdkit-isomer-generator\n```\n\nInstall the required Python packages (assuming you have Python installed):\n\n```shell\npip install rdkit-pypi\n```\n\n## Usage\nEdit the `input_smiles` variable in the script to specify the SMILES notation of the molecule for which you want to generate isomers. For example:\n\n```python\ninput_smiles = \"CCC(Cl)C(Cl)C\"\n```\n\nRun the script using the following command:\n\n```shell\npython isomer_generator.py\n```\n\nAfter running the script, you will get the following output:\n\n- A JSON file named `isomer_data.json` containing information about the generated isomers and their IUPAC-like names.\n- PNG image files for each isomer, e.g., `Isomer_1.png`, `Isomer_2.png`, etc., showing the visual representation of each isomer.\n\n## Generated Output\nThe script generates two types of output:\n\n### JSON Data\nThe JSON file `isomer_data.json` contains a dictionary with information about each generated isomer, including its SMILES notation and an IUPAC-like name.\n\n```json\n{\n  \"Isomer_1\": {\n    \"SMILES\": \"CCC(Cl)C(Cl)C\",\n    \"IUPAC_Like_Name\": \"CCC(Cl)[C@H](C)Cl\"\n  },\n  \"Isomer_2\": {\n    \"SMILES\": \"CCC(Cl)[C@H](C)Cl\",\n    \"IUPAC_Like_Name\": \"CCC(Cl)[C@@H](C)Cl\"\n  },\n  ...\n}\n```\n\n### Isomer Images\nPNG images are generated for each isomer, showing their structural representation. These images are saved as `Isomer_1.png`, `Isomer_2.png`, etc.\n\n![Isomer_1.png]\n\n![Isomer_2.png]\n\n...\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiohacker0%2Fisomer_generator","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbiohacker0%2Fisomer_generator","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiohacker0%2Fisomer_generator/lists"}