{"id":32920690,"url":"https://github.com/preghosh/3dmolviewer","last_synced_at":"2026-05-17T19:03:37.834Z","repository":{"id":323553200,"uuid":"1071477207","full_name":"pregHosh/3DMolViewer","owner":"pregHosh","description":" A Streamlit application for interactively visualizing and analyzing molecular structures and their properties.","archived":false,"fork":false,"pushed_at":"2025-11-10T19:06:12.000Z","size":867,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":0,"default_branch":"main","last_synced_at":"2025-11-10T21:07:43.156Z","etag":null,"topics":["cheminformatics","computational-chemistry","molecular-visualization","molecule"],"latest_commit_sha":null,"homepage":"","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/pregHosh.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,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2025-10-07T12:02:56.000Z","updated_at":"2025-11-10T19:06:17.000Z","dependencies_parsed_at":null,"dependency_job_id":null,"html_url":"https://github.com/pregHosh/3DMolViewer","commit_stats":null,"previous_names":["preghosh/3dmolviewer"],"tags_count":null,"template":false,"template_full_name":null,"purl":"pkg:github/pregHosh/3DMolViewer","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pregHosh%2F3DMolViewer","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pregHosh%2F3DMolViewer/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pregHosh%2F3DMolViewer/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pregHosh%2F3DMolViewer/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/pregHosh","download_url":"https://codeload.github.com/pregHosh/3DMolViewer/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pregHosh%2F3DMolViewer/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":33151625,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-17T09:28:26.183Z","status":"ssl_error","status_checked_at":"2026-05-17T09:27:52.702Z","response_time":107,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"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":["cheminformatics","computational-chemistry","molecular-visualization","molecule"],"created_at":"2025-11-10T23:00:46.828Z","updated_at":"2026-05-17T19:03:37.828Z","avatar_url":"https://github.com/pregHosh.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# 🧬 Lite Molecular Viz\n\nLite Molecular Viz is a standalone Streamlit application for interactively browsing and analyzing molecular structures and their associated properties. It's designed as a lightweight, easy-to-use tool for researchers and developers in computational chemistry and drug discovery.\n\n\nIntended to be used with [![Code](https://img.shields.io/badge/MolCraftDiffusion-GitHub-red)](https://github.com/pregHosh/MolCraftDiffusion)\n\nThe paper: [![arXiv](https://img.shields.io/badge/PDF-arXiv-blue)](https://chemrxiv.org/engage/chemrxiv/article-details/6909e50fef936fb4a23df237)\n\n\n## Features\n\n-   **Multiple Data Sources**: Load your data with flexibility.\n    -   **ASE Database**: For large datasets, use a highly efficient `.db` file.\n    -   **CSV Files**: Upload directly, or provide a local file path.\n    -   **XYZ Directory**: Point to a directory of `.xyz` or `.pdb` files.\n-   **Dynamic Visualization Modes**:\n    -   **Plotting Interface**: If your data includes numeric properties, explore it with interactive plots (scatter, line, histogram, box, parity). Selecting data points on a plot instantly displays the corresponding 3D molecule.\n    -   **Molecule Gallery**: If your dataset only contains molecule identifiers, the app provides a clean, grid-based gallery of all 3D structures.\n-   **Interactive 3D Viewer**:\n    -   Powered by `3Dmol.js` for high-quality rendering.\n    -   View molecules in stick, sphere, or line styles.\n    -   Zoom, pan, and rotate structures.\n-   **Extensible Plugin System**:\n    -   Enhance the app's functionality with optional plugins for on-demand data analysis.\n    -   **Dataset Statistics Plugin**: Compute and visualize summary statistics, element distributions, and property histograms for your dataset.\n\n## Quick Start\n\n1.  **Set up the environment**:\n    ```bash\n    # Clone the repository (if you haven't already)\n    # git clone ...\n    # cd 3DMolViewer\n\n    # Create and activate a virtual environment\n    python -m venv .venv\n    source .venv/bin/activate\n    ```\n\n2.  **Install dependencies**:\n    ```bash\n    pip install -r requirements.txt\n    ```\n\n3.  **Launch the app**:\n    ```bash\n    streamlit run app.py\n    ```\n\n4.  Once the app is open in your browser, use the sidebar to select your data source and start exploring.\n\n## Data Sources\n\nThe application supports several methods for loading molecular data.\n\n### ASE Database (Recommended for large datasets)\n\nFor the best performance with large datasets, consolidate your molecules and properties into a single ASE database (`.db`) file.\n\nA utility script is provided to make this easy. It takes a directory of molecule files (`.xyz`, `.pdb`, etc.) and a CSV file with properties, and merges them into a `.db` file. The CSV must contain a column that matches the molecule filenames.\n\n**Usage:**\n```bash\npython scripts/create_database.py [path/to/your.csv] [path/to/molecule/dir] [output_database.db]\n```\n\n**Example:**\n```bash\n# Create a database from the example data\npython scripts/create_database.py examples/sampled_molecules_descriptors.csv examples/ molecules.db --overwrite\n```\nAfter creating the database, select \"ASE Database\" in the app's data source options and provide the path to your `.db` file.\n\n### CSV File\n\nYou can load properties from a CSV file by either uploading it directly in the app or by providing a local file path. If the CSV contains a column with molecule names, you can link it to a separate **Molecule Data Source** (like an XYZ directory or an ASE DB) in the sidebar to visualize the structures.\n\n### XYZ Directory\n\nFor smaller datasets, you can simply point the application to a directory containing your molecule files (e.g., `.xyz`, `.pdb`). The app will read the files from the directory.\n\n## Project Structure\n\n```\n.\n├── app.py                # Main Streamlit application\n├── requirements.txt      # Python dependencies\n├── README.md             # This file\n├── core/                 # Core application logic\n│   ├── molecule_viz.py   # 3Dmol.js visualization\n│   ├── plotting.py       # Plotly interactive plots\n│   └── utils.py          # Data processing and configuration\n├── plugins/              # Extensible plugin modules\n│   ├── base_plugin.py\n│   └── statistics_plugin.py\n├── scripts/              # Utility scripts\n│   └── create_database.py\n├── examples/             # Example molecule files and data\n└── tests/                # Application tests\n```\n\n## Contributing\n\nIssues and pull requests are welcome. Please ensure that new features are documented and that the code follows the existing style.\n\n## License\n\nThis project is released under the MIT License.","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpreghosh%2F3dmolviewer","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpreghosh%2F3dmolviewer","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpreghosh%2F3dmolviewer/lists"}