{"id":18978274,"url":"https://github.com/autodesk/notebook-molecular-visualization","last_synced_at":"2025-07-23T17:06:01.782Z","repository":{"id":50387483,"uuid":"63356717","full_name":"Autodesk/notebook-molecular-visualization","owner":"Autodesk","description":"2D and 3D molecular visualization in Jupyter notebooks using 3DMol.js and D3.js","archived":false,"fork":false,"pushed_at":"2018-03-30T15:55:15.000Z","size":15822,"stargazers_count":80,"open_issues_count":15,"forks_count":21,"subscribers_count":10,"default_branch":"master","last_synced_at":"2025-04-19T19:37:55.536Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"http://moldesign.bionano.autodesk.com","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Autodesk.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2016-07-14T17:36:39.000Z","updated_at":"2025-03-26T07:50:07.000Z","dependencies_parsed_at":"2022-08-02T22:45:59.743Z","dependency_job_id":null,"html_url":"https://github.com/Autodesk/notebook-molecular-visualization","commit_stats":null,"previous_names":[],"tags_count":20,"template":false,"template_full_name":null,"purl":"pkg:github/Autodesk/notebook-molecular-visualization","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Autodesk%2Fnotebook-molecular-visualization","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Autodesk%2Fnotebook-molecular-visualization/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Autodesk%2Fnotebook-molecular-visualization/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Autodesk%2Fnotebook-molecular-visualization/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Autodesk","download_url":"https://codeload.github.com/Autodesk/notebook-molecular-visualization/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Autodesk%2Fnotebook-molecular-visualization/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":266717708,"owners_count":23973383,"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","status":"online","status_checked_at":"2025-07-23T02:00:09.312Z","response_time":66,"last_error":null,"robots_txt_status":null,"robots_txt_updated_at":null,"robots_txt_url":"https://github.com/robots.txt","online":true,"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":[],"created_at":"2024-11-08T15:32:52.579Z","updated_at":"2025-07-23T17:06:01.755Z","avatar_url":"https://github.com/Autodesk.png","language":"Python","readme":"notebook-molecular-visualization\n===============================\n[![PyPI version](https://badge.fury.io/py/nbmolviz.svg)](https://badge.fury.io/py/nbmolviz)\n\nJupyter notebook add-ons for the [Molecular Design Toolkit](https://github.com/Autodesk/molecular-design-toolkit). NBMolViz provides visualization and interactivity for 3D Molecular Structures in Jupyter notebooks.\n\nAfter installing it, you'll never need to use the NBMolViz package directly. It's instead called through MDT to provide enhanced functionality in notebooks. \n\n## Installation\nWhen you install `nbmolviz`, you'll need to both install the python library _and_ enable the notebook extensions. \n\n1. **Install the python library:**\n```bash\n    $ pip install nbmolviz\n```\n    \n2. **Activate notebook extensions:**\nTo enable for your user account:\n```bash\n    $ python -m nbmolviz activate --user\n```\n       \nTo enable within your current virtual environment:\n```bash\n    $ python -m nbmolviz activate --sys-prefix\n```\n\nTo globally enable for all users (use with caution! This may require `sudo`):\n```bash\n    $ python -m nbmolviz activate --global\n```\n\n## Upgrading from older versions\n\n1. **Upgrade the library to the newest version**\n    $ pip install --upgrade nbmolviz\n\n2. **Remove old notebook extensions (you will be notified if it's necessary to run with `sudo`)**:\n```bash\n    $ python -m nbmolviz uninstall\n```\n\n3. Activate the notebook extension as above\n\n\n## Examples\n\nDraw a small molecule:\n```python\nimport moldesign as mdt\nmol = mdt.from_name('ethylene')\nmol.draw()\n```\n\u003cimg src=\"img/smallmol.png\" style=\"width: 600px;\"/\u003e\n\nDraw a protein:\n```python\nimport moldesign as mdt\nmol = mdt.from_pdb('3aid')\nmol.draw()\n```\n\u003cimg src=\"img/protein.png style=\"width: 600px;\"/\u003e\n\n\nInteractively select atoms (the currently selected atoms will be available as `selector.selected_atoms`)\n```python\nimport moldesign as mdt\nmol = mdt.from_pdb('3aid')\nselector = mdt.widgets.ResidueSelector(mol)\nselector\n```\n\u003cimg src=\"img/selector.png\" style=\"width: 600px;\"/\u003e\n\n\n## Dev install\nRequires npm.\n\n    $ git clone https://github.com/autodesk/notebook-molecular-visualization\n    $ cd notebook-molecular-visualization\n    # ./set_filters.sh  # tells git to clean up notebooks before committing\n    $ python setup.py jsdeps\n    $ pip install -e .\n    $ jupyter nbextension install --py --symlink --user nbmolviz\n    $ jupyter nbextension enable --py --user nbmolviz\n    $ cd tests/galileo \u0026\u0026 npm install\n    \nThis will build your widgets into a folder at `notebook-molecular-visualization/nbmolviz/static`\n\nDuring development, to see the effects of changes to any javascript files (in notebook-molecular/visualization/js/src), run `python setup.py jsdeps` and reload any notebook browser windows.\n\n## To run visual tests\n`cd tests/nb \u0026\u0026 ../galileo/bin/galileo --launchnb`\n\n## Releasing a new version\nTravis automatically releases commits that are tagged, so to trigger a new release, just do:\n\n    git tag \u003cnew tag version\u003e\n    git push origin --tags\n\nIf you want to see what will be included in a release, run `check-manifest`.  You could also manually build a release with `python setup.py sdist` and manually release with `python setup.py sdist upload -r pypi`.\n\n## Contributing\n\nThis project is developed and maintained by the [Molecular Design Toolkit](https://github.com/autodesk/molecular-design-toolkit) project. Please see that project's [CONTRIBUTING document](https://github.com/autodesk/molecular-design-toolkit/CONTRIBUTING.md) for details.\n\n\n## About\nThis package started life as hackathon project for the \u003ca href=\"http://www.cecam.org/workshop-1214.html\"\u003eCECAM 2015 Macromolecular Simulation Workshop.\u003c/a\u003e It's since undergone a complete source rewrite, and is being released by BioNano Research at Autodesk as part of our suite of Molecular Design Tools.\n\nThe visualizers offered by this library were built using:\n  - \u003ca href=\"https://github.com/jupyter/ipywidgets\"\u003eipywidgets\u003c/a\u003e - UI library for interactivity in Jupyter notebooks\n  - \u003ca href=\"http://3dmol.csb.pitt.edu/doc/index.html\"\u003e3Dmol.js\u003c/a\u003e - 3D molecular visualization library for web browsers\n  - \u003ca href=\"http://d3js.org/\"\u003eD3.js\u003c/a\u003e - javascript library for graph visualization\n\n\n\n## License\n\nCopyright 2017 Autodesk Inc.\n\nLicensed under the Apache License, Version 2.0 (the \"License\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at\n\nhttp://www.apache.org/licenses/LICENSE-2.0\n\nUnless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fautodesk%2Fnotebook-molecular-visualization","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fautodesk%2Fnotebook-molecular-visualization","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fautodesk%2Fnotebook-molecular-visualization/lists"}