{"id":15018298,"url":"https://github.com/tridentbio/trident-chemwidgets","last_synced_at":"2025-10-23T17:31:48.365Z","repository":{"id":37784654,"uuid":"462835118","full_name":"tridentbio/trident-chemwidgets","owner":"tridentbio","description":"Jupyter Widgets to interact with molecular datasets.","archived":false,"fork":false,"pushed_at":"2022-06-24T14:07:20.000Z","size":10372,"stargazers_count":31,"open_issues_count":2,"forks_count":2,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-02-05T11:11:19.209Z","etag":null,"topics":["chemistry","jupyter","jupyter-notebook","molecule","notebook","visualization"],"latest_commit_sha":null,"homepage":"","language":"CSS","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/tridentbio.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":"LICENSE.txt","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2022-02-23T17:19:03.000Z","updated_at":"2025-02-05T03:18:40.000Z","dependencies_parsed_at":"2022-06-23T22:13:25.759Z","dependency_job_id":null,"html_url":"https://github.com/tridentbio/trident-chemwidgets","commit_stats":null,"previous_names":[],"tags_count":3,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tridentbio%2Ftrident-chemwidgets","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tridentbio%2Ftrident-chemwidgets/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tridentbio%2Ftrident-chemwidgets/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tridentbio%2Ftrident-chemwidgets/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/tridentbio","download_url":"https://codeload.github.com/tridentbio/trident-chemwidgets/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":237869068,"owners_count":19379259,"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":["chemistry","jupyter","jupyter-notebook","molecule","notebook","visualization"],"created_at":"2024-09-24T19:51:48.255Z","updated_at":"2025-10-23T17:31:43.560Z","avatar_url":"https://github.com/tridentbio.png","language":"CSS","funding_links":[],"categories":["Molecular Visualization"],"sub_categories":["Force Fields"],"readme":"\u003cbr/\u003e\u003cbr/\u003e\n\n\u003cdiv align=\"center\"\u003e\n    \u003cimg width=\"300px\" src=\"https://github.com/tridentbio/trident-chemwidgets/raw/master/logo.svg\"/\u003e\n\u003c/div\u003e\n\n\u003cbr/\u003e   \n\n\u003c!-- \u003ch1 align=\"center\"\u003eTrident Chemwidgets\u003c/h1\u003e --\u003e\n\n![License](https://img.shields.io/badge/license-BSD--3-lightgrey?style=for-the-badge)\n![Version](https://img.shields.io/badge/version-0.2.1-blue?style=for-the-badge)\n![PRs](https://img.shields.io/badge/PRs-welcome-green?style=for-the-badge)\n\n## Summary\n\n- [About](#About)\n- [Installation](#Installation)\n- [Documentation](#Documentation)\n- [Usage](#Usage)\n\u003c!-- - [Tests](#Tests) --\u003e\n\u003c!-- - [Roadmap](#Roadmap) --\u003e\n\n\n## About\n\nThe Trident Chemwidgets (TCW) package provides a set of Jupyter widgets to improve data visibility in cheminformatics and molecular machine learning. \n\nTrident Chemwidgets is a product of Trident Bioscience. Trident Bioscience builds machine learning applications for the biotech and pharmaceutical industries. If you're interested in learning more, you can visit us at [trident.bio](https://www.trident.bio) or email us at [info@trident.bio](mailto:info@trident.bio).\n\n## Installation\n\nTrident Chemwidgets is available from pip and conda:\n\npip:\n```bash\npip install trident-chemwidgets\n```\n\nconda:\n```\nconda install -c conda-forge trident-chemwidgets\n```\n\nThen, for Jupyter Lab, run:\n\n```\njupyter labextension install trident-chemwidgets\n```\n\n[Full instructions here.](https://www.trident.bio/trident-chemwidgets/html/installing.html)\n\n## [Documentation](https://www.trident.bio/trident-chemwidgets)\n\nClick the link above to access the [documentation](https://www.trident.bio/trident-chemwidgets). If you're looking for example notebooks, check out the links below (clone this repository to use them directly).\n\n- [JSME widget](https://github.com/tridentbio/trident-chemwidgets/raw/master/examples/JSME_widget.ipynb)\n- [Histogram widget](https://github.com/tridentbio/trident-chemwidgets/raw/master/examples/Histogram_widget.ipynb)\n- [Scatter widget](https://github.com/tridentbio/trident-chemwidgets/raw/master/examples/Scatter_widget.ipynb)\n- [InteractiveMolecule widget](https://github.com/tridentbio/trident-chemwidgets/raw/master/examples/InteractiveMolecule_widget.ipynb)\n\n## Usage\n\nWe suggest importing Trident Chemwidgets using the convention `tcw`, as shown below. \n\n```python\nimport trident_chemwidgets as tcw\n```\n\n---\n\n### Input functions\n\n#### JSME\n\nTo facilitate molecular input, TCW provides an interface to the [JSME Molecule Editor](https://jsme-editor.github.io/) with added functionality.\n\n```python\neditor = tcw.JSME()\neditor\n```\n\n\u003cdiv align=\"center\"\u003e\n    \u003cimg width=\"600px\" src=\"https://github.com/tridentbio/trident-chemwidgets/raw/master/examples/gifs/jsme_demo_small.gif\"/\u003e\n\u003c/div\u003e\n\nYou can play with JSME widget in this [notebook](https://github.com/tridentbio/trident-chemwidgets/raw/master/examples/JSME_widget.ipynb).\n\n---\n\n### Plotting functions\n\nUnderstanding the distribution of your data is critical to many cheminformatic tasks. To this end, we supply a number of interactive plotting functions that allow you to display both the data and underlying molecular structures. You can even subset and save the data based on the property values for use in downstream analysis.\n\n#### Histogram\n\nFor 1-dimensional datasets, TCW provides a histogram plot function:\n\n```python\nhistogram = tcw.Histogram(data=data, smiles='smiles', x='tpsa', x_label='TPSA')\nhistogram\n```\n\n\u003cdiv align=\"center\"\u003e\n    \u003cimg width=\"600px\" src=\"https://github.com/tridentbio/trident-chemwidgets/raw/master/examples/gifs/histogram_demo_small.gif\"/\u003e\n\u003c/div\u003e\n\n\nYou can play with Histogram widget in this [notebook](https://github.com/tridentbio/trident-chemwidgets/raw/master/examples/Histogram_widget.ipynb).\n\n#### Scatter plot\n\nFor 2-dimensional datasets, TCW provides a scatter plot function:\n\n```python\nscatter = tcw.Scatter(data=data, smiles='smiles', x='mwt', y='logp',\n                      x_label='Molecular Weight', y_label='logP')\n```\n\n\u003cdiv align=\"center\"\u003e\n    \u003cimg width=\"600px\" src=\"https://github.com/tridentbio/trident-chemwidgets/raw/master/examples/gifs/scatter_demo_small.gif\"/\u003e\n\u003c/div\u003e\n\n\nYou can play with Scatter widget in this [notebook](https://github.com/tridentbio/trident-chemwidgets/raw/master/examples/Scatter_widget.ipynb).\n\n---\n\n### Output functions\n\n#### Interactive molecule\n\nTo examine features at the atom level, TCW provides a function to plot a molecule and allow users to explore the atom-specific features:\n\n```python\nmol = tcw.InteractiveMolecule('CC(C)CC1=CC=C(C=C1)C(C)C(=O)O', data=atom_data)\nmol\n```\n\n\u003cdiv align=\"center\"\u003e\n    \u003cimg width=\"600px\" src=\"https://github.com/tridentbio/trident-chemwidgets/raw/master/examples/gifs/interactive_molecule_demo_small.gif\"/\u003e\n\u003c/div\u003e\n\n\nYou can play with InteractiveMolecule widget in this [notebook](https://github.com/tridentbio/trident-chemwidgets/raw/master/examples/InteractiveMolecule_widget.ipynb).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftridentbio%2Ftrident-chemwidgets","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftridentbio%2Ftrident-chemwidgets","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftridentbio%2Ftrident-chemwidgets/lists"}