{"id":15063801,"url":"https://github.com/avrabyt/st-speckmol","last_synced_at":"2026-04-23T15:01:17.369Z","repository":{"id":37476628,"uuid":"494125258","full_name":"avrabyt/st-speckmol","owner":"avrabyt","description":"Streamlit Component for creating Speck molecular structures within Streamlit Web app.","archived":false,"fork":false,"pushed_at":"2025-12-17T16:53:24.000Z","size":77573,"stargazers_count":32,"open_issues_count":2,"forks_count":17,"subscribers_count":1,"default_branch":"main","last_synced_at":"2026-03-19T06:28:36.825Z","etag":null,"topics":["bioinformatics","molecules","pdb","python","streamlit","streamlit-component","visualization"],"latest_commit_sha":null,"homepage":"https://hellostspeckmol.streamlitapp.com","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/avrabyt.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","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}},"created_at":"2022-05-19T15:20:34.000Z","updated_at":"2025-12-17T16:53:29.000Z","dependencies_parsed_at":"2024-05-16T19:50:15.937Z","dependency_job_id":null,"html_url":"https://github.com/avrabyt/st-speckmol","commit_stats":null,"previous_names":["avrabyt/specklit"],"tags_count":4,"template":false,"template_full_name":null,"purl":"pkg:github/avrabyt/st-speckmol","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/avrabyt%2Fst-speckmol","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/avrabyt%2Fst-speckmol/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/avrabyt%2Fst-speckmol/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/avrabyt%2Fst-speckmol/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/avrabyt","download_url":"https://codeload.github.com/avrabyt/st-speckmol/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/avrabyt%2Fst-speckmol/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":32185320,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-23T11:42:27.955Z","status":"ssl_error","status_checked_at":"2026-04-23T11:42:18.877Z","response_time":53,"last_error":"SSL_read: 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":["bioinformatics","molecules","pdb","python","streamlit","streamlit-component","visualization"],"created_at":"2024-09-25T00:07:20.563Z","updated_at":"2026-04-23T15:01:17.358Z","avatar_url":"https://github.com/avrabyt.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Stspeckmol\nA Streamlit Component for creating Speck molecular structures within Streamlit Web app.\n\n[![PyPI version](https://badge.fury.io/py/st-speckmol.svg)](https://pypi.org/project/st-speckmol/)\n[![Downloads](https://pepy.tech/badge/st-speckmol)](https://pepy.tech/project/st-speckmol)\n[![Downloads](https://pepy.tech/badge/st-speckmol/month)](https://pepy.tech/project/st-speckmol)\n[![Website shields.io](https://img.shields.io/website-up-down-green-red/http/shields.io.svg)](https://hellostspeckmol.streamlitapp.com)\n![GitHub last commit](https://img.shields.io/github/last-commit/avrabyt/st-speckmol?style=plastic)\n![GitHub Release Date](https://img.shields.io/github/release-date/avrabyt/st-speckmol)\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.11205344.svg)](https://doi.org/10.5281/zenodo.11205344)\n\n\n\n## Installation \n```console\npip install st-speckmol\n```\nto upgrade use,\n```console\npip install --upgrade st-speckmol\n```\n\u003e:warning: https://github.com/avrabyt/st-speckmol/issues/20 In case of `ModuleNotFoundError: No module named 'ipython_genutils'` :\n\u003e```console\n\u003e pip install ipython_genutils\n\u003e```\n\u003e **Future release of st-speckmol, will support this module natively.**\n\n## Update (v0.0.7 - Dec 2024)\nFor Streamlit Cloud compatibility, `st-speckmol` now uses [ipyspeck](https://github.com/denphi/speck)'s native Streamlit component. All existing APIs remain unchanged.\n\n## Example\n\nTry the app, for different examples. \n\n[![Streamlit App](https://static.streamlit.io/badges/streamlit_badge_black_white.svg)](https://hellostspeckmol.streamlitapp.com)\n\n\n## Quickstart\n\n``` python\nimport streamlit as st\nimport glob\nfrom st_speckmol import speck_plot\n\n# Example files path\nex_files = glob.glob(\"examples/*.xyz\")\nwith st.sidebar:\n    example_xyz = st.selectbox(\"Select a molecule\",ex_files)\n    f = open(example_xyz,\"r\")\n    example_xyz = f.read()\n\nres = speck_plot(example_xyz)\n\n```\n\n![Speclit demo](https://github.com/avrabyt/Specklit/blob/main/Resources/SpeckLit_demo.gif)\n\n## Video tutorial\n\u003cdetails\u003e\n  \u003csummary\u003eSee the tutorial video\u003c/summary\u003e\n\n[![How to Build PROTEIN VISUALIZATION WEB-APP using PYTHON and STREAMLIT | PART 1](https://github.com/avrabyt/st-speckmol/blob/main/Resources/Speck-Thumbnail.png)](https://youtu.be/jUh923Z4fuk)\n\n\u003c/details\u003e\n\n[Blog Post](https://medium.com/@avra42/how-to-build-molecular-structures-visualizing-web-application-using-python-and-streamlit-5ec9da86550c) \n\n\n## Scientfic usage\nTo cite any scientific usage, please refer to the following citation:\n\n```\n@software{Biswas_2024,\n  author = {Avratanu Biswas},\n  title = {st-speckmol},\n  version = {v0.0.7},\n  doi = {10.5281/zenodo.11205344},\n  url = {https://github.com/avrabyt/st-speckmol},\n  date = {2024-12-17}\n}\n\n```\nFor additional assistance, feel free to reach out to me directly.\n\n## Related library - [Stmol](https://github.com/napoles-uach/stmol) \nDuring the development of the related library [Stmol](https://github.com/napoles-uach/stmol), we introduced the convenient `speck_plot()` function, allowing seamless integration of both libraries. \n\u003e ℹ️\n\u003e The complete integration of StSpeckmol **has not yet been finalized**, and any additional (or recently implemented) functionalities like `add_speck_param` will exclusively be accessible through this library.\"\n\n```python\n# Installation of Stmol\npip install stmol==0.0.9\n\n# Import Speck plot\nfrom stmol import speck_plot\n\n```\n\n## References\n\n[Speck Online](http://wwwtyro.github.io/speck/) - Original WebGL molecular viewer by [@wwwtyro](https://github.com/wwwtyro)\n\n[ipyspeck](https://pypi.org/project/ipyspeck/) - Jupyter/Streamlit widget by [@denphi](https://github.com/denphi)\n\n[Example-Source](https://github.com/wwwtyro/speck/tree/gh-pages/static/samples)\n\n[Stmol](https://github.com/napoles-uach/stmol)\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Favrabyt%2Fst-speckmol","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Favrabyt%2Fst-speckmol","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Favrabyt%2Fst-speckmol/lists"}