https://github.com/avrabyt/st-speckmol

Streamlit Component for creating Speck molecular structures within Streamlit Web app.
https://github.com/avrabyt/st-speckmol

bioinformatics molecules pdb python streamlit streamlit-component visualization

Last synced: 7 months ago
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Streamlit Component for creating Speck molecular structures within Streamlit Web app.

• Host: GitHub
• URL: https://github.com/avrabyt/st-speckmol
• Owner: avrabyt
• License: mit
• Created: 2022-05-19T15:20:34.000Z (over 3 years ago)
• Default Branch: main
• Last Pushed: 2024-05-16T18:35:11.000Z (over 1 year ago)
• Last Synced: 2025-03-24T10:12:11.345Z (7 months ago)
• Topics: bioinformatics, molecules, pdb, python, streamlit, streamlit-component, visualization
• Language: Python
• Homepage: https://hellostspeckmol.streamlitapp.com
• Size: 74 MB
• Stars: 31
• Watchers: 1
• Forks: 15
• Open Issues: 4
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# Stspeckmol

A Streamlit Component for creating Speck molecular structures within Streamlit Web app.

[![PyPI version](https://badge.fury.io/py/st-speckmol.svg)](https://pypi.org/project/st-speckmol/)

[![Downloads](https://pepy.tech/badge/st-speckmol)](https://pepy.tech/project/st-speckmol)

[![Downloads](https://pepy.tech/badge/st-speckmol/month)](https://pepy.tech/project/st-speckmol)

[![Website shields.io](https://img.shields.io/website-up-down-green-red/http/shields.io.svg)](https://hellostspeckmol.streamlitapp.com)

![GitHub last commit](https://img.shields.io/github/last-commit/avrabyt/st-speckmol?style=plastic)

![GitHub Release Date](https://img.shields.io/github/release-date/avrabyt/st-speckmol)

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.11205344.svg)](https://doi.org/10.5281/zenodo.11205344)

## Installation 

```console

pip install st-speckmol

```

to upgrade use,

```console

pip install --upgrade st-speckmol

```

>:warning: https://github.com/avrabyt/st-speckmol/issues/20 In case of `ModuleNotFoundError: No module named 'ipython_genutils'` :

>```console

> pip install ipython_genutils

>```

> **Future release of st-speckmol, will support this module natively.**

## Example

Try the app, for different examples. 

[![Streamlit App](https://static.streamlit.io/badges/streamlit_badge_black_white.svg)](https://hellostspeckmol.streamlitapp.com)

## Quickstart

``` python

import streamlit as st

import glob

from st_speckmol import speck_plot

# Example files path

ex_files = glob.glob("examples/*.xyz")

with st.sidebar:

    example_xyz = st.selectbox("Select a molecule",ex_files)

    f = open(example_xyz,"r")

    example_xyz = f.read()

res = speck_plot(example_xyz)

```

![Speclit demo](https://github.com/avrabyt/Specklit/blob/main/Resources/SpeckLit_demo.gif)

## Video tutorial

  See the tutorial video

[![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)

[Blog Post](https://medium.com/@avra42/how-to-build-molecular-structures-visualizing-web-application-using-python-and-streamlit-5ec9da86550c) 

## Scientfic usage

To cite any scientific usage, please refer to the following citation:

```

@software{Biswas_2024,

  author = {Avratanu Biswas},

  title = {st-speckmol},

  version = {v0.0.6.1},

  doi = {10.5281/zenodo.11205344},

  url = {https://github.com/avrabyt/st-speckmol},

  date = {2024-05-16}

}

```

For additional assistance, feel free to reach out to me directly.

## Related library - [Stmol](https://github.com/napoles-uach/stmol) 

During 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. 

> ℹ️

> 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."

```python

# Installation of Stmol

pip install stmol==0.0.9

# Import Speck plot

from stmol import speck_plot

```

## References

[Speck Online](http://wwwtyro.github.io/speck/)

[Speck Python package](https://pypi.org/project/ipyspeck/)

[Example-Source](https://github.com/wwwtyro/speck/tree/gh-pages/static/samples)

[Stmol](https://github.com/napoles-uach/stmol)