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https://github.com/napoles-uach/stmol
This is the repository for the Stmol project, a Streamlit component that uses py3Dmol to render molecules.
https://github.com/napoles-uach/stmol
molecular protein-structure streamlit visualization
Last synced: 5 days ago
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This is the repository for the Stmol project, a Streamlit component that uses py3Dmol to render molecules.
- Host: GitHub
- URL: https://github.com/napoles-uach/stmol
- Owner: napoles-uach
- License: mit
- Created: 2020-07-29T19:00:23.000Z (over 4 years ago)
- Default Branch: master
- Last Pushed: 2023-12-06T15:50:28.000Z (about 1 year ago)
- Last Synced: 2024-12-05T06:04:29.739Z (17 days ago)
- Topics: molecular, protein-structure, streamlit, visualization
- Language: Python
- Homepage: https://github.com/napoles-uach/stmol
- Size: 11.1 MB
- Stars: 195
- Watchers: 5
- Forks: 36
- Open Issues: 13
-
Metadata Files:
- Readme: README.md
- Changelog: changelog.md
- License: LICENSE
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README
# Stmol
[  ](https://www.frontiersin.org/articles/10.3389/fmolb.2022.990846/full)\
A component for building interactive molecular visualizations within Streamlit web-applications. It is designed to provide a state of the art visualizing and rendering 3D molecular structures for researchers, in a user-friendly manner.
------------------------------
## Note: Due to recent changes in the 3Dmol.js package, it is recomended to install py3DMol in the following way,
```
pip install py3Dmol==2.0.0.post2
```
## Stmol features
- An easy-to-use component for rendering interactive 3D molecular visualizations of protein and ligand structures within Streamlit web-apps
- `stmol` can render protein and ligand structures with just a few lines of Python code by utilizing popular visualization libraries, currently Py3DMol and Speck.
- On the user-end, `stmol` does not require expertise to interactively navigate.
- On the developer-end, `stmol` can be easily integrated within structural bioinformatic and cheminformatic pipelines to provide a simple means for user-end researchers to advance biological studies and drug discovery efforts.
------------------------------
## Stmol installation
`stmol` runs with traditional Python stack.
To install `stmol` from [pypi](https://pypi.org/project/stmol/), run this command in your terminal:
``` console
pip install stmol==0.0.9
```
Since the end goal of `stmol` plugin, is to enable easy rendering of molecular structure within the streamlit applicaton, libraries such as
[streamlit](https://github.com/streamlit/streamlit) and [py3Dmol](https://pypi.org/project/py3Dmol/) are crucial to work with.
Run this command in your terminal to install the latest release of Streamlit,
``` console
pip install streamlit
```
Run this command in your terminal to install the latest release of py3Dmol,
``` console
pip install py3Dmol
```
A recent addition to `stmol` project, in a form of static HTML wrapper is the `speck_plot()` function, which helps in rendering [Speck](https://github.com/wwwtyro/speck) structures within the Streamlit web-application, is dependent on the following libraries,
```console
ipyspeck(==0.6.1)
ipywidgets(==7.6.3)
ipython_genutils
```
-----------------
## Quickstart
##### 1. Protein visualization using `showmol()`function
- **Using `py3Dmol object`**
To visualize any protein structure, all we need is the PDB ID of the protein.
```python
from stmol import showmol
import py3Dmol
# 1A2C
# Structure of thrombin inhibited by AERUGINOSIN298-A from a BLUE-GREEN ALGA
xyzview = py3Dmol.view(query='pdb:1A2C')
xyzview.setStyle({'cartoon':{'color':'spectrum'}})
showmol(xyzview, height = 500,width=800)
```
- **Using the `render_pdb()` function**
The `render_pdb()` function accepts any PDB ID and returns a py3Dmol object.
```python
from stmol import *
showmol(render_pdb(id = '1A2C'))
```
[](https://github.com/napoles-uach/stmol/blob/master/Resources/Quickstart-1.gif)
##### 2. Labelling protein using `render_pdb_resn()`function
Inorder to mark the residues, we can use the `render_pdb_resn()` function, which in this example marks the *Alanine* [ALA] residues,
```python
showmol(render_pdb_resn(viewer = render_pdb(id = '1A2C'),resn_lst = ['ALA',]))
```
[](https://github.com/napoles-uach/stmol/blob/master/Resources/Quickstart-2.png)
###### Refer to the documentation [here](https://napoles-uach-stmol-home-pom051.streamlitapp.com/Documentation)
----------
## Examples
You can find several `stmol` examples [here](https://napoles-uach-stmol-home-pom051.streamlitapp.com/Examples).
### Browser support
- Chrome, Edge, Firefox - [link](https://napoles-uach.github.io/stmol/)
- Safari - [link](https://napoles-uach-stmol-home-pom051.streamlitapp.com)
----------------
## Dependencies
- [py3Dmol](https://pypi.org/project/py3Dmol/)
- [ipyspeck](https://pypi.org/project/ipyspeck/)
- [ipywidgets](https://github.com/jupyter-widgets/ipywidgets)
- [streamlit](https://github.com/streamlit/streamlit)
- [ipython_genutils](https://github.com/ipython/ipython_genutils)
-----------------
## Contribution to the project
We appreciate contributions from the community! Every little bit helps, and credit will always be given.
- **Reporting Bugs** - Report bugs at https://github.com/napoles-uach/stmol/issues
- **Fix Bugs** - Look through the GitHub issues for bugs. Anything tagged with “bug” and “help wanted” is open to whoever wants to help with it.
- **Implement Features** - Look through the GitHub issues for features. Anything tagged with “enhancement” and “help wanted” is open to whoever wants to implement it.
- **Submit Feedback** - The best way to send feedback is to file an issue at https://github.com/napoles-uach/stmol/issues
--------------
## Authors
- J. M. Nápoles-Duarte
- Avratanu Biswas
- Mitchell I. Parker
## Aknowledgments
We thank the authors of 3dmol.js and py3Dmol.
Nicholas Rego, David Koes, 3Dmol.js: molecular visualization with WebGL, Bioinformatics, Volume 31, Issue 8, 15 April 2015, Pages 1322–1324, https://doi.org/10.1093/bioinformatics/btu829
## How to cite
Please include this citation if Stmol is used in an academic study:
Nápoles-Duarte JM, Biswas A, Parker MI, Palomares-Baez JP, Chávez-Rojo MA and Rodríguez-Valdez LM (2022) Stmol: A component for building interactive molecular visualizations within streamlit web-applications. Front. Mol. Biosci. 9:990846. doi: 10.3389/fmolb.2022.990846
Or use the following bibtex format,
```
@ARTICLE{stmol,
AUTHOR={Nápoles-Duarte, J.M. and Biswas, Avratanu and Parker, Mitchell I. and Palomares-Baez, J.P. and Chávez-Rojo, M. A. and Rodríguez-Valdez, L. M.},
TITLE={Stmol: A component for building interactive molecular visualizations within streamlit web-applications},
JOURNAL={Frontiers in Molecular Biosciences},
VOLUME={9},
YEAR={2022},
URL={https://www.frontiersin.org/articles/10.3389/fmolb.2022.990846},
DOI={10.3389/fmolb.2022.990846},
ISSN={2296-889X},
}
```