https://github.com/jhsmit/ipymolstar
PDBeMolstar as anywidget
https://github.com/jhsmit/ipymolstar
anywidget molstar pdbe
Last synced: 6 months ago
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PDBeMolstar as anywidget
- Host: GitHub
- URL: https://github.com/jhsmit/ipymolstar
- Owner: Jhsmit
- License: mit
- Created: 2024-02-14T10:00:22.000Z (over 1 year ago)
- Default Branch: master
- Last Pushed: 2025-04-09T15:14:14.000Z (6 months ago)
- Last Synced: 2025-04-09T15:23:46.003Z (6 months ago)
- Topics: anywidget, molstar, pdbe
- Language: Jupyter Notebook
- Homepage:
- Size: 642 KB
- Stars: 32
- Watchers: 3
- Forks: 5
- Open Issues: 4
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# ipymolstar
## Live Demos
Give `ipymolstar` a spin without even installing python!
- Try it in jupyter lab via [JupyterLite](https://github.com/Jhsmit/ipymolstar-demo) 🌍🚀
- Explore the solara ☀️ [demo application](https://github.com/Jhsmit/ploomber-solara-ipymolstar) on [Ploomber-cloud](https://hidden-resonance-5816.ploomberapp.io) ⛅
- Grab a cup and play with the [solara](https://app.py.cafe/jhsmit/ipymolstar-solara), [pyshiny](https://py.cafe/jhsmit/ipymolstar-shiny) or [panel](https://app.py.cafe/jhsmit/ipymolstar-panel) live demo's on PyCafé ☕
- Upload your Alphafold3 .zip result and view plddt or chain colors in the `solarafold` result viewer on [huggingface](https://huggingface.co/spaces/Jhsmit/solarafold) 🤗
- Control the camera 📷 with [MolViewSpec](https://pypi.org/project/molviewspec/) from python 🐍 in a solara ☀️ dashboard on [PyCafé](https://py.cafe/jhsmit/molviewspec-protein-visualization) ☕
You can find other examples in the examples directory.
## Preview
You can run a quick preview of `ipymolstar` in a notebook with [juv](https://github.com/manzt/juv):
```sh
juv run example.ipynb
```
## Installation
```sh
pip install ipymolstar
```
> [!WARNING]
> Make sure you install ipymolstar in an environment that contains your installation of Jupyter. If you have installed Jupyter in a different environment from your project (requiring you to use a named, non-default kernel), you will have to install ipymolstar (or only anywidget) in your Jupyter environment as well.
## Use
```python
from ipymolstar import PDBeMolstar
view = PDBeMolstar(molecule_id='1qyn', theme='light', hide_water=True)
view
```
Loading local data, hiding the buttons:
```python
from pathlib import Path
fpth = Path().resolve() / 'assets' / '6vsb.bcif'
custom_data = {
'data': fpth.read_bytes(),
'format': 'cif',
'binary': True,
}
view = PDBeMolstar(
custom_data=custom_data,
hide_controls_icon=True,
hide_expand_icon=True,
hide_settings_icon=True,
hide_selection_icon=True,
hide_animation_icon=True,
hide_water=True,
hide_carbs=True,
)
view
```
See the example notebook for more advanced usage.
Solara example code can be found [here](https://github.com/Jhsmit/ploomber-solara-ipymolstar)
## Citing
`ipymolstar` uses [anywidget](https://github.com/manzt/anywidget) to create a widgets based on [Mol*](https://molstar.org/)
To cite Mol*:
> David Sehnal, Sebastian Bittrich, Mandar Deshpande, Radka Svobodová, Karel Berka, Václav Bazgier, Sameer Velankar, Stephen K Burley, Jaroslav Koča, Alexander S Rose: Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures, Nucleic Acids Research, 2021; [10.1093/nar/gkab31](https://doi.org/10.1093/nar/gkab314).
### PDBeMolstar
The PDBeMolstar widget is based on the [PDBe integration](https://github.com/molstar/pdbe-molstar) of Mol*.
### MolViewSpec
The MolViewSpec widget is based on [MolViewSpec](https://github.com/molstar/mol-view-spec). To cite MolViewSpec:
> Sebastian Bittrich, Adam Midlik, Mihaly Varadi, Sameer Velankar, Stephen K. Burley, Jasmine Y. Young, David Sehnal, Brinda Vallat: Describing and Sharing Molecular Visualizations Using the MolViewSpec Toolkit, Current Protocols, 2024; [10.1002/cpz1.1099](https://doi.org/10.1002/cpz1.1099)
See also the [RCSB citation policies](https://www.rcsb.org/pages/policies) for additional citation information.
## Development
The molviewspec widget front-end code bundles it's JavaScript dependencies. After setting up Python,
make sure to install these dependencies locally:
```sh
npm install
```
While developing, you can run the following in a separate terminal to automatically
rebuild JavaScript as you make changes:
```sh
npm run dev
```
### Creating a new release
- update `__version__` in `__init__.py`
- create a new release on GitHub, choose as tag 'v' + `__version__`; ie 'v0.0.3'
- GitHub actions should automatically deploy to PyPi
### Hot reloading
To enable anywidget hot reloading, you need to set the env var `ANYWIDGET_HMR` to 1.
Windows:
```bash
set ANYWIDGET_HMR=1
jupyter lab
```