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https://github.com/jhsmit/ipymolstar

PDBeMolstar as anywidget
https://github.com/jhsmit/ipymolstar

anywidget molstar pdbe

Last synced: 2 months ago
JSON representation

PDBeMolstar as anywidget

Host: GitHub
URL: https://github.com/jhsmit/ipymolstar
Owner: Jhsmit
Created: 2024-02-14T10:00:22.000Z (10 months ago)
Default Branch: master
Last Pushed: 2024-10-04T09:19:38.000Z (3 months ago)
Last Synced: 2024-10-05T00:13:49.854Z (3 months ago)
Topics: anywidget, molstar, pdbe
Language: Jupyter Notebook
Homepage:
Size: 514 KB
Stars: 22
Watchers: 2
Forks: 3
Open Issues: 4
Metadata Files:
- Readme: README.md

Awesome Lists containing this project

README

# ipymolstar

![image](https://github.com/Jhsmit/ipymolstar/assets/7881506/589a94d5-2647-4977-90aa-c886c10cacb9)

## 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 app demo code in [PyCafe](https://app.py.cafe/snippet/solara/v1?c=H4sIAN-cF2YAA8VZCW_bNhT-K5wKDErnOHGbLKsBYWuObgOWLluyAUMUGJRE20JkUqUoJ0aW_76PpCRT8tG0TTEasWTy8fHdB_PgxSJh3tBLZ7mQihQio5KGfCzFjKT5YiayQlFJquWL02N2bqd65OqXs_Ozywo2oYrGGS0KVtTAzVSP0CJJY1WB2jP6NEtpAyvvekTOQ94io5_RKOT681ODK-TmYSg5xeQw5AQDdLK4zNgoTYakUJIEJPQGHxY89CxAXBZKzEYaz5BoYsi_5L3gDID6YYGiySgWmZBLFC_eHelPjaXIUz4kkRAZVt_RrKg2TtOEjXKRLWYMmzes31G1ZXXKsCooiCw2wsRURptXueAjaIYnVEIIm1AIKgvWXdYfLRrMVKL_k9FYpXPm14L2d3ZCPk-LNEqzVC1GcVQA-jr0KrZDrwd5GR7tq8OQnTDU21eX1GrR0BV6N5qUXArFUg0ipNYQThn88c97C_nq4uzAwDU6r8EeLJ-h93NWxkJjs6r27bwepcwCkKZUXgz39vIyiqds1udxlPZ5hpd02p-I-Z5khcLqZC8WfCwk2Cv29jEG378d6Kd-3bs8ffcjAHPBCzZSi5wFBZ2zb5upiBaM0xkLTmokr09HJ7-fX_z-13u8_Ho6Ojx68xpMLcnTYFSBwiIZtxailFO5CIy6qumd6hl6b68unoVV-F7Jkz1Qtnf45vAIS7GQScWnfrVcvk6WPH4e20D-DGyf0PEYVvI8anZ4f3U4ePPVeNfIn4H3SyUX8ZRv4558JvsHB4P9o8FXE4BFDxa-QAaPVVaoYpUhnzOOBJOwMbmw0ePvlN35CDC3IwY7McHMhr2dKmfcpWpah7sTBCI_9KqtZI69oVcD6qEgQR1jQk-jhHTTMRKci5wwEIn1LJ1MVZ0w9HCSZp9lQMOV__KlTYkgUNH-nGYl2-nZQwLzjWC7jUU6YX5NXgzVIdT2SMEU4rv5sQzkJbSCoxXz94FTw3fIbiCRbQ10e91fu2uUSzZPRalzgHNQPduRu2HG5E8ly1iV0tpOe6-sM06jBmjAbqvzQZps2NJKGNf7N9W-JkPcssWGnZzdKz-FxPx2OuljS4Gcp7OeRbaq8G-CTVJxDGdlm7Nm5QoDKHM8mF_XH4EtrZD2rLHd4K1ew6-KOz20zX0Swso6VzFWWoZx2b2jRh4aoW9M1NRFPaId3Ly6DgI-9TwJtI8sFYbw1CZvudSHvVq8LYZaiFwNrqByF5-CrG19K-jayy2ELTY7cAbGHtDYbQfzC8KxMHSrVJIWBIaYECW032rXr0XT3VswNivg5XxcFimfkClDtROxmGI_uWMajVveGoxTcdechpp5k304BAWOYgxL_UzcwS0QlhzkgS6Wn25_Ln6ERNRvLq62x1231GlIWNqlG6vf5vkxBWHOuU4Eu9LR80pMJpkJXWtCvcjKGS_864Me-eHGxbImISCNKYnYbZNBh1H4CupYQ6l_b91C57COlbkn1GOti1UoWubWJcsydlwqhXR7CWsAl6voDUnBOjt1cms9ahaC-mUNTNXZBToi7Y4zdm9Lcf22KwVS5U1n0zqmKxYs8T50xXSZ0vgMbGN5isE8AerdQTvgbUeGNGsE-jFsHce3uE7TuV-oRaaVOGU6Tg7Jq_0cvK7seHIUWCV8g9W4EXOd8PT4JKtxGLtE1dEqEN3R6OH0mOjD12hfD2si3RixDbhooI17bwB9ivV11F_FnCeLtp1D_hfhOna5TbyrEXC7gLO0UBvqli8T91r_OJmy-DYS92t4rfnU9yNrebSHLovdvobcFowyOosSSu7R3Dj5RO8K7rvMrRCMfsL650jX28QU9O7FxRoToMrc-KD9MNckD8vtj7qW_7ixaQSB_tpkYC4fL18-aNAhuX_cZltbJL6UekUyaZO81c4mDA2Bkk7zYel_VquJFF_W3FWcRtFJ41tEYjSbqGhM8dkjUSbi2-BKtmo3PdzMp3P7OeOlbwp3XCvJACfoMI-bnhEIQ4Gk0CCN4iwFNtMyrlOFnOsKQMgLQKG82SAmxIEEsnUMtq6Wt4io2rTedJtSfMV8t_lcLbeVDaEnWSIpUm9Pn22ZtiejNF82gn7dEH5HBijllqLe4kIvPq01fmG-n9rl7ugI5cNoq6vl3YeKQhito37bsQGsWR49tPso45c1-Oae356Hvw6LdUGl-z94Ti2nHQhK_-wg2d6O_0YXolR-PE2zRDJeCwdmruBZ5tFplM3c-tb6qQ25ZKg-uFMUV1QsmazpCeoX3DDg_iOi0qCEdbt44UrGPpfX4TtaThvvOXKZznA5Y7Tm9WCOH8pUGr0X-v8Jzf8OsKYrJMxZUvGb5rnWlDccm4sdjyWpOuM0ygCFIMYe_wOmoGbMlxgAAA) ☕
- Upload your Alphafold3 .zip result and view plddt or chain colors in the `solarafold` result viewer on [huggingface](https://huggingface.co/spaces/Jhsmit/solarafold) 🤗

## Installation

```sh
pip install ipymolstar
```

## 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)

## Cite

`ipymolstar` uses [anywidget](https://github.com/manzt/anywidget) to create a widget based on the [PDBe integration](https://github.com/molstar/pdbe-molstar) of [Mol*](https://molstar.org/).

When using `ipymolstar`, please cite:

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).

See also the [RCSB citation policies](https://www.rcsb.org/pages/policies) for additional citation information.

## Development

### 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 th env var `ANYWIDGET_HMR` to 1.

Windows:
```bash
set ANYWIDGET_HMR=1
jupyter lab
```