dsxksss/ipymolstar

PDBeMolstar as anywidget

ipymolstar

Live Demo

Give ipymolstar a spin without even installing python!

• Try it in jupyter lab via JupyterLite 🌍🚀
• Explore the solara ☀️ demo application on Ploomber-cloud ⛅
• Grap a cup and play with the solara app demo code in PyCafe ☕

Installation

pip install ipymolstar

Use

from ipymolstar import PDBeMolstar
view = PDBeMolstar(molecule_id='1qyn', theme='light', hide_water=True)
view

Loading local data, hiding the buttons:

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

Cite

ipymolstar uses anywidget to create a widget based on the PDBe integration of Mol*.

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.

See also the RCSB citation 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:

set ANYWIDGET_HMR=1
jupyter lab