JSmol bokeh extension

Custom extension to bokeh for JSmol.

• Based on the surface3d example and extension widget
• works both using bokeh and bokeh server

Installation

pip install jsmol-bokeh-extension

Usage

Below a complete example.py demonstrating how to use the jsmol bokeh extension:

rom bokeh.models import ColumnDataSource
from bokeh.io import show, curdoc
from bokeh.models.widgets import Button, TextInput
from bokeh.layouts import layout, widgetbox

from jsmol_bokeh_extension import JSMol

script_source = ColumnDataSource()

info = dict(
    height="100%",
    width="100%",
    serverURL="https://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php",
    use="HTML5",
    j2sPath="https://chemapps.stolaf.edu/jmol/jsmol/j2s",
    script=
    "background black;load https://chemapps.stolaf.edu/jmol/jsmol-2013-09-18/data/caffeine.mol",
)

applet = JSMol(
    width=600,
    height=600,
    script_source=script_source,
    info=info,
)

button = Button(label='Execute')
inp_script = TextInput(value='background white;')


def run_script():
    script_source.data['script'] = [inp_script.value]


button.on_click(run_script)

ly = layout([applet, widgetbox(button, inp_script)])

show(ly)
curdoc().add_root(ly)

Note: The example can be run both using bokeh and bokeh server:

# run locally (displays structure but button won't work)
python example.py

# run using bokeh server (displays structure and button should work)
bokeh serve example.py --show

Links

• the JSmol Info dict