MolBokeh

MolBokeh is a simple package for viewing the image of molecules in interactive graphics from the Bokeh package without the need to run a web application such as flask or dash in the backend, thus facilitating integration with other tools and codes.

Installation

pip3 install molbokeh

Simple usage

For more detailed usage examples, look the notebook at example/how_to_use.ipynb or open in Google Colab (Opt1), Colab (Opt2)

import pandas as pd
from MolBokeh import MolBokeh
from bokeh.plotting import figure,show
from bokeh.models import ColumnDataSource

path = 'data.csv'
df = pd.read_csv(path)

source = ColumnDataSource(df)
fig = figure(width=600, height=500,tools="pan,box_zoom,wheel_zoom,zoom_in,zoom_out,reset,save,hover")
fig.scatter(x='MolWt', y='MolLogP', source=source, size=12,alpha=0.6)

## Adding molecules
fig = MolBokeh().add_molecule(fig=fig,
                              source=source,
                              smilesColName='Smiles_canon',
                              hoverAdditionalInfo=['MolWt','MolLogP','nRing','qed','TPSA'],
                              molSize=(100,100))
show(fig)

Parameters info

Parameter	Type	Default	Description
fig	bokeh.plotting._figure.figure	required	Bokeh plot object created from source(df)
source	bokeh.models.sources.ColumnDataSource	required	Bokeh data type used to plot initial chart.
smilesColName	str	required	Smiles column name in dataframe used to create source object
hoverAdditionalInfo	None or list	None	List of column names (variables) to be shown within the graphs hover.
molSize	tuple	(150,150)	Size of the image of the molecule to be shown within the hover, also changes the size of the hover frame