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A python package for generating interactive views of chemical spaces.

Project description

Faerun (Python)

Faerun (Python) is based on the Lore.js 3D WebGL engine for interactive big data rendering and the FUn project. It facilitates the creation of interactive (2D and 3D) HTML plots of chemical data (or chemical spaces). Molecular structures are rendered using SmilesDrawer.

Associated Publication: https://academic.oup.com/bioinformatics/article/34/8/1433/4657075

Faerun Python

Examples

The code of the examples shown above for creating interactive 2D and 3D maps from Drugbank can be found in the examples directory. Following, a simple example of plotting any data:

import numpy as np
from faerun import Faerun

faerun = Faerun(view='free', shader='circle')

t = np.linspace(0, 12.0, 326)
s = np.sin(np.pi * t)
c = np.cos(np.pi * t)

faerun.plot({ 'x': t, 'y': s, 'z': c, 'c': t / max(t) })

TODO

  • [ ] Add the abilty to draw shapes as well as colours
  • [ ] Make output templatable

Documentation

Faerun(title='python-faerun', point_size=5, tree_color='#aaaaaa', clear_color='#111111', fog_intensity=2.6, coords=True, coords_color='#888888', view='free', shader='circle')
Parameter Default Description
title 'python-faerun' The title of the HTML document.
point_size 5 The size of the points.
tree_color '#aaaaaa' Not yet implemented.
clear_color '#111111' The clear colour, or background colour is used to clear the canvas after each rendering step.
fog_intensity 2.6 Fog is used to darken / lighten far away points depending on the clear_color. This is a visual cue helpful for depth perception in orthogonal projections.
coords True Whether or not to draw the coordinate axes.
coords_color '#888888' The colour used to draw the coordinate axes.
view 'free' The view mode. Available options: free, front, back, left, right, bottom, top
shader circle The name of the shader used to draw the points. Available options: circle, legacyCircle, sphere
Faerun.plot(path, data, x='x', y='y', z='z', c='c', colormap='plasma', smiles='smiles', tree=None)
Parameter Default Description
data A dict or a Pandas DataFrame containing the data.
x x The name of the column containing the x-coordinates.
x y The name of the column containing the y-coordinates.
x z The name of the column containing the z-coordinates.
c c The name of the column containing the values by which the points are coloured. Has to be normalized between 0.0 and 1.0
smiles smiles The name of the column containing the SMILES strings with which the points are annotated.
path '' The path to which the HTML and data files will be written.
tree None Not yet implemented.

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