Scaffold Graph Adapter

Common Scaffolds around molecule datasets is becoming very common to find basically a lowest common denominator. Luckily, there is a tool from the University College London that accomplishes just that. The ScaffoldGraph:

GitHub - UCLCheminformatics/ScaffoldGraph: ScaffoldGraph is an open-source cheminformatics library, built using RDKit and NetworkX, for the generation and analysis of scaffold networks and scaffold trees.GitHub

Import Package

from global_chem import GlobalChem
from global_chem_extensions import GlobalChemExtensions

gc = GlobalChem()
cheminformatics = GlobalChemExtensions().cheminformatics()

Connect the ScaffoldGraph Adapter

Install the additional Scaffold Graph Visualizer Adapter

!pip install -q ipycytoscape

Fetch Node Data and Create the Scaffold Graph with IUPAC/SMILES

Code

from scaffoldgraph.vis.notebook import cytoscape

adapter = cheminformatics.create_scaffold_graph(
            node_key = 'rings_in_drugs'
)

tree = adapter.connect()
print (tree)

Output