Symmetry Analysis

The symmetry module converts molecular structures into networkx graphs and applies Weisfeiler–Lehman (WL) refinement to discover atoms that share identical local environments. This is particularly helpful when analysing RESP results, because the buckets returned by the WL procedure highlight atoms that can share constrained charges.

from pathlib import Path

from symmetry import buckets_from_pdb

buckets = buckets_from_pdb(Path("data/raw/1.pose.pdb"), radius=10)
print(f"Identified {len(buckets)} equivalence classes")

Each bucket contains the indices of atoms that are indistinguishable after r rounds of WL refinement. Increase radius when you need a deeper comparison of atomic environments.

Hydrogen-less molecular network used for WL refinement.

Radius 10	Radius 15

The figure above starts from the hydrogen-less network of the biliverdin fragment. The colourings correspond to WL buckets evaluated at radii 10 and 15, respectively.