Visualize dynophores: 2D ligand view

In this notebook, we will show how to view the dynophore’s superfeatures mapped onto a 2D view of the structure-bound ligand. This visualization uses the `rdkit library <>`__.

%load_ext autoreload
%autoreload 2
from pathlib import Path

from dynophores import Dynophore
from dynophores.viz import view2d

Set paths to data files

DATA = Path("../../dynophores/tests/data")
dyno_path = DATA / "out"
pdb_path = DATA / "in/startframe.pdb"

Load data as Dynophore object

dynophore = Dynophore.from_dir(dyno_path)

Show 2D ligand view

Static view

Note that you can toogle the superfeature highlights and PDB serial atom numbers on or off.

[5]:, show_superfeatures=True, show_pdb_serial_numbers=False)

Interactive view