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 <https://www.rdkit.org/docs/index.html>`__.

[1]:

%load_ext autoreload
%autoreload 2

[2]:

from pathlib import Path

from dynophores import Dynophore
from dynophores.viz import view2d

Set paths to data files

[3]:

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

Load data as Dynophore object

[4]:

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]:

view2d.static.show(dynophore, show_superfeatures=True, show_pdb_serial_numbers=False)

[5]:
../_images/tutorials_explore_view2d_9_0.png

Interactive view

[6]:

view2d.interactive.show(dynophore)