Visualize proteins and ligands

This document describes how to visualize proteins and ligands constructed using the Protein and Ligand classes, and tools to visualize SDF files.

Visualizing a protein¶

Browser support

These visualizations work best on Google Chrome. We are aware of issues on other browsers, especially Safari on macOS.

A protein object can be visualized using show:

from deeporigin.drug_discovery import Protein

protein = Protein.from_pdb_id("1EBY")

protein.show()

A visualization such as this will be shown:

Jupyter notebook required

Visualizations such as these require this code to be run in a jupyter notebook. We recommend using these instructions to install Jupyter.

The Ligand class is the primary way to work with ligands in Deep Origin.

Browser support

These visualizations work best on Google Chrome. We are aware of issues on other browsers, especially Safari on macOS.

A ligand object can be visualized using show:

from deeporigin.drug_discovery import Ligand

serotonin = Ligand.from_identifier("serotonin")

serotonin.show()

If a ligand is backed by a SDF file, a 3D visualization will be shown, similar to:

A visualization such as this will be shown:

Jupyter notebook required

Visualizations such as these require this code to be run in a jupyter notebook. We recommend using these instructions to install Jupyter.

If a ligand is not backed by a SDF file, a 2D visualization will be shown:

Molecules in SDF files can be visualized the show_molecules_in_sdf_file function as follows:

from deeporigin.drug_discovery.chemistry import show_molecules_in_sdf_file
show_molecules_in_sdf_file("path/to/file.sdf")