Work with proteins

This document describes how to work with proteins and use them in Deep Origin tools.

The Protein class

The Protein class is the primary way to work with proteins in Deep Origin.

Constructing a protein

From a file

A protein can be constructed from a file:

from deeporigin.chemistry import Protein
protein = Protein("/path/to/pdb")

From a PDB ID

A protein can also be constructed from a PDB ID:

from deeporigin.chemistry import Protein
protein = Protein(pdb_id="1EBY")

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:

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.