Getting started

BiochemicalVisualization.jl provides graphical representations of molecular systems. In the following example, a sample structure is loaded through BiochemicalAlgorithms.jl and prepared for visualization later on.

using BiochemicalAlgorithms, BiochemicalVisualization

# Read PDB file from the BiochemicalAlgorithms.jl repository
sys = load_pdb(ball_data_path("../test/data/AlaAla.pdb"))

# Prepare molecule
infer_topology!(sys)
assign_radii!(sys)

Available representations

The following code examples showcase all currently available representations. Please note that, on this page, all interactive widgets are replaced by screenshots thereof. When executed locally, e.g., in a Julia REPL or in a Jupyter notebook, the code examples should open a browser window with the correpsonding widget or embed the widget into the notebook, respectively.

Ball-and-stick representation

ball_and_stick(sys)

Ball-and-stick representation of a simple molecule

Stick representation

stick(sys)

Stick representation of a simple molecule

Van-der-Waals surface representation

van_der_waals(sys)

Van-der-waals representation of a simple molecule

Please note that the sphere radii are currently not automatically assigned by atom type but rather read from the corresponding Atom object (i.e., from its radius field).