Video Tutorials

Below is a list of video tutorials made by Andrew Tarzia, which provide a thorough introduction to stk. More videos can be found here.

Basics of stk

Video 1 is an overview of the 2021 publication covering the capability of stk and the docs of stk. The Jupyter notebook is available here.

Functional Groups in stk

Video 2 is an overview of defining FunctionalGroup instances in stk. It includes an example of the versatility of stk for unique problems. The Jupyter notebook is available here.

Cage Building

Video 3 is an overview of organic and metal-organic cage construction in stk. This example covers how stk handles isomerism and the concept of hierarchical construction. The Jupyter notebook is available here.

Hierarchical Construction with stk

Video 4 expands on the use of hierarchical construction in stk. It includes an implementation of the example from the 2021 publication and the construction of a rotaxane/cage hybrid! The Jupyter notebbok is available here.

Using stko with stk

Video 5 shows the usage of the stko package to optimize and calculate the properties of stk molecules. The Jupyter notebook is available here.

Databases and stk-vis in stk

Video 6 is a short introduction to databasing and the use of StkVis with stk molecules! The Jupyter notebook is available here.

Host-Guest Conformers with stk

Video 7 shows an example of the generation of stk host-guest complexes using the software SpinDry. The Jupyter notebook is available here.

Swapping Hosts and Guests in Complexes

The new video shows an example of loading an existing host-guest complex into stk, extracting the different molecules (with networkx), and then building new complexes from that. The code is available here.

Processing stk building blocks before construction

This video shows the use of the new bbprepared library that helps to process automatically generated stk BuildingBlock conformers to be better fit for construction.