structure generation of (supra)molecular materials

I am a developer of stk for the generation of molecular and periodic material structures. I recently put together a play list of tutorials on stk usage: stk tutorials and have some examples of stk usage here.

I have some code available on GitHub Gists.

stko contains wrappers for optimisation and property calcualtion of stk molecules

I have also developed some low-cost Monte Carlo-based algorithms for optimisation stk molecule optimisation (MCHammer) and host-guest conformer generation/optimisation (SpinDry).

preparing building blocks for structure generation

I recently developed bbprepared that contains algorithms and tests (examples) for preparing building blocks for stk usage.

Here is a video on its usage.

coarse-grained structure generation

CGExplore is a library for using stk with coarse-grained molecules to afford more efficient high-throughput screening and rational design. This library is under-development but it’s first usage is written up here.

calculating molecular size

mol-ellipsize is an efficient method for calculating molecular size based on fitting an ellipsoid to the vdw cloud of a molecule. Examples are provided within the github repository. See a blog post here.

visualising molecular pores

PoreMapper is a very efficient way to map the inside of a molecular pore for visualisation and analysis. See a blog post here.