software

open-source 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
• stko : Wrappers for optimisation and property calcualtion of stk molecules
• MCHammer : Efficient MC-based optimisation of chemical structures based on alchemical bond and nonbonded potential functions (implemented into stk as an Optimizer class)
• SpinDry : Efficient MC-based host-guest conformer generation of stk molecules based on alchemical potential functions
• I also have some examples of stk usage 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.