Welcome to stko’s documentation!

GitHub: https://github.com/JelfsMaterialsGroup/stko

Install

stko can be installed directly with pip:

$ pip install stko

Dependencies

The software packages we offer optimizers are also depencies depending on the desired functions used. These are:

• MacroModel

• GULP

• XTB

• OpenBabel

Overview

stko is a Python library which performs optimizations and calculations on complex molecules built using stk. In the case of optimizations, a clone of stk.Molecule is returned. For calculators, a Results class are used to calculate and extract properties of an stk.Molecule.

Examples

For every class (including Calculator, Optimizer), there are small examples of usage on the associated docs page. We have a page dedicated to analysing cage structures. There are also some examples for stko usage available here. These cover:

• Basic examples

• Molecule alignment

• Using calculators

• Cage analysis

• Using Gulp

• Splitting molecules

• Interfacing with MDAnalysis

• Interfacing with OpenBabel

• Interfacing with Orca

• Calculating molecular shape with RDKit

• Extracting stk topology graphs from molecules

• Analysing torsions

• Converting molecules to their Zmatrix

Indices and Tables

• Index

• Module Index

• Search Page