sire is a powerful Python/C++ module for loading and manipulating
molecular (predominantly biomolecular) systems.
Calculate alchemical free energies using GPU-accelerated molecular dynamics simulations.
Load and save molecules from a number of molecular file formats. This includes Amber, CHARMM and GROMACS files.
This includes loading, editing and saving trajectory files!
Create 2D structure views of molecules, including automatically deriving bond orders, formal charges and stereochemistries from molecules where that information is not present.
Search for molecules, atoms etc using a powerful search engine.
Convert molecules to and from BioSimSpace, thereby opening the way for automatic parameterisation of ligands, solvation of molecules, and running of complex simulation workflows.
A powerful property system that lets you associate nearly any data with nearly any molecular view or sub-view. For example, you can assign multiple different coordinate properties for atoms based on their different frames or perturbation states.
A comprehensive units system that lets you choose you own physical units, and that interpret units from strings and convert from popular units packages.