sire is a powerful Python/C++ module for loading and manipulating
molecular (predominantly biomolecular) systems.
Load and save molecules from a number of molecular file formats. This includes Amber, CHARMM and GROMACS files.
This includes loading trajectory files!
View molecules (or subsets) using nglviewer. This includes creating complex multi-representation views.
Create 2D structure views of molecules, including automatically deriving bond orders, formal charges and stereochemistries from molecules where that information is not present.
Convert molecules to and from RDKit, and easily create molecules from smiles strings or generate smiles strings from molecules.
Convert molecules to OpenMM, and run molecular dynamics and minimisation via an intuitive interface.
Convert molecules to and from BioSimSpace, thereby opening the way for automatic parameterisation of ligands, solvation of molecules, and running of complex simulation workflows.
Edit molecules, move them, recombine them into new molecular systems.
Calculate energies of molecular systems (or subsets) using the forcefield parameters read from the input files. Calculate energies across trajectories (or subsets of trajectories).
Measure distances, angles, dihedrals etc, including across frames of trajectories (or subsets of trajectories).
Search for molecules, atoms etc using a powerful search engine.
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.
and lots more! Take a look at the quick overview for a flavour of what
sirecan do, or take a look at the tutorial for more detail.