Features

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!

• 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).

• View molecules (or subsets) using nglviewer.

• 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 sire can do, or take a look at the tutorial for more detail.