Features

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!

• 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.

• Search for molecules, atoms etc using a powerful search engine.

• Convert molecules to and from RDKit, and easily create molecules from smiles strings or generate smiles strings from molecules.

• Convert molecules to and from smarts strings too!. Use smarts (and smiles) in your searches.

• 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).

• Create merged molecules that represent perturbations for relative and absolute free energy calculations.

• Create merged molecules that represnet perturbations of residues in proteins.

• Mutate residues or parts of molecules via copy-and-pasting bits of molecules.

• 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.

• 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.