Tutorial

This tutorial will take you through most aspects of running, understanding, analysing and customising Sire. The tutorial is designed to be run through in order.

This tutorial assumes that you have installed Sire following the instructions here, and have activated the Anaconda / miniconda Python environment into which Sire was installed. You can test this by starting python and typing

>>> import sire as sr

If sire imports without error, then everything is working.

If you can’t import sire, or have any other problems, then please ask for support.

• Part 1 - Loading and Saving
  • Importing sire
  • Loading a molecule
  • Simple indexing
  • Saving a molecule
  • Loading from multiple files
  • Loading and saving trajectories
  • Supported file formats
• Part 2 - Indexing and Searching
  • Indexing Atoms
  • Indexing Residues
  • Indexing Chains
  • Indexing Segments
  • Indexing Molecules
  • Indexing Bonds
  • Indexing Angles
  • Indexing Dihedrals
  • Indexing Impropers
  • Searching
• Part 3 - Molecular Properties
  • Atom Properties
  • Cursors and Editing Properties
  • Residue, Chain and Segment Properties
  • Molecule Properties
  • Bond Views and Properties
  • Angle Views and Properties
  • Dihedral Views and Properties
  • Improper Views and Properties
• Part 4 - Measurement, Trajectories and Movement
  • Measuring Distances and Angles
  • Measuring Trajectories
  • Measuring Energies
  • Measuring Energies Across Trajectories
  • Moving Atoms and Molecules
  • Moving Bonds, Angles and Dihedrals
• Part 5 - Interconverting with other Packages
  • Converting Molecules
  • Viewing Molecules in 2D
  • Creating Molecules from Smiles Strings
  • Searching for Fragments using Smarts Strings
  • Molecular Dynamics and Minimisation
• Part 6 - Morphs and Alchemical Free Energies
  • Merged Molecules
  • Alchemical Dynamics
  • Restraints
  • Alchemical Restraints
  • Running a Free Energy Perturbation Simulation
  • Running Faster Free Energy Simulations
• Part 7 - Merged Molecules and Lambda Levers
  • Perturbation
  • Lambda schedules and levers
  • Ghost Atoms and Softening Potentials
  • Creating merge molecules
  • Perturbation Files (pertfiles)
  • Annihilation and Decoupling
  • Residue mutations
• Part 08 - QM/MM
  • Introduction
  • Sire-EMLE
  • Alanine-dipeptide conformational landscape
  • Diels-Alder reaction