Contents

• TIES
• Installation
• Examples - Command Line
• Examples - Python
• TIES Protocol
  • Superimposition and defining the alchemical region
  • Charge treatment
    • Joint region: matched atoms and their charges
• Classes
  • Ligand
  • Protein
  • Pair
  • Config
• API
  • ties.Ligand
  • ties.Protein
  • ties.Pair
  • ties.Config
  • ties.topology_superimposer
  • ties.helpers
  • ties.generator