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openbiosim - sire
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  • Features
  • Installation
  • Quick Start Guide
  • Tutorial
    • 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 8 - QM/MM
      • Introduction
      • Sire-EMLE
      • Alanine-dipeptide conformational landscape
      • Diels-Alder reaction
  • Diaries
  • Detailed Guides
    • Searching
    • Trajectories
    • Viewing Molecules
    • OpenMM Integration
    • Units
  • Documentation
    • sire module
    • Sub-modules
      • sire.base
        • Public API
      • sire.cas
        • Public API
      • sire.convert
        • Public API
      • sire.io
        • Public API
        • Public API
      • sire.maths
        • Public API
      • sire.mm
        • Public API
      • sire.mol
        • Public API
      • sire.morph
        • Public API
      • sire.restraints
        • Public API
      • sire.search
        • Public API
      • sire.stream
        • Public API
      • sire.system
        • Public API
      • sire.units
        • Public API
      • sire.utils
        • Public API
      • sire.vol
        • Public API
  • How to ask for help
  • Contributing
    • Developer’s guide
    • Coding Style
    • Packaging releases
    • Roadmap
  • Contributors
  • Code of Conduct
  • Changelog
  • Acknowledgements
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sire.mol¶

  • Public API
    • Atom
    • AtomIdx
    • AtomMapping
    • AtomMatch
    • AtomMatchM
    • AtomName
    • AtomNum
    • BondOrder
    • Chain
    • ChainIdx
    • ChainName
    • Cursor
    • Cursors
    • CursorsM
    • Dynamics
    • Element
    • Minimisation
    • MolIdx
    • MolName
    • MolNum
    • Molecule
    • ResIdx
    • ResName
    • ResNum
    • Residue
    • SegIdx
    • SegName
    • Segment
    • SelectorMol
    • Stereochemistry
    • TrajectoryIterator
    • get_alignment()
    • is_water()
    • selection_to_atoms()
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Last updated on Oct 12, 2025