MolecularGraph.jl

MolecularGraph.jl is a graph-based molecule modeling and chemoinformatics analysis toolkit fully implemented in Julia.

draw3d_rotation.mp4

Documentation and API Reference

Documentation and API Reference

How to use

Pluto.jl notebook tutorials

To run codes in your environment, see Edit or run this notebook instruction shown in the top-right of the tutorial pages below.

• Getting started
• Molecular graph basics
  • Scope of MolecularGraph.jl
  • Considerations in molecular graph implementation
  • Basic operations provided by Graphs.jl interface
  • MolGraph type and atom/bond properties
• Properties and descriptors
  • Built-in molecule properties and descriptors
    • Lipinski's Rule of five (RO5)
    • Molecular formula
    • Atom and bond properties
    • Graph topology (ring and fused ring)
  • Auto-update mechanism of properties
• Preprocessing
  • Remove hydrogen vertices
  • Extract molecules of interest
  • Standardize charges
  • Dealing with resonance structure
  • Customize property updater
• Mass and isotopes
  • Molecular weight and exact mass
  • Uncertainty
  • Isotopic composition
  • Simulate mass spectrum
• Substructure and query
  • Substructure match
  • InChI and InChIKey
  • SMARTS query
  • Structural alerts (e.g. PAINS)
  • Functional group analysis
  • Query containment
• Maximum common substructure (MCS)
  • Maximum common induced substructure (MCIS)
  • Maximum common edge-induced substructure (MCES)
  • Connected or disconnected MCS
  • Working with larger molecules
  • Topological constraint (tdMCS)
• Drawing molecule
  • 2D structure images
    • Display and export in SVG format
    • Display and export in PNG format
    • Layout for Pluto notebook
    • Regenerate coordinates
  • 3D molecule rendering using Makie.jl
• Stereochemistry
  • Stereochemistry as a molecular graph property
  • Stereospecific implicit hydrogens

Features

• Chemical structure file I/O

  • 2D structure image drawing and export to SVG
  • 3D structure drawing (Makie.jl)
  • SDFile reader/writer (.sdf, .mol)
  • SMILES/SMARTS reader
  • SMILES writer (RDKitMinimalLib.jl)
  • Coordinates generation (coordgenlibs)

• Properties and descriptors

  • H-bond donor/acceptor
  • rotatable bonds
  • Aromaticity
  • Wildman-Crippen logP
  • Fingerprints (RDKitMinimalLib.jl)

• Substructure and query

  • InChI (InChI)
  • Serialization (molecule object <-> loss-less format or CommonChem JSON)
  • Subgraph isomorphism detection with VF2 algorithm
    • SMARTS query match
    • Monomorphism, node-induced and edge-induced match
    • Constraints (mandatory/forbidden vertex mapping)
  • Functional group query set
  • Structural alerts detection with ChEMBL dataset
  • SMARTS query containment

• Atomic mass

  • standard atomic/molecular weight
  • relative atomic/molecular mass
  • isotopic composition

• Molecular graph topology

  • Ring, scaffold, connected components
  • Minimum cycle basis (de Pina algorithm)
    • Smallest set of smallest rings (SSSR)
  • Planarity (left-right planarity test)
  • Maximum matching
    • Kekulization
  • Graph traversal

• Maximum common substructure (MCS)

  • By clique detection algorithm
  • Node-induced (MCIS) and edge-induced (MCES)
  • Connected and disconnected
  • Topological constraint (known as tdMCS)
  • Diameter restriction (MCS-DR) and graph-based local similarity (GLS)

License

MIT license
See Assets/README.md for details of external data sets and their licenses.

Copyright

(C) 2018-2025 Seiji Matsuoka and contributors