Graph-based molecule modeling toolkit for cheminformatics
73 Stars
Updated Last
1 Year Ago
Started In
October 2018


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



  • Chemical structure file I/O

    • Structure image drawing and export to SVG
    • SDFile import/export (.sdf, .mol)
    • SMILES/SMARTS parser
  • Database

    • InChI
    • Serialization (molecule object <-> JSON)
  • Basic descriptors

    • H-bond donor/acceptor
    • rotatable bonds
    • Aromaticity
    • Wildman-Crippen logP
  • Atomic mass

    • standard atomic/molecular weight
    • relative atomic/molecular mass
    • isotopic composition
  • Molecular graph topology

    • Ring, scaffold, connectivity
    • Graph traversal
  • 2D geometry

    • Stereochemistry drawing
    • Coordinates generation (coordgenlibs)
  • Sub(super)structure

    • Library search by using SMARTS query
    • Subgraph isomorphism detection with VF2 algorithm
    • Node-induced and edge-induced
    • Constraints (mandatory/forbidden mapping)
  • SMARTS and terminology graph-based functional group analysis

  • 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)


MIT license


(C) 2018-2020 Seiji Matsuoka

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