MolecularGraph.jl

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

Usage

• Try it with Jupyter notebook tutorials
• Documentation and API Reference

Features

• Chemical structure file I/O

  • 2D structure image drawing and export to SVG
  • 3D structure drawing
  • SDFile import/export (.sdf, .mol)
  • SMILES/SMARTS parser

• Database

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

• 2D geometry

  • Stereochemistry drawing
  • Coordinates generation (coordgenlibs)

• Sub(super)structure

  • Library search by using SMARTS query
  • Subgraph isomorphism detection with VF2 algorithm
  • Monomorphism, node-induced and edge-induced
  • Constraints (mandatory/forbidden mapping)

• SMARTS query-based substructure analysis

  • functional group mining
  • structural alerts (by using ChEMBL dataset)

• 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) 2018-2021 Seiji Matsuoka and contributors