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Graph-based molecule modeling toolkit for cheminformatics

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hs-heddy/MolecularGraph.jl

 
 

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MolecularGraph.jl

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

Installation

 (v1.0) pkg> add MolecularGraph

Usage

Features

  • Chemical structure file I/O

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

    • Molecular weight, composition and formula
    • H-bond donor/acceptor
    • rotatable bonds
    • Aromaticity
    • Wildman-Crippen logP
  • Molecular graph topology

    • Ring, scaffold, connectivity
    • Graph traversal
  • Sub(super)structure

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

License

MIT license

Copyright

(C) 2018-2019 Seiji Matsuoka

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Graph-based molecule modeling toolkit for cheminformatics

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  • Jupyter Notebook 57.3%
  • Julia 42.5%
  • Other 0.2%