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https://github.com/mojaie/MolecularGraph.jl

Graph-based molecule modeling toolkit for cheminformatics
https://github.com/mojaie/MolecularGraph.jl

cheminformatics chemistry graph julia julia-language mcs molecular-modeling molecule toolkit

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Graph-based molecule modeling toolkit for cheminformatics

Lists

README 

        

MolecularGraph.jl

===================================================



[![DOI](https://zenodo.org/badge/151080560.svg)](https://zenodo.org/badge/latestdoi/151080560)

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









Documentation and API Reference

------------------------------------



[Documentation and API Reference](https://mojaie.github.io/MolecularGraph.jl/dev)



How to use

------------------------------------



[Pluto.jl notebook tutorials](https://github.com/mojaie/MolecularGraph.jl_notebook)



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](https://mojaie.github.io/MolecularGraph.jl_notebook/getting_started.html)

- [Molecular graph basics](https://mojaie.github.io/MolecularGraph.jl_notebook/molecular_graph_basics.jl.html)

  - 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](https://mojaie.github.io/MolecularGraph.jl_notebook/properties_and_descriptors.jl.html)

  - 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](https://mojaie.github.io/MolecularGraph.jl_notebook/preprocessing.jl.html)

  - Remove hydrogen vertices

  - Extract molecules of interest

  - Standardize charges

  - Dealing with resonance structure

  - Customize property updater

- [Mass and isotopes](https://mojaie.github.io/MolecularGraph.jl_notebook/mass_and_isotopes.jl.html)

  - Molecular weight and exact mass

  - Uncertainty

  - Isotopic composition

  - Simulate mass spectrum

- [Substructure and query](https://mojaie.github.io/MolecularGraph.jl_notebook/substructure_and_query.jl.html)

  - Substructure match

  - InChI and InChIKey

  - SMARTS query

  - Structural alerts (e.g. PAINS)

  - Functional group analysis

  - Query containment

- [Maximum common substructure (MCS)](https://mojaie.github.io/MolecularGraph.jl_notebook/maximum_common_substructure.html)

  - Maximum common induced substructure (MCIS)

  - Maximum common edge-induced substructure (MCES)

  - Connected or disconnected MCS

  - Working with larger molecules

  - Topological constraint (tdMCS)

- [Drawing molecule](https://mojaie.github.io/MolecularGraph.jl_notebook/drawing_molecule.jl.html)

  - Settings of 2D structure images

    - Change image size

    - Layout for web and Pluto notebook

  - Regenerate 2D coordinates

  - 3D molecule rendering using Makie.jl

- [Stereochemistry](https://mojaie.github.io/MolecularGraph.jl_notebook/stereochemistry.jl.html)

  - 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](https://github.com/MakieOrg/Makie.jl))

  - SDFile reader/writer (.sdf, .mol)

  - SMILES/SMARTS parser (only reader)

  - Coordinates generation ([coordgenlibs](https://github.com/schrodinger/coordgenlibs))



- Properties and descriptors

  - H-bond donor/acceptor

  - rotatable bonds

  - Aromaticity

  - Wildman-Crippen logP



- Substructure and query

  - InChI ([InChI](https://www.inchi-trust.org/))

  - Serialization (molecule object <-> 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



- 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](http://opensource.org/licenses/MIT)  

See [Assets/README.md](https://github.com/mojaie/MolecularGraph.jl/tree/master/assets) for details of external data sets and their licenses.



Copyright

-----------------



(C) 2018-2023 Seiji Matsuoka and contributors