MolecularGraph.jl tutorial notebooks (Pluto.jl)

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

Legacy tutorials (MolecularGraph.jl v0.13 and below)

1. Install Julia kernel to Jupyter Notebook

If you are new to Jupyter Notebook with Julia kernel, please set up Julia kernel according to IJulia instruction.
https://github.com/JuliaLang/IJulia.jl

1. Clone the repository

% cd your_workspace
% git clone https://github.com/mojaie/MolecularGraph.jl_notebook.git
Cloning into 'MolecularGraph.jl_notebook'...

2. Launch Julia REPL

% cd MolecularGraph_notebook
% julia

               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.6.0 (2021-03-24)
 _/ |\__'_|_|_|\__'_|  |  Official https://julialang.org/ release
|__/                   |

julia>

3. Type ] to enter Pkg mode and create project

(@1.6) pkg> activate .
Activating new environment at `your_workspace/MolecularGraph_notebook/Project.toml`

4. Install packages

instantiate the notebook tutorial project. If you do not have 'Plot.jl' yet, it may take several minites to install.

(MolecularGraph) pkg> instantiate
  Progress [========================================>]  1/1
1 dependency successfully precompiled in 8 seconds (16 already precompiled)

• Getting started
• Basics of molecular graph
• Preprocessing
• Calculation of descriptors
• Molecular/atomic mass and isotopes
• Search molecules from database
• Maximum common substructure (MCS)

License

CC-by-4.0

Copyright

(C) 2020-2024 Seiji Matsuoka