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
- Built-in molecule properties and descriptors
- 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
- 2D structure images
- Stereochemistry
- Stereochemistry as a molecular graph property
- Stereospecific implicit hydrogens
- 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
- Clone the repository
% cd your_workspace
% git clone https://github.com/mojaie/MolecularGraph.jl_notebook.git
Cloning into 'MolecularGraph.jl_notebook'...
- 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>
- Type
]
to enter Pkg mode and create project
(@1.6) pkg> activate .
Activating new environment at `your_workspace/MolecularGraph_notebook/Project.toml`
- 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)
(C) 2020-2024 Seiji Matsuoka