MolecularGraph.jl
MolecularGraph.jl is a graph-based molecule modeling and chemoinformatics analysis toolkit fully implemented in Julia.
Installation
(@v1.8) pkg> add MolecularGraph
Usage
See Pluto.jl notebook tutorials
- 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
- Settings of 2D structure images
- Change image size
- Layout for web and Pluto notebook
- Regenerate 2D coordinates
- 3D molecule rendering using Makie.jl
- Settings of 2D structure images
License
MIT license See Assets/README.md for details of external data sets and their licenses.
Copyright
(C) 2018-2023 Seiji Matsuoka and contributors