https://github.com/mojaie/moleculargraph.jl_notebook
Notebook tutorials for MolecularGraph.jl
https://github.com/mojaie/moleculargraph.jl_notebook
Last synced: 12 months ago
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Notebook tutorials for MolecularGraph.jl
- Host: GitHub
- URL: https://github.com/mojaie/moleculargraph.jl_notebook
- Owner: mojaie
- License: cc-by-4.0
- Created: 2020-03-13T04:11:49.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2024-07-21T05:37:43.000Z (almost 2 years ago)
- Last Synced: 2025-05-07T08:08:57.704Z (about 1 year ago)
- Language: Jupyter Notebook
- Size: 2.17 MB
- Stars: 11
- Watchers: 1
- Forks: 3
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
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](https://mojaie.github.io/MolecularGraph.jl_notebook/getting_started.html)
- [Molecular graph basics](https://mojaie.github.io/MolecularGraph.jl_notebook/molecular_graph_basics.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.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.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.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.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.html)
- 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](https://mojaie.github.io/MolecularGraph.jl_notebook/stereochemistry.html)
- 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](https://nbviewer.jupyter.org/github/mojaie/MolecularGraph.jl_notebook/blob/master/notebook_v0_13/gettingStarted.ipynb)
- [Basics of molecular graph](https://nbviewer.jupyter.org/github/mojaie/MolecularGraph.jl_notebook/blob/master/notebook_v0_13/molecularGraphBasics.ipynb)
- [Preprocessing](https://nbviewer.jupyter.org/github/mojaie/MolecularGraph.jl_notebook/blob/master/notebook_v0_13/preprocess.ipynb)
- [Calculation of descriptors](https://nbviewer.jupyter.org/github/mojaie/MolecularGraph.jl_notebook/blob/master/notebook_v0_13/calculateDescriptors.ipynb)
- [Molecular/atomic mass and isotopes](https://nbviewer.jupyter.org/github/mojaie/MolecularGraph.jl_notebook/blob/master/notebook_v0_13/massAndIsotopes.ipynb)
- [Search molecules from database](https://nbviewer.jupyter.org/github/mojaie/MolecularGraph.jl_notebook/blob/master/notebook_v0_13/substructureSearch.ipynb)
- [Maximum common substructure (MCS)](https://nbviewer.jupyter.org/github/mojaie/MolecularGraph.jl_notebook/blob/master/notebook_v0_13/mcs.ipynb)
License
------------------------
[CC-by-4.0](https://creativecommons.org/licenses/by/4.0/)
Copyright
------------------------
(C) 2020-2024 Seiji Matsuoka