https://github.com/tpfto/MoleculeViewer

A package for visualizing molecules.
https://github.com/tpfto/MoleculeViewer

chemistry mathematica molecular-graphics visualizing-molecules wolfram-language wolfram-mathematica

Last synced: about 1 month ago
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A package for visualizing molecules.

• Host: GitHub
• URL: https://github.com/tpfto/MoleculeViewer
• Owner: tpfto
• License: mit
• Created: 2017-09-23T14:54:55.000Z (about 7 years ago)
• Default Branch: master
• Last Pushed: 2019-09-29T13:30:18.000Z (about 5 years ago)
• Last Synced: 2024-08-05T09:11:32.174Z (5 months ago)
• Topics: chemistry, mathematica, molecular-graphics, visualizing-molecules, wolfram-language, wolfram-mathematica
• Language: Mathematica
• Size: 3.39 MB
• Stars: 11
• Watchers: 3
• Forks: 5
• Open Issues: 4
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.txt

Awesome Lists containing this project

• awesome-wolfram-language - MoleculeViewer

README

        
# MoleculeViewer

### A package for visualizing molecules.

[![DOI](https://zenodo.org/badge/104575485.svg)](https://zenodo.org/badge/latestdoi/104575485)

![cucurbituril rendered using MoleculeViewer](https://user-images.githubusercontent.com/13274842/65828934-ed138600-e2d2-11e9-9b07-32fb147249d1.png)

MoleculeViewer is a *Mathematica* package that renders molecules in a manner resembling physical molecular models. In particular, multiple bonds are depicted as out-of-plane bonds.

The package supports additional features like stylized molecule depictions (ball-and-stick, spacefilling, etc.), multiple atom legends, custom coloring of atoms, atom highlighting and tooltips.

The package also provides a number of auxiliary functions that use the services of [Open Babel](http://openbabel.org/), [Imago OCR](https://lifescience.opensource.epam.com/imago/index.html), [JME](http://www.molinspiration.com/jme/), [Accelrys JDraw](http://download.accelrys.com/freeware/accelrys_draw/ReleaseNotes_AccelrysDraw_4.1.pdf), [JChemPaint](https://jchempaint.github.io/), [ChEMBL Beaker](https://github.com/chembl/chembl_beaker), [ChemSpider](http://www.chemspider.com/), [NCI CACTUS](https://cactus.nci.nih.gov/chemical/structure), [PubChem](https://pubchem.ncbi.nlm.nih.gov/), [RCSB PDB](https://www.rcsb.org/), and [ZINC](https://zinc.docking.org/).

Download the paclet from the [releases](https://github.com/tpfto/MoleculeViewer/releases) page, and install it by evaluating the following in *Mathematica*:

    Needs["PacletManager`"]

    PacletInstall["/path/to/paclet/MoleculeViewer-1.0.paclet"]

where `"/path/to/paclet/MoleculeViewer-1.0.paclet"` should be replaced with the actual path to the downloaded paclet file. 

See the file `molviewer.nb` for more detailed information on the package. A molecule gallery `gallery.nb` is also provided.