https://github.com/zachcp/chemdoodle

htmlwidgets for chemdoodle web components
https://github.com/zachcp/chemdoodle

Last synced: 3 months ago
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htmlwidgets for chemdoodle web components

• Host: GitHub
• URL: https://github.com/zachcp/chemdoodle
• Owner: zachcp
• Archived: true
• Created: 2015-05-27T04:02:45.000Z (over 9 years ago)
• Default Branch: master
• Last Pushed: 2021-04-11T22:43:33.000Z (over 3 years ago)
• Last Synced: 2024-05-14T13:31:48.215Z (6 months ago)
• Language: R
• Homepage: http://zachcp.github.io/chemdoodle/
• Size: 664 KB
• Stars: 18
• Watchers: 3
• Forks: 9
• Open Issues: 5
• Metadata Files:
  • Readme: README.Rmd

Awesome Lists containing this project

• awesome-shiny-extensions - chemdoodle - HTML widget for visualizing and drawing molecules. (Visualization / Chemical Data)

README

        
---

output: github_document

---

```{r, include = FALSE}

knitr::opts_chunk$set(

  collapse = TRUE,

  eval=FALSE,

  comment = "#>",

  fig.path = "man/figures/README-",

  out.width = "100%"

)

```

# chemdoodle

This repo is for the creation of an HTMLWidget for visualizing

moleules based on the [ChemDoodle WebComponent](http://web.chemdoodle.chttps://github.com/rajarshi/cdkr/tree/master/rcdkom/) library,

the [HTMLWidgets](http://www.htmlwidgets.org/) package, and the

[Chemistry Development Kit](https://github.com/cdk) via [rCDK](https://github.com/rajarshi/cdkr/tree/master/rcdk). **Warning: development in flux and liable to break until version 1.0!**

### Install

And the development version from [GitHub](https://github.com/) with:

```{r}

# install.packages("devtools")

# devtools::install_github("zachcp/chemdoodle")

```

### Basic Viewer

```{r}

library(chemdoodle)

chemdoodle_viewer("C1CCCCC1", width = 100, height = 100)

```

### Transform Canvas

```{r}

chemdoodle_transform("C1CCCCC1", width = 100, height = 100)

```

### Slideshow Canvas

```{r}

chemdoodle_slideshow(c("C1CCCCC1", "CNCNCNC1CCCCC1", "CN1C=NC2=C1C(=O)N(C(=O)N2C)C",

                       "CC1=C(C=C(C2=C1C(=C)OC2=O)OC)OC"), 200,200, bondscale=15)

```

### Sketcher

The ChemDoodle Sketcher needs extra work for functionality. You can use `drawMolecule()` to create a seketcher and the molecule is captured as ChemDoodle JSON which can be converted to

a CDK Atom and be passed around, converter or whatever. Currently round-tripping (putting the molecule back) doesn't work because there are some issues around properly scaling the compound.

```{r, eval=FALSE}

#experimetal/new features

# gets a molecule from the chemdoodle sketcher

moljson <- drawMolecule()

# processed the Molecule JSON to a CDK AtomContainer - this can be saved,

# written to Smiles etc.

mol <- processChemDoodleJson(moljson)

# convert to SMILES

smi <- toSmiles(mol)

# convert to InChi

inchi <- toInChi(mol)

# try sending a molecule to the sketcher (needs work)

drawMolecule(mol=mol)

```

### Access the Sketcher as a ShinyApp 

```{r, eval=FALSE}

# you can also try a minimal shiny example

shiny::runApp(appDir = "examples/minimalshinyapp/")

```