README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  eval=FALSE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# chemdoodle

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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/")
```