openBabelPlot {ChemmineR} | R Documentation

## Plot compound structures

### Description

Plots compound structure(s) for molecules stored in SDF and SDFset containers.

### Usage

    	openBabelPlot(sdfset, height=600, noHbonds = TRUE, regenCoords=FALSE)

### Arguments

`sdfset` | Object of class `SDFset`
`height` | The height of the image in pixels. The generated image is always square, so this will also be the width.
`noHbonds` | If `TRUE`, then the C-hydrogens and their bonds - explicitly defined in an SDF - are excluded from the plot.
`regenCoords` | If ChemmineOB is installed and this option is TRUE, then Open Babel will be used to re-generate the 2D coords for each compound before plotting it. This often results in a nicer layout. If you want to save the results of the coord re-generation, call the `regenerateCoords` function first yourself and save the result.

### Details

The function `openBablePlot` depicts a 2D compound structure based on the XY-coordinates specified in the atom block of an SDF. If more than one compound is given in the SDFset, they will be arranged in a grid layout.

### Author(s)

Kevin Horan

### See Also

`sdf.visualize`

### Examples

    	## Not run:
    	## Import SDFset sample set
    	data(sdfsample)
    	(sdfset <- sdfsample)

    	## Plot single compound structure
    	openBabelPlot(sdfset[1])

    	## Plot several compounds structures
    	openBabelPlot(sdfset[1:4])

    ## End(Not run)

[Package ChemmineR version 3.39.2 Index]