renderSMILES.CDKdepict: Render SMILES into 2D image for plotting via CDK Depict

In schymane/RChemMass: Various Cheminformatic, Curation and Mass Spectrometry Functions

Description

This function uses the URL built with buildCDKdepictURL to create an image for direct use in plotting, via a temporary svg file and given coordinates. Output requires that plot.new has been called.

Usage

renderSMILES.CDKdepict(depictURL,coords=c(0,0,100,100), filename="tmp.svg")

Arguments

depictURL	A URL created with buildCDKdepictURL
coords	This is used to control the size of the image within the plot. Values c(xmin,ymin,xmax,ymax).
filename	Name of the temporary svg file for saving the image. Can be used to save all image files if renamed for every instance.

Value

Returns an image for use during plotting

Author(s)

Emma Schymanski <[e-mail]>

See Also

buildCDKdepictURL to create the URL, renderSMILES.rcdk for alternative plotting direct from SMILES.

Examples

plot.new()
plot.window(xlim=c(0,200), ylim=c(0,100))
test_url <- buildCDKdepictURL("OS(=O)(=O)c1ccc(cc1)C(CC(=O)O)CC(=O)O |Sg:n:15:m:ht,Sg:n:11:n:ht|",
style="cow",title="SPADCs, n+m=0-5", abbr="off",suppressh=TRUE,showtitle=TRUE,zoom=5,annotate="off",
smarts="C(=O)O")
renderSMILES.CDKdepict(test_url)

schymane/RChemMass documentation built on Jan. 25, 2021, 5:45 a.m.