Just my opinion, but I think you would be better off to draw the structures using a drawing program like MarvinSketch (free, java based) and save the structure as a SMILES file, MOL file, or SDF. You should be able to import any of those into R. A program like MarvinSketch will check the structure for errors as you draw it and keep to standardized formats.
By the way, I see no error in the SMILEA string for the structure in your expamle so your error is not in the drawing part of the process. Even so, I try to keep to well established tools for basic tasks and Marvin as is well established as it gets. I would look for an example of what you are trying and see if you can get the example to work. LMH Luigi Marongiu wrote: > Hello,' > I have seen from this link > https://cran.r-project.org/web/packages/rcdk/vignettes/using-rcdk.html > that there is a way to draw chemical structures using R via rcdk package. > I tried to draw a simple structure but I got an error. What is it > missing? What is the correct syntax? > Thanks > > ``` > library(rcdk) > smile <- 'c1ccccc1CC(=O)C(N)CC1CCCCOC1' > mol <- parse.smiles(smile)[[1]] > view.molecule.2d(mol) >> Error in view.molecule.2d(mol) : java.lang.NoSuchMethodError: <init> > ``` > > ______________________________________________ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
