Thanks for the tip! I think the problem is all Java-based, the SMILES structure comes from the example in the template, it should work. There is something missing in the execution...
On Tue, Dec 6, 2022 at 3:12 AM LMH <lmh_users-gro...@molconn.com> wrote: > > 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. > > > -- Best regards, Luigi ______________________________________________ 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.
