Thanks, I will. On Tue, Dec 6, 2022 at 7:21 AM Jeff Newmiller <jdnew...@dcn.davis.ca.us> wrote: > > I have never seen this package mentioned on this list. You should contact the > package maintainer. > > On December 5, 2022 9:59:34 PM PST, Luigi Marongiu <marongiu.lu...@gmail.com> > wrote: > >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. > >> > > >> > > > > > > -- > Sent from my phone. Please excuse my brevity.
-- 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.
