[R] How to draw chemical structures with R?

[Luigi Marongiu]

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-groups using 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>
> > ```
> >
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> >
>


-- 
Best regards,
Luigi