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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