[R] How to draw chemical structures with R?
jdnewm|| @end|ng |rom dcn@d@v|@@c@@u@
Tue Dec 6 07:21:27 CET 2022
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.luigi using 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-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.
>> 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)[]
>> > view.molecule.2d(mol)
>> >> Error in view.molecule.2d(mol) : java.lang.NoSuchMethodError: <init>
>> > ```
>> > ______________________________________________
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>> > and provide commented, minimal, self-contained, reproducible code.
Sent from my phone. Please excuse my brevity.
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