How to draw chemical structures with R?
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 at 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