cdkr

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- Do you use rcdk or depend on it? - I'm looking to hand off the maintenance reins. - If you're interested, comment on this thread or shoot me an...

zachcp

Implement [Release note figures as vignettes](https://github.com/cdk/cdk/releases). - [2.9 Release Notes](https://github.com/cdk/cdk/releases/tag/cdk-2.9) - [2.8 Release Notes](https://github.com/cdk/cdk/releases/tag/cdk-2.8) - [2.5 Release Notes](https://github.com/cdk/cdk/wiki/2.5-Release-Notes) - [2.4 Release Notes](https://github.com/cdk/cdk/wiki/2.3-Release-Notes) - [2.2 Release Notes](https://github.com/cdk/cdk/wiki/2.2-Release-Notes)

zachcp

visualization with `view.molecule.2d` fails with an `<init>` error message

11

Given this code (in RStudio): ``` library(rcdk) cxSMILES = "O=C(*)Oc1ccc(cc1)C(C)(C)c1ccc(O*)cc1 |Sg:n:0,1,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20::ht| Poly(bisphenol-A-carbonate" mol = rcdk::parse.smiles(cxSMILES) rcdk::view.molecule.2d(mol) ``` The last code fails with this exception: ``` Error in rcdk::view.molecule.2d(mol) : java.lang.NoSuchMethodError:...

egonw

Only "0" returned for AromaticAtomsCountDescriptor and AromaticBondsCountDescriptor

4

Hello rcdk, I am querying the CDK chemical properties using smiles generated using the CSI:FingerID module of Sirius. For some reason, I get "0" for number of aromatic atoms and...

bsedio

This works.... ```R > formula isvalid.formula(formula,rule=c("nitrogen","RDBE")) [1] FALSE ``` But when I try.... ```R > formula isvalid.formula(formula,rule=c("nitrogen","RDBE")) Error in .jcall(rdbeRule, "D", "validate", molecularFormula) : java.lang.NullPointerException ``` I'm trying to validate...

arthuc01

Isotope labels for get.isotope.pattern

1

Hi, I'm using the rCDK package and I'm getting the isotope pattern for a given molecular formula, but they have no labels as to what combination of isotopes each line...

gjgfml

Compounds that contain covalently bound Boron have an issue with calculating all BCUT descriptors. A warning is returned and all the BCUT values are NA. Example of Epetraborole: qsar_p

dischiessel

InChIKey functionality crashes with "Exception: java.lang.StackOverflowError thrown from the UncaughtExceptionHandler in thread "process reaper""

6

I describe the issue here because `rinchi` is just a wrapper around this functionality, and nothing we can change in `rinchi` would make a difference to this issue: ``` library(rcdk)...

meowcat

rcdk::matches() function bugs

3

There is an issue for substructure match function. I got true value even if the substructure is not in the query molecule. Please include a minimal reproducible example (AKA a...

YANGJJ93MS

view.molecule.2D not working on Rstudio

5

mols view.molecule.2d(m) Error in view.molecule.2d(m) : java.lang.NoSuchMethodError:

garimaloh