Uli

breaking change in SeedGenerator?

10

I updated my project to cdk28 and realized that the hash values for `IAtomContainer`s changed. It took me a while to track this down. I finally figured out that a...

for a negative and a positive return value from AtomEncoder

added test case for initial cycles oom

4

test case for #976

OOM in InitialCycles when applying aromaticity

8

I experience an OOM when applying the aromaticity for this (slightly?) symmetrical structure:  `C1=CC2=CC3=C1C1=C4C=C(C=C1)C1=CC=C(C=C1)C1=CC=C(C=C1)C1=CC=C(C=C1)C1=CC=C(C=C1)C1=CC=C(C=C1)C1=CC=C(C=C1)C1=CC=C(C=C1)C1=CC=C(C=C1)C1=CC=C(C=C1)C1=CC=C(C=C1)C1=CC5=C(C=C1)C1=C(C=C(C=C1)C1=CC=C(C=C1)C1=CC=C(C=C1)C1=CC=C(C=C1)C1=CC=C(C=C1)C1=CC=C(C=C1)C1=CC=C(C=C1)C1=CC=C(C=C1)C1=CC=C(C=C1)C1=CC=C(C=C1)C1=CC=C2C=C1)C345` Here is the stacktrace: ``` Exception in thread "main" java.lang.OutOfMemoryError: Java heap space at org.openscience.cdk.graph.InitialCycles.indexOfEdge(InitialCycles.java:228)...

I use the download grype subaction to download grype and then run it locally (i.e., on the github runner): ``` - name: 💾 Install grype uses: anchore/scan-action/download-grype@v3 id: grype_install -...

support for bond types >4 in MDLV3000Reader and MDLV3000Writer

6

I would like to read a MDL V3000 file that has a bond type >4, that is, a query bond type. Looking at the code, an exception is raised for...

My gradle build requires the full git history to be available as a version string is inferred from the git history based on tags and commits using the gradle plugin...

callout boxes are not rendered in html

1

Github flavored markdown support callout boxes such as: ``` > [!WARNING] > Text goes here. ``` > [!WARNING] > Text goes here. ``` > [!IMPORTANT] > Text goes here. ```...