John Mayfield

Oh grrr... not finished yet but can see it still didn't pickup the SonarCloud token. This is infuriating, we could just expose the token publicly but I thought how I...

Yes it uses secrets, however since the branch is in your fork it will not see the secret. So o thought the work around was you define a secret in...

We renderer them as paths otherwise we don’t have correct sizing information and we want things to be consistent. We could make an option to not do this for the...

There is no way to currently do it then, a new option "NonRenderedTitle" option which by passes the rendering would do the trick. Please feel free to submit a patch

Interesting, the issue with the "phane" structures are there are an exponential amount of essential cycles. If you call the lower level cycles method directly I think you can see...

Scrap that, it's relavent cycles I was thinking off and that number is fine: ```java IAtomContainer mol = smipar.parseSmiles("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"); Cycles cycles = Cycles.relevant().find(mol); System.err.println(cycles.numberOfCycles()); ``` Essential: 26 Relevant: 2074

Actually when you remove the C D4 atom (the cross over bit) you end up with: 16,777,240 cycles which is why the you get out of memory. I'm not really...

Yeah we can check how many there are before and throw and exception if it's too many (5> million is probably reasonable)

> option to go all the way if desired. tricky without an an API change

Ah it's another bug when trying to actually generate them, I'll try and find time to take a look. Thanks.