John Mayfield

SMIRKS is like a programming language, doing things you didn't ask for is dangerous. But yes it is a common requirement that users want to write loose patterns that will...

That is completely not valid, you generated it with ChemAxon Marvin and there is no linkage between the left and right side since the link atoms are handled with recursive...

You should use more of the expressions, v/D/X/H to constrain the pattern and you can do a generalised one like this. Any atom which isn't present in the pattern is...

Thanks will take a look, probably just the container one is reusing atoms. You can probably fix it by calling atom typing/add hydrogens but should clean it up as we...

Yes it is as I expected, basically internally it does this before generating each fragment: ```java AtomContainerManipulator.clearAtomConfigurations(frag); for (IAtom atom : frag.atoms()) atom.setImplicitHydrogenCount(null); AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(frag); CDKHydrogenAdder.getInstance(frag.getBuilder()).addImplicitHydrogens(frag); Aromaticity.cdkLegacy().apply(frag); ``` I'll look a...

Sure, I think actually you just remove the code I pasted above... perhaps add an option for it though.

Isn’t this what the obabel command line is for? 😃

White on transparent wot: is already implemented and we used in Arthor for dark mode :) my plan was to refactor this and make it more tuneable, still have presets...

Here is the gist of the canonical bond code/expressions. Something I forgot to add is there is subtle semantics between SMARTS and MDL, in MDL SINGLE_OR_DOUBLE may match aromatic bonds...

We don't enforce this but you shouldn't really be mixing query atoms/bonds and regular atoms/bonds. That's not how the CDK APIs are intended to be used - it would be...