John Mayfield
John Mayfield
Close as stale... I don't think parameterised tests make sense here. Particularly because you would have to test them all in a module which included all dependencies. I prefer it...
Somewhere they could/should be used is AtomTyping...
Sounds good, hard to decide where they would go. FuncGroups is sort a descriptor and SugarRemoval is sort of a standardisation (which we don't have a module for).
Thanks for the feedback, this would be quite simple. Ironically I never liked those APIs as I think it should just return a normal ``Set`` or ``List``
Something you might find useful Uli is we can store reactions as molecules. See [ReactionManipulator](http://cdk.github.io/cdk/latest/docs/api/index.html?org/openscience/cdk/tools/manipulator/ReactionManipulator.html).toMolecule(); and toReaction();
No worries, I was going to use sed as I think most of it is find/replace the package names :-)
@uli-f Thanks for the offer to help. Some of these we need to "start" a v3.0 branch for which we're not quite at yet. However the Stream API for ACSet...
Perhaps: ``` if (atom.isDefined(IAtom.HydrogenCount)) { // do the "special case" } ```
I think this was perhaps based on the restricted documentation from MDL/Daylight. i.e. Coming from SDF/SMILES everything is set by design. I guess CML you have missing fields though? Anyways...
> * AtomContainerManipulator::perceiveAtomTypesAndConfigureAtoms Indeed, I always thought that was too long a name but I can't think of a better one :-)