John Mayfield

Doh I didn't mean to check in the options yet as they don't do anything. I really am hesitant about recalculate H, Evan Bolton at pubchem likes the term RoboChemistry...

Wait for my ACS talk and I will show the Wild West of SMIRKS bespoke variations. I think having another variant, does not help the situation, however some middle ground...

Are you manually writing these SMIRKS or generating them, if the later then can make the generate write them better.

Matches https://www.daylight.com/dayhtml/javadocs/index.html?com/daylight/Transform.html https://www.daylight.com/dayhtml/doc/man/man3/dt_xtransform.html https://www.daylight.com/dayhtml/doc/man/man3/dt_utransform.html https://www.daylight.com/dayhtml/doc/man/man3/dt_transform.html xtransform is the only one you apply them all at once, the others have overlaps so you need to rematch.

What would expect the unique/all options. As described in the doc these are the "iterate possible matches options" and control which matches you apply them to. You can only do...

Mostly finished my RDKit talk prep now so will try and catch up on this PR/others

SMILES: CCOCCF SMIRKS: [O:1][C:2][C:3]>>[OH1:1].[CH3:2][C:3] Expected outcome with Transform.Mode.Unique: CC.OCCF and CCO.CCF Actual outcome with Transform.Mode.Unique: CC.O[CH3]CF and C[CH3]O.CCF SMILES: CCOCCF SMIRKS: [C:4][O:1][C:2][C:3]>>[C:4][OH1:1].[CH3:2][C:3] Expected outcome with Transform.Mode.Unique: CCO.CCF and CC.OCCF Actual...

I think the issue is newAtomContainer(mol) does a shallow copy... doing a clone fixes the issue but really we just need a deep copy ``` private static IAtomContainer copyOf(IAtomContainer mol)...

Main usages are cdk-dict and pcore, so should be easy(ish) to remove.

I think also cmlxom>xom>cmlxom which is harder to remove.