Hi All,

I think I've run into either some unexpected behavior or misleading
documentation in the MCS module. In the guide it reads: "An atomCompare of
'any' says that any atom matches any other atom, 'elements' compares by
element type, and 'isotopes' matches based on the isotope label. Isotope
labels can be used to implement user-defined atom types." I've created a
sort of hash based on the element and hybridization of the atom and stored
it in the isotope label. FindMCS generates the correct results but the
SMARTS in the MCSResult is garbage.

MCSResult(numAtoms=35, numBonds=39,

My isotope label has overwritten the other element information. The SMILES
I'm comparing are
"COc1ccc(C(Nc2nc3c(ncn3COCC=O)c(=O)[nH]2)(c2ccccc2)c2ccccc2)cc1" and

Is there a way to produce the same matching behavior (hybridization and
element must match) and still produce usable SMARTS? I specifically wanted
to be able to use a hash so that I could extend this to other features.

I can't seem to find any discussion of this in any of the mailing lists or
API, but I may have missed something.

Bests and Thanks for any help,

Liz Wylie
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