On Dec 8, 2012, at 7:01 AM, Greg Landrum wrote:
> It's a pretty small API change, but there's a huge amount of code that needs 
> to be changed in the back and lots and lots of testing that has to be done, 
> so this is going to take a while.

Speaking of hydrogens, I came across a strange query (part of the
BindingDB_structure set from my Structure Query Collection).


Because of RDKit's sanitization, the '[H]' gets absorbed into the atoms.
This breaks a bond, so what started as a ring with poor chemistry ends
up as two linear pieces with sane chemistry.

>>> mol = Chem.MolFromSmiles("C1N[H]OC[H]1")
>>> Chem.MolToSmiles(mol)

The above query is nonsensical, but I don't think sanitization should
modify the topology of the input.

Divalent hydrogen does exist in a very small number of real records.
I once came across a couple of structure with a 4-membered boron/hydrogen
ring, like this:

>>> mol = Chem.MolFromSmiles("[B]1[H][B][H]1")
>>> Chem.MolToSmiles(mol)

I am unable to find a public record with that core, to act as a
more realistic test case.


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