On Dec 16, 2016, at 3:27 PM, Andrew Dalke wrote:
> 2013 RDKit didn't preserve the atom order between labeled and unlabeled atoms.
...
> I no longer have an older version of RDKit installed.
My memory is wrong. I have rebuilt a version from 2013 and been unable to find
a failure case.
That is, overnight I had it fragment every bond from about 450,000 structures
and make either "[*:1].[*:1]" or "[*:1].[*:2]" pairs, then compared the
canonical "de-labeled" SMILES (the canonical labeled SMILES with the :1/:2
removed) to the unlabeled canonical SMILES. (I also specified the isotope as
2*atomic number so there wouldn't be a problem with the brackets.)
In every case the unlabeled and delabled SMILES were identical.
I tried some other variations but still found no mismatches.
> Going through my notes, here was one of the failure cases:
>
> core =>
> Cc1cc2c3c(c1)C[N@]([*])CCN(C)CC[N@@]([*])Cc1cc(C)cc(c1OCCCO3)C[N@@](C)CCN(C)CC[N@](C)C2
> syntax =>
> Cc1cc2c3c(c1)C[N@]([*:1])CCN(C)CC[N@@]([*:2])Cc1cc(C)cc(c1OCCCO3)C[N@](C)CCN(C)CC[N@@](C)C2
> canonical =>
> Cc1cc2c3c(c1)C[N@]([*:2])CCN(C)CC[N@@]([*:1])Cc1cc(C)cc(c1OCCCO3)C[N@@](C)CCN(C)CC[N@](C)C2
It appears this was from another problem. I wanted to fragment the structure
and produce a canonical fragmented structure. The problem in the above is that
the labels of "1" and "2" break the symmetry and lead to different canonical
outputs.
It is not related to the question you [Stephen] asked.
It may be that I did my analysis of canonical atom order in labeled/unlabeled
SMILES with a newer version of the toolkit than 2013. In any case, I am
surprised to find how stable those labels are in the 2013 release.
Cheers,
Andrew
[email protected]
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