Hi Pat,
On Sat, May 5, 2018 at 4:12 AM Patrick Walters <[email protected]> wrote:
> Hi All,
>
> I've been playing around with some of the structural alerts from ChEMBL
> and noticed that on alert was generating a SMARTS Parse Error with the
> RDKit.
>
> [2H,3H,13C,14C,15N,125I,23F,22Na,32P,33P,35S,45Ca,57Co,103Ru,141Ce]
>
This should be parseable, but the effect of the "[2H,3H..." part of the
query is almost certainly not what is intended. The RDKit's interpretation
of this is explained here:
https://github.com/rdkit/rdkit/issues/1719
with a reference to the daylight documentation.
In short:
[2H] -> [2#1]
[3H] -> [3#1]
[2H, 3H] -> [2*H, 3*H]
There's a bit more discussion of this point here:
https://github.com/rdkit/rdkit/issues/1404
@Michał Nowotka <[email protected]> : who would be the right person in the
ChEMBL group to let know about this?
> It appears that the issue was reported previously and that Greg fixed the
> bug.
>
> https://github.com/rdkit/rdkit/issues/1719
>
> It seems like the problem is still there in 2018.03
>
Yep, looks like I fixed it and then forgot to create a pull request. The PR
is in now.
-greg
> >>> from rdkit import rdBase
> >>> rdBase.rdkitVersion
> '2018.03.1'
> >>> from rdkit import Chem
> >>> Chem.MolFromSmarts('[2H,13C]')
> [22:06:46] SMARTS Parse Error: syntax error for input: '[2H,13C]'
>
>
> Pat
>
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