On Nov 9, 2017, at 21:49, Brian Cole wrote:
> Certainly, but thousands of lines of Python doesn't fit in an email in an
> easily digestible way. :-)
I'll restate things since I wasn't clear. While this step may be what you need
for the way you structure things, there might be a better way to st
>
> Somehow you got the code to generate a "9" for that ring closure, which is
> not something that RDKit does naturally, so we are only seeing a step in
> the larger part of your goal.
>
Certainly, but thousands of lines of Python doesn't fit in an email in an
easily digestible way. :-)
> Since
On Nov 9, 2017, at 16:09, Brian Cole wrote:
> Here's an example of why this is useful at maintaining molecular
> fragmentation inside your molecular representation:
>
> >>> from rdkit import Chem
> >>> smiles = 'F9.[C@]91(C)CCO1'
> >>> fluorine, core = smiles.split('.')
> >>> fluorine
> 'F9
Trouble is, you're mixing chemical operations and lexical ones. It
might be handy if this 'just worked' but in practice it's not going to
produce valid SMILES without more work.
I've written code in the past to do this kind of thing for virtual
library building, using dummy atoms to mark link posi
Here's an example of why this is useful at maintaining molecular
fragmentation inside your molecular representation:
>>> from rdkit import Chem
>>> smiles = 'F9.[C@]91(C)CCO1'
>>> fluorine, core = smiles.split('.')
>>> fluorine
'F9'
>>> fragment = core.replace('9', '([*:9])')
>>> fragment
'[C@]([*
On Nov 9, 2017, at 08:13, Greg Landrum wrote:
> As was discussed in the comments of
> https://github.com/rdkit/rdkit/issues/786, I think it's pretty gross that the
> second syntax is even legal. But that's a side point.
To belabor that point. Neither Daylight SMILES nor OpenSMILES accept it, wh
Hi
Surely the problem is that some of these SMILES aren't really valid. From
the Daylight theory manual: '*The bonds are numbered in any order,
designating ring opening (or ring closure) bonds by a digit immediately
following the atomic symbol at each ring closure'* (my emphasis).
So the behavio
On Thu, Nov 9, 2017 at 6:32 AM, Brian Cole wrote:
> Hi Cheminformaticians,
>
> This is an extreme subtlety in the interpretation of SMILES atom
> stereochemistry and I think a bug in RDKit. Specifically, I think the
> following SMILES should be the same molecule:
>
> >>> rdkit.__version__
> '2017
Hi Cheminformaticians,
This is an extreme subtlety in the interpretation of SMILES atom
stereochemistry and I think a bug in RDKit. Specifically, I think the
following SMILES should be the same molecule:
>>> rdkit.__version__
'2017.09.1'
>>> Chem.CanonSmiles('F[C@@]1(C)CCO1')
'C[C@]1(F)CCO1'
>>>
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