Dissent is fine, but it's important to remember that there are *always*
going to be edge cases and that we're not trying to model something
physically observable here. The concept of aromaticity is primarily there
to make canonicalization easier. Section 3.4.2 here:
http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html has more info
about this, as does the RDKit documentation:
http://rdkit.org/docs/RDKit_Book.html#aromaticity
I'm willing to change the current behavior, but someone would need to
explain what it should be changed to in a way that is clear, unambiguous,
and that would allow a human being looking at the structure to relatively
easily figure out whether or not a given ring is aromatic.
On Tue, Oct 23, 2018 at 1:17 PM Chris Earnshaw <cgearns...@gmail.com> wrote:
> Sorry about this, but I think that 'perhaps sub-optimal' should be
> replaced by 'definitely wrong'. The 'quasi-aromatic' system in these two
> structures is identical and should behave as such, but in practice one of
> them matches a pyridine SMARTS pattern and the other doesn't. That
> shouldn't be affected by whether the saturated substituents form a ring or
> not. I do appreciate that it gets messy to deal with as fused rings may be
> fully conjugated, but the current behaviour seems to be disturbingly
> inconsistent. It would be suboptimal to say that no exocyclic bond is
> allowed to steal electrons, but that may be better than what's happening
> here.
>
> Apologies for the dissent!
>
> Chris Earnshaw
>
>
>
> On Tue, 23 Oct 2018 at 11:57, Greg Landrum <greg.land...@gmail.com> wrote:
>
>> The current implementation requires "exocyclic" bonds to actually be
>> *non-ring* bonds in order to be recognized as such.
>> This is perhaps sub-optimal, but it's clearly defined and avoids
>> arguments about when exactly an "exocyclic" bond starts stealing electrons.
>>
>> -greg
>>
>> On Tue, Oct 23, 2018 at 12:46 PM Francis Atkinson <fran...@ebi.ac.uk>
>> wrote:
>>
>>> Ian,
>>>
>>> I make it 6 electrons: two from the N, none from the C double bonded
>>> to the exocyclic N, and one each from four other carbons in the ring. It's
>>> isoelectronic with *e.g.* pyridone, which is aromatic in RDKit...
>>>
>>> In [1]: from rdkit import Chem
>>>
>>> In [2]: Chem.MolToSmiles(Chem.MolFromSmiles('O=c1[nH]cccc1'))
>>> Out[2]: 'O=c1cccc[nH]1'
>>>
>>> The protonated/tautomerised version are indeed aromatic
>>> (interconverting bewteen these species was actually how I came across this
>>> issue), but I still reckon the unprotonated bicyclic should be aromatic
>>> too...
>>>
>>> Francis
>>> On 23/10/2018 11:18, Ian Tickle wrote:
>>>
>>>
>>> Hi, it seems to me that neither is aromatic since the N-substituted
>>> hetero ring breaks the Huckel rule by having 7 e- (2 from the N and 1 each
>>> from the 5 Cs). If you remove 1 e- from the N (so it's [n+]) and also make
>>> the external double bond into a single (picking up a proton on the other N)
>>> it becomes pyridinium which is certainly aromatic.
>>>
>>> [n+]12ccccc1NCCC2
>>>
>>> [n+]12ccccc1NC.CC2
>>>
>>> What does it make of those?
>>>
>>> Cheers
>>>
>>> -- Ian
>>>
>>>
>>> On Tue, 23 Oct 2018 at 10:37, Francis Atkinson <fran...@ebi.ac.uk>
>>> wrote:
>>>
>>>> Hello,
>>>>
>>>> In the following pair of molecules, the bicyclic is non-aromatic,
>>>> whereas the 'ring-opened' analogue is aromatic...
>>>>
>>>> In [1]: from rdkit import Chem
>>>>
>>>> In [2]: Chem.MolToSmiles(Chem.MolFromSmiles('n12ccccc1=NCCC2'))
>>>> Out[2]: 'C1=CC2=NCCCN2C=C1'
>>>>
>>>> In [3]: Chem.MolToSmiles(Chem.MolFromSmiles('n12ccccc1=NC.CC2'))
>>>> Out[3]: 'CCn1ccccc1=NC'
>>>>
>>>> Notebook version:
>>>>
>>>> https://nbviewer.jupyter.org/gist/flatkinson/b88eb42510a79594a9e37042eeb7e224
>>>>
>>>> This seems counter-intuitive to me: I don't see why the pyridine in the
>>>> first molecule shouldn't be aromatic, just as it is in the second.
>>>>
>>>> Am I missing something here?
>>>>
>>>> Thanks,
>>>>
>>>> Francis
>>>>
>>>> --
>>>> Dr Francis L Atkinson
>>>>
>>>> Chemogenomics Group
>>>> European Bioinformatics Institute (EMBL-EBI)
>>>> European Molecular Biology Laboratory
>>>> Wellcome Genome Campus
>>>> Hinxton
>>>> Cambridge CB10 1SD
>>>> United Kingdom
>>>>
>>>> (01223) 494473
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Rdkit-discuss mailing list
>>>> Rdkit-discuss@lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>>
>>> --
>>> Dr Francis L Atkinson
>>>
>>> Chemogenomics Group
>>> European Bioinformatics Institute (EMBL-EBI)
>>> European Molecular Biology Laboratory
>>> Wellcome Genome Campus
>>> Hinxton
>>> Cambridge CB10 1SD
>>> United Kingdom
>>>
>>> (01223) 494473
>>>
>>> _______________________________________________
>>> Rdkit-discuss mailing list
>>> Rdkit-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>
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