Greg,
That fixed it! Thanks so much, that makes a lot more sense now.
-Chris
On Fri, Oct 6, 2017 at 1:25 AM, Greg Landrum <greg.land...@gmail.com> wrote:
> Hi Chris,
>
> There's an additional step performed during sanitization that recognizes
> that the implicit H needs to be on the N. The steps of a normal full
> molecular sanitization operation are documented here:
> http://www.rdkit.org/docs/RDKit_Book.html#molecular-sanitization
>
> The adjustHs() function is not exposed directly to Python, but you can
> take care of aromaticity assignment and adjustHs in a single call with the
> SanitizeMol() function:
>
> In [21]: m = Chem.MolFromMolBlock(mb,sanitize=False)
>
> In [22]: Chem.SanitizeMol(m,sanitizeOps=Chem.SANITIZE_SETAROMATICITY|
> Chem.SANITIZE_ADJUSTHS)
> Out[22]: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE
>
> In [23]: Chem.MolToSmiles(m)
> Out[23]: 'CC(C)c1cccc2c(Cl)cc(-c3ccc(-c4ccc(C(=O)O)cc4)[nH]3)nc12'
>
> I highlighted the N in the heterocyle with the implicit H.
>
> Hopefully this helps.
>
> Best,
> -greg
> p.s. Note: while testing parts of this answer I uncovered a bug in
> AdjustHs() that causes it to fail for molecules that include atoms with
> "bad valences": https://github.com/rdkit/rdkit/issues/1605 This looks
> like it should be easy to fix for the upcoming release.
>
>
> On Thu, Oct 5, 2017 at 11:06 PM, Chris Murphy <
> chris.mur...@schrodinger.com> wrote:
>
>> Hi!
>>
>> I'm running at an issue with implicit hydrogens on aromatic heteroatoms.
>> I am feeding the following sdf into a mol object:
>>
>>
>> Mrv16c5 10021719092D
>>
>> 28 31 0 0 0 0 999 V2000
>> -2.9000 0.2076 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> -2.1871 0.6228 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
>> 0.0063 0.2957 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
>> -0.7486 0.6354 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> -1.4657 0.2118 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> 0.5599 0.9164 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> -2.9000 -0.6228 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> -2.1829 -1.0380 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> -1.4657 -0.6228 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> -3.6214 0.6228 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> -0.6731 1.4574 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> 0.1405 1.6335 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> 3.8646 0.5976 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> 1.3860 0.8367 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> 3.0384 0.6731 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> 4.3469 1.2687 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
>> 1.7257 0.0818 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> 1.8641 1.5161 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> 2.6861 1.4322 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> 2.5477 -0.0021 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> -2.1829 -1.8683 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
>> -3.6297 1.4532 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> 4.2085 -0.1656 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
>> -3.6214 -1.0463 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> -4.3385 0.1992 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> -4.3385 -0.6311 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> -4.3469 1.8600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> -2.9042 1.8683 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> 2 1 1 0 0 0 0
>> 3 4 1 0 0 0 0
>> 4 5 1 0 0 0 0
>> 5 2 2 0 0 0 0
>> 6 3 1 0 0 0 0
>> 7 1 1 0 0 0 0
>> 8 7 1 0 0 0 0
>> 9 8 2 0 0 0 0
>> 10 1 2 0 0 0 0
>> 11 4 2 0 0 0 0
>> 12 11 1 0 0 0 0
>> 13 15 1 0 0 0 0
>> 14 6 1 0 0 0 0
>> 15 19 1 0 0 0 0
>> 16 13 2 0 0 0 0
>> 17 14 2 0 0 0 0
>> 18 14 1 0 0 0 0
>> 19 18 2 0 0 0 0
>> 20 17 1 0 0 0 0
>> 21 8 1 0 0 0 0
>> 22 10 1 0 0 0 0
>> 23 13 1 0 0 0 0
>> 24 7 2 0 0 0 0
>> 25 10 1 0 0 0 0
>> 26 25 2 0 0 0 0
>> 27 22 1 0 0 0 0
>> 28 22 1 0 0 0 0
>> 24 26 1 0 0 0 0
>> 9 5 1 0 0 0 0
>> 6 12 2 0 0 0 0
>> 20 15 2 0 0 0 0
>> M END
>> $$$$
>>
>> The nitrogen in the heterocycle should have 1 implicit hydrogen on it,
>> and when I look at it after initially creating the mol object, it does. I
>> want to convert it to aromatic form, so I am calling
>> rdmolops.SetAromatize(mol). Once I do this however, it seems that the
>> implicit hydrogen on the nitrogen is removed, which then causes an error to
>> be thrown if I ever try to convert it back to kekule form or do any kind of
>> sanitization. Maybe my understanding of aromaticity is wrong, but shouldn't
>> the hydrogen be on the nitrogen regardless of whether or not it is
>> considered to be in an aromatic form?
>>
>> I could be misunderstanding rdkit's aromaticity models, but for my
>> purposes, I want to be able to convert the mol to either kekule or aromatic
>> form depending on some configuration settings. Is there a way to manipulate
>> the hydogrens on an atom in this case?
>>
>> Thanks!
>> Chris
>>
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