Re: [Rdkit-discuss] Nitrogen Valence

[Yuran W. <wan...@gm...>]

Hi Peter,
Thank you for your reply. I did not quite understand what you mean by 'But
this makes no sense'.
Also the SMILES you tested are zwitterionic form. In this link
http://www.rdkit.org/docs/RDKit_Book.html#molecular-sanitization, the
zwitterionic form seems suitable for N=O, N#N, not for N=N. But I may just
have a very limited knowledge of RDkit.

This is how it looks like in ChemDraw:
[image: Inline image 1]


Thanks,
Yuran

On Thu, May 11, 2017 at 1:33 PM, Peter S. Shenkin <sh...@gm...> wrote:

> The problematic part is just the beginning of your would-be SMILES:
> N=N(C)(C)C. The rest is correctly parsed. But this makes no sense. Perhaps
> you mean one of the substructures illustrated in the attached (which at
> least satisfy normal valence rules). If not, perhaps you could attach a
> structural diagram of what you do mean.
>
> -P.
>
>
> On Thu, May 11, 2017 at 11:02 AM, Yuran Wang <wan...@gm...>
> wrote:
>
>> Dear Greg,
>> Thank you very much for the suggestions. It works for me!
>> Here is the SMILES of one molecule that I am looking
>> at: N=N(C)(C)CC(CN1N=CN=C1)(O)C2=C(C=C(C=C2)F)F
>> Any better alternative will be appreciated.
>>
>> Thanks,
>> Yuran
>>
>> On Thu, May 11, 2017 at 10:49 AM, Greg Landrum <gre...@gm...>
>> wrote:
>>
>>>
>>>
>>> On Thu, May 11, 2017 at 4:24 PM, Yuran Wang <wan...@gm...>
>>> wrote:
>>>
>>>> I have a question regarding the available valence of Nitrogen. It seems
>>>> only 3 is available in the default setting (atomic_data.cpp). Why is it
>>>> kept to only 3, and not extended to include 4 and 5? If I change it locally
>>>> to include 4 and 5, will it cause any problems?
>>>>
>>>
>>> Aside from generating molecules that don't make any chemical sense?
>>> Probably not, but the lack of chemical sense may cause some unexpected
>>> behavior.
>>>
>>>
>>>> I am aware that I could turn off the sanitization to get a mol object,
>>>> however, it cannot be further processed to get fingerprints, which is what
>>>> I need.
>>>>
>>>
>>> Well, you could turn off the sanitization on molecule construction and
>>> then manually sanitize with the valence check turned off. Here's a simple
>>> example of that:
>>>
>>> In [11]: m = Chem.MolFromSmiles('CN(C)(C)(C)C',sanitize=False)
>>>
>>> In [12]: m.UpdatePropertyCache(strict=False)
>>>
>>> In [13]: Chem.SanitizeMol(m,Chem.SANITIZE_SYMMRINGS|Chem.SANITIZE_SET
>>> CONJUGATION|Chem.SANITIZE_SETHYBRIDIZATION)
>>> Out[13]: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE
>>>
>>> In [14]: rdMolDescriptors.GetMorganFingerprint(m,2)
>>> Out[14]: <rdkit.DataStructs.cDataStructs.UIntSparseIntVect at
>>> 0x10b0ab350>
>>>
>>>
>>> But, again, the RDKit's valence rules tend to reflect real chemistry.
>>> What are you trying to represent that you need 5 coordinate neutral
>>> nitrogen atoms? There may be a better way.
>>>
>>> -greg
>>>
>>>
>>
>>
>>
>> --
>> Best,
>> Yuran Wang
>>
>> ------------------------------------------------------------
>> ------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> Rdkit-discuss mailing list
>> Rdk...@li...
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>>
>


-- 
Best,
Yuran Wang