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 <wangyuran...@gmail.com> 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 <greg.land...@gmail.com>
> wrote:
>
>>
>>
>> On Thu, May 11, 2017 at 4:24 PM, Yuran Wang <wangyuran...@gmail.com>
>> 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_
>> SETCONJUGATION|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
>
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