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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