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
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