Dear all,
After reading through this, thinking about it, and searching some more, I
decided to adopt an alternate solution.
Instead of removing the stereochemistry of the P=C double bond in in
molecules like:
C/C=P(=O)/OC1=CC=CC=C1
I added that substructure to the list of things that sanitization
"corrects". It now yields the zwitterionic [P+]-[O-] form. Here's an
example:
In [*4*]: m = Chem.MolFromSmiles('C/C=P(=O)/OC1=CC=CC=C1')
In [*5*]: print(Chem.MolToSmiles(m,True))
C/C=[P+](\[O-])Oc1ccccc1
Best,
-greg
On Thu, Mar 10, 2016 at 8:11 PM, Greg Landrum <greg.land...@gmail.com>
wrote:
> Dear all,
>
> Here's a question for the chemists in the group: do we need to be
> concerned about representing the stereochemistry of the P=C bond in
> substructures like O=P(/O)=C/C under normal circumstances?
>
> Here's a pubchem compound example that has the double bond crossed
> (possibly leading one to believe that it could have stereochemistry):
> https://pubchem.ncbi.nlm.nih.gov/compound/56981965
> Here's the corresponding substance record (which is how PubChem received
> the structure):
> https://pubchem.ncbi.nlm.nih.gov/substance/135741697
>
> Another example, this time without the crossed bond in the compound record:
> https://pubchem.ncbi.nlm.nih.gov/compound/87396055
>
> Best,
> -greg
>
>
>
>
>
>
------------------------------------------------------------------------------
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://pubads.g.doubleclick.net/gampad/clk?id=278785231&iu=/4140
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
