Thread: [Rdkit-discuss] Number of sp3 atoms

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rdkit-discuss

[Rdkit-discuss] Number of sp3 atoms

From: Chris S. <sw...@ma...> - 2020-05-31 13:24:14

Hi,

I’ve written a Jupyter notebook to calculate a variety of calculated properties of molecules (MWt, TPSA, HAC, HBD/A etc.)

I’d like to include the number of sp3 atoms, is there an easy way to do this?

Cheers,

Chris

Re: [Rdkit-discuss] Number of sp3 atoms

From: Andrew D. <da...@da...> - 2020-05-31 15:10:25

On May 31, 2020, at 15:23, Chris Swain via Rdkit-discuss <rdk...@li...> wrote:
> I’d like to include the number of sp3 atoms, is there an easy way to do this?

I don't easily see a function for that. There's rdMolDescriptors.CalcFractionCSP3() which "returns the fraction of C atoms that are SP3 hybridized".

You can do it yourself by looking at the atom's hybridization:

>>> mol = Chem.MolFromSmiles("CN1C=NC2=C1C(=O)N(C(=O)N2C)C")
>>> sum((a.GetHybridization() == Chem.HybridizationType.SP3) for a in mol.GetAtoms())
3

Cheers,

				Andrew
				da...@da...

Re: [Rdkit-discuss] Number of sp3 atoms

From: Jean-Marc N. <jm....@un...> - 2020-05-31 16:23:00

Le 31/05/2020 à 16:52, Andrew Dalke a écrit :
> On May 31, 2020, at 15:23, Chris Swain via Rdkit-discuss <rdk...@li...> wrote:
>> I’d like to include the number of sp3 atoms, is there an easy way to do this?
> I don't easily see a function for that. There's rdMolDescriptors.CalcFractionCSP3() which "returns the fraction of C atoms that are SP3 hybridized".
>
> You can do it yourself by looking at the atom's hybridization:
>
>
>>>> mol = Chem.MolFromSmiles("CN1C=NC2=C1C(=O)N(C(=O)N2C)C")
>>>> sum((a.GetHybridization() == Chem.HybridizationType.SP3) for a in mol.GetAtoms())
> 3
>
> Cheers,
>
> 				Andrew
> 				da...@da...
>
>
>
>
> _______________________________________________
> Rdkit-discuss mailing list
> Rdk...@li...
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Yes, but

 >>> mol = Chem.MolFromSmiles("O=COC")
 >>> sum((a.GetHybridization() == Chem.HybridizationType.SP3) for a in 
mol.GetAtoms())
1

because the two oxygen atoms are SP2.

Best regards,

Jean-Marc


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