Answering this may require a long explanation, or it could be really
quick.... let's see where we end up. :-)
If you replace "a.GetTotalNumHs()" with
"a.GetTotalNumHs(includeNeighbors=True)", do the results then make sense to
you?
-greg
On Tue, Jun 21, 2016 at 4:50 PM, David Cosgrove <davidacosgrov...@gmail.com>
wrote:
> Hi All,
>
> I'm a bit confused about counting hydrogen atoms. It's a perennial
> problem with cheminformatics toolkits in my experience, but this seems
> particularly perverse. If I run the code:
>
> from rdkit import Chem
> from rdkit.Chem import AllChem
>
> mol = Chem.MolFromSmiles( 'CCO' )
> mol = Chem.AddHs( mol )
> cids = AllChem.EmbedMultipleConfs(mol , useExpTorsionAnglePrefs=True ,
> useBasicKnowledge=True , numConfs=1 )
> AllChem.MMFFOptimizeMoleculeConfs( mol , mmffVariant='MMFF94s' )
>
> for a in mol.GetAtoms() :
> num_heavy = a.GetTotalDegree() - a.GetTotalNumHs()
> print '%d : %d num_heavy = %d num_H = %d %d %d' % ( a.GetIdx() ,
> a.GetAtomicNum() , num_heavy , a.GetTotalNumHs() , a.GetNumImplicitHs() ,
> a.GetNumExplicitHs() )
> for nb in a.GetNeighbors() :
> print ' %d : %d' % ( nb.GetIdx() , nb.GetAtomicNum() )
>
> I get the output
>
> 0 : 6 num_heavy = 4 num_H = 0 0 0
> 1 : 6
> 3 : 1
> 4 : 1
> 5 : 1
> 1 : 6 num_heavy = 4 num_H = 0 0 0
> 0 : 6
> 2 : 8
> 6 : 1
> 7 : 1
> 2 : 8 num_heavy = 2 num_H = 0 0 0
> 1 : 6
> 8 : 1
> 3 : 1 num_heavy = 1 num_H = 0 0 0
> 0 : 6
> 4 : 1 num_heavy = 1 num_H = 0 0 0
> 0 : 6
> 5 : 1 num_heavy = 1 num_H = 0 0 0
> 0 : 6
> 6 : 1 num_heavy = 1 num_H = 0 0 0
> 1 : 6
> 7 : 1 num_heavy = 1 num_H = 0 0 0
> 1 : 6
> 8 : 1 num_heavy = 1 num_H = 0 0 0
> 2 : 8
>
>
> It seems that in a 3D mol, after embedding and minimisation, an H atom is
> just like any other atom, and is ignored in the various H atom counting
> functions. Is that expected behaviour? Depending on the answer, either
> the documentation or the behaviour is incorrect.
>
> Cheers,
> Dave
>
>
>
> ------------------------------------------------------------------------------
> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
> Francisco, CA to explore cutting-edge tech and listen to tech luminaries
> present their vision of the future. This family event has something for
> everyone, including kids. Get more information and register today.
> http://sdm.link/attshape
> _______________________________________________
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
------------------------------------------------------------------------------
Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
Francisco, CA to explore cutting-edge tech and listen to tech luminaries
present their vision of the future. This family event has something for
everyone, including kids. Get more information and register today.
http://sdm.link/attshape
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
