Re: [Rdkit-discuss] Lipinski HBD count

2011-09-30 Thread James Davidson
Hi Greg, Greg wrote: > For what it's worth: the results here are definitely not > correct for the SMILES as provided. Atoms in SMILES that are > in square brackets have no implicit Hs, so [N+] actually has > zero hydrogens. I guess you actually provided the molecules > to MOE in some other fo

Re: [Rdkit-discuss] Lipinski HBD count

2011-09-30 Thread Greg Landrum
James, On Fri, Sep 30, 2011 at 8:48 AM, James Davidson wrote: > > Greg wrote: >> You actually don't need to add the Hs: >> >>> p1 = Chem.MolFromSmarts('[#7,#8;H1]') >> >>> p2 = Chem.MolFromSmarts('[#7,#8;H2]') >> >>> p3 = Chem.MolFromSmarts('[#7,#8;H3]') m = >> >>> Chem.MolFromSmiles('CC(=O)N') >

Re: [Rdkit-discuss] Lipinski HBD count

2011-09-29 Thread James Davidson
Hi Greg, Greg wrote: > You actually don't need to add the Hs: > >>> p1 = Chem.MolFromSmarts('[#7,#8;H1]') > >>> p2 = Chem.MolFromSmarts('[#7,#8;H2]') > >>> p3 = Chem.MolFromSmarts('[#7,#8;H3]') m = > >>> Chem.MolFromSmiles('CC(=O)N') > >>> m2 = Chem.MolFromSmiles('OCC(=O)N') > >>> def NHOHCount(

Re: [Rdkit-discuss] Lipinski HBD count

2011-09-29 Thread Greg Landrum
On Fri, Sep 30, 2011 at 4:44 AM, Greg Landrum wrote: > >> The MOE descriptor lip_don seems to exactly reproduce these 'bond count' >> numbers for my set of compounds.  So I guess my question is - shouldn't >> we be counting the NH and OH bonds for Lipinski-like counting? (and I >> guess this is wh

Re: [Rdkit-discuss] Lipinski HBD count

2011-09-29 Thread Greg Landrum
Dear James, On Wed, Sep 28, 2011 at 8:04 PM, James Davidson wrote: > > Apologies for posting on a rather well-trodden (and tedious?) topic... > I have just spent some time counting H-bond donors in a variety of ways > for a 4000 compound data set - to see how our calculations could best > match t