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
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')
>
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(
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
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
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