Marshall,
On Thu, Apr 16, 2009 at 5:57 AM, Marshall Levesque
wrote:
> Greg-
>
> Both the chirality-AddHs() and memory leak fixes to RDKit seem to be
> working perfectly by my tests. Great work and thanks again for being
> so quick with responses to questions and updating RDKit with solutions!
G
Greg-
Both the chirality-AddHs() and memory leak fixes to RDKit seem to be
working perfectly by my tests. Great work and thanks again for being
so quick with responses to questions and updating RDKit with solutions!
-Marshall
On Apr 14, 2009, at 9:43 PM, Greg Landrum wrote:
Marshall,
O
Marshall,
On Tue, Apr 14, 2009 at 11:35 PM, Marshall Levesque
wrote:
>
> Here is the file and the output of a short test with the molecules, which
> match visual inspection of produced 3D structures via AddHs() and
> EmbedMolecule:
>
supp = Chem.SDMolSupplier('4aminoacids.separated.sdf')
>>>
On Apr 14, 2009, at 8:17 PM, Marshall Levesque wrote:
Here is an attempt to try to use OpenBabel's addH functionality and
checking stereochemistry with RDKit:
Ooh. Now that's an exciting bug. The hydrogen addition code is
designed for 3D molecules... I'll go file that in the bug database.
Here is an attempt to try to use OpenBabel's addH functionality and
checking stereochemistry with RDKit:
babel 4aminoacids.separated.sdf 4aminoacids.H.sdf -h
>>> supp = Chem.SDMolSupplier('4aminoacids.separated.sdf')
>>> suppH = Chem.SDMolSupplier('4aminoacids.H.sdf')
>>> for m in supp:
...
Greg-
Here is the file and the output of a short test with the molecules,
which match visual inspection of produced 3D structures via AddHs()
and EmbedMolecule:
>>> supp = Chem.SDMolSupplier('4aminoacids.separated.sdf')
>>> for m in supp:
... Chem.FindMolChiralCenters(m)
...
[(2, 'S')]
On Tue, Apr 14, 2009 at 10:04 PM, Marshall Levesque
wrote:
> Greg-
>
> As always... thank you for the detailed response.
>
> I have been trying to look in detail at some amino acid structures going
> from 2D->3D. Here are my results using RDKit's methods of investigating
> chirality of alanine:
>
Greg-
As always... thank you for the detailed response.
I have been trying to look in detail at some amino acid structures
going from 2D->3D. Here are my results using RDKit's methods of
investigating chirality of alanine:
>>> suppl = Chem.SDMolSupplier('4aminoacids.separated.sdf')
>>>
>>
On Tue, Apr 14, 2009 at 7:38 AM, Greg Landrum wrote:
>
> To answer the overall question: yes the embedding process *should*
> preserve stereochemistry. Having said that, the area of chirality is
> where one is the most likely to encounter "correctness bugs" in the
> RDKit.
Since I'm probably more
Dear Marshall,
To answer the overall question: yes the embedding process *should*
preserve stereochemistry. Having said that, the area of chirality is
where one is the most likely to encounter "correctness bugs" in the
RDKit.
I think there may be some confusion about representation of
stereochem
Greg-
Looping over the atoms of 1000 molecules with
mol.GetAtomWithIdx(i).GetChiralTag() gave me the statistic of ~58%
stereocenters being preserved after the molecules were embedded (2D-
>3D), creating multiple conformers (about 2 conformers per rotatable
bond) and UFFOptimized. So my qu
Just to include other thoughts on the topic... can this issue come
from the Chem.AddHs(mol) step that is performed pre-embed for 2D->3D
generation?
Since the conformers of a single starting 2D structure don't all see
flipping of stereochemistry when a single structure has Hs added and
is
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