That's a nice Python implementation of the logic that's used in
prepareMolForDrawing that does the same thing. It probably makes sense for
there to be an easy single function that you can call to do this, but that
should definitely work.
-greg
On Thu, Oct 19, 2017 at 6:43 PM, Chris Murphy
wrote
I did need to add hydrogens for it work correctly, since the exocyclic
hydrogens needed to be there to be wedged/dashed, however I used these two
lines to ensure I only added the ones I needed:
On Thu, Oct 19, 2017 at 2:41 PM, Chris Murphy
wrote:
> Greg,
>
> That did the trick, thanks so much f
chiral_atoms = [center[0] for center in Chem.FindMolChiralCenters(mol)]
mol = Chem.AddHs(mol, explicitOnly=False, addCoords=True,
onlyOnAtoms=chiral_atoms)
On Thu, Oct 19, 2017 at 2:43 PM, Chris Murphy
wrote:
> I did need to add hydrogens for it work correctly, since the exocyclic
> hydr
Greg,
That did the trick, thanks so much for the help!
On Wed, Oct 18, 2017 at 2:13 AM, Greg Landrum
wrote:
>
>
> On Tue, Oct 17, 2017 at 8:16 PM, Chris Murphy <
> chris.mur...@schrodinger.com> wrote:
>
>>
>> I am trying to implement a function that cleans up chiral centers by
>> moving the wed
On Tue, Oct 17, 2017 at 8:16 PM, Chris Murphy
wrote:
>
> I am trying to implement a function that cleans up chiral centers by
> moving the wedged/dashed stereo bond out of a ring and onto a function
> group or hydrogen if possible.
>
As a general thing: the existing function Chem.WedgeMolBonds()
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