That did the trick, thanks so much for the help!
On Wed, Oct 18, 2017 at 2:13 AM, Greg Landrum <greg.land...@gmail.com>
> 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 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() should
> already handle assigning wedged bonds to exocyclic atoms. It does not,
> however, remove existing wedging. I think that this is probably what you
> should be using, but for that to be useful you first need to have a
> molecule with atomic stereochemistry assigned and wedging info removed from
> If you skip sanitization when processing a mol block (which is what I
> suspect based on your previous messages), you end up with a molecule that
> has the atomic stereochemistry assigned, but with the wedging information
> still there. Removing the existing wedging info and then calling
> Chem.WedgeMolBonds() should get you what you're looking for.
> The function to remove bond wedging isn't currently exposed to Python, I
> can do that, but in the meantime a python translation isn't complicated:
> In : def ClearSingleBondDirFlags(m):
> ...: for bond in m.GetBonds():
> ...: if bond.GetBondType() == Chem.BondType.SINGLE:
> ...: if bond.GetBondDir() == Chem.BondDir.UNKNOWN:
> ...: bond.SetProp("_UnknownStereo",1)
> ...: bond.SetBondDir(Chem.BondDir.NONE)
> The piece with the _UnknownStereo property is important to make sure info
> about wavy (I call them "squiggle") bonds is maintained.
> If the combination of this function and Chem.WedgeMolBonds() isn't enough
> to solve the problem, I'll get into the rest of your question, but I
> think/hope that this might do it and save you some time and effort.
> P.S. If anyone could offer a good suggestion for how to determine if the
>> bond I am moving the dash/wedge to should be dashed or wedged that would
>> also be super helpful.
> That's a non-trivial bit of C++ code that isn't currently exposed to the
> python interface. I don't think it would be hard to do that if it would be
>> I have been able to successfully identify the wedged bonds and the
>> adjacent bond to move the wedge/dash stereo bond to and move the stereo
>> bond off of the ring bond, but when I check the result, I notice that I
>> assigned the wrong wedge/dash form to one of the bonds, so I want to check
>> the chirality of the atoms after doing my changes and flip the ones that
>> are wrong.
>> However, I am noticing that the output of Chem.FindMolChiralCenters(mol)
>> does not change (as well as atom.GetProp('_CIPCode')), even if I change all
>> of the bonds to either dashed or wedged, or another combination that should
>> clearly change the original chirality of the stereocenters. I tried
>> calling rdmolops.AssignStereochemistry(mol), but the result of
>> FindMolChiralCenters and atom.GetProp('_CIPCode') still does not change.
>> Does SetBondDir actually affect the R/S chiral tags on the atoms? Is
>> there a good way to check if the changes in the bonds have changed the
>> chirality at a given chiral center?
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