This isn't an area I've thought much about, so this may be a bit naive.
It seems like the interesting atom from the perspective of perception is
the carbon that the Hs are attached to, not the Hs themselves; it's the
carbon that will become a chiral center.
If we neglect dependent stereochemistry for the moment, can't we just find
carbon atoms that have two hydrogen substituents and then look to see if
they (the carbons) have two differently ranked neighbors? The advantage to
this is that it saves the addHs step and will generally be a lot faster to
execute.
Here's a quick code snippet, it lets you choose between using CIP ranks to
distinguish atoms or just using their canonical rankings.
def findProchiral(mol,useCIPRanks=False):
if not useCIPRanks:
ranks = Chem.CanonicalRankAtoms(mol,breakTies=False)
else:
Chem.AssignStereochemistry(mol)
ranks = [x.GetProp('_CIPRank') for x in mol.GetAtoms()]
res = []
for atom in mol.GetAtoms():
# only consider atoms with two heavy neighbors and two Hs.
# could probably be further limited to just consider carbons
if atom.GetTotalDegree()!=4 or atom.GetTotalNumHs()!=2:
continue
hvyNbrRanks=[]
for nbr in atom.GetNeighbors():
if nbr.GetAtomicNum()>1:
hvyNbrRanks.append(ranks[nbr.GetIdx()])
if len(hvyNbrRanks)==2:
break
if hvyNbrRanks[0] != hvyNbrRanks[1]:
res.append(atom.GetIdx())
return res
Is that headed in the right direction?
-greg
On Thu, Mar 10, 2016 at 5:30 PM, Peter S. Shenkin <[email protected]> wrote:
> Is the canonical rank of prochiral H's different or the same? (For example
> the rank of the H's on C-1 of ethyl chloride.)
>
> Thanks,
> -P.
>
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