Hi Dave,
Thanks for the suggestion about mutating the atom in-place then pruning the
rest of the R-group away.
This will work, but it's inelegant and slow. Here's why.
I'm trying to construct an R-group table for each core, for up to 3 R-groups,
of a data set. For that, I need to know the canonical core and the canonical
side groups.
What makes this more tricky is that "[H]" is a reasonable side-group, so I may
need to map a 3-cut system with a 2-cut+hydrogen one.
My plan is to construct one form of the core where the R-groups were replaced
with a "*", and another form where the R-groups were replaced with "[H]". I can
group everything by the hydrogen core, then limit my match attempts to that
subset.
If I use your technique, I'll have to copy & prune up to four times per
molecule (because R-groups can be chiral too), rather than do everything in one
swoop.
Of course, "inelegant and slow" beats "doesn't work at all"! I'm still trying
to see if I can make it work.
Andrew
da...@dalkescientific.com
On Feb 4, 2016, at 2:10 PM, David Cosgrove wrote:
> HI Andrew,
>
> I don't have a solution for RDKit, because I don't know if you can do this
> sort of thing. But when I've tackled this in OEChem, I've changed the atomic
> number of the substituent atom to something else (I always use Xe, because I
> know that will never be anything other than a marker atom, but you might
> change it to 0 for *) and then trim the atoms off that one (other than the
> parent chiral atom). That way, you never break the bond between the core and
> the substituent and the chirality is preserved - it might change from R to S,
> because that depends on the atomic numbers of the atoms on the chiral atom
> (CPK rules) but the relative orders should remain the same.
>
> Hope that helps,
>
> Dave
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