On Mon, Dec 2, 2013 at 1:03 PM, Michal Krompiec
<[email protected]>wrote:
>
> > ReplaceSubstructs() is designed for the very simple case of replacing a
> > piece of the molecule that is connected via one bond. It has the
> significant
> > limitation that it (currently) assumes that the bond will be formed to
> the
> > first atom in the replacement.
> It would be useful to remove this limitation, that is to add the index
> of the bonding atom in the replacement to the arguments.
>
Yeah, there's a feature request in github for this already:
https://github.com/rdkit/rdkit/issues/171
It will almost certainly make it into the next release.
> > The most general and flexible approach to this is almost definitely to
> use
> > reactions. However, these are somewhat trickier to encode and do not
> > preserve conformations.
>
> In my project (combinatorial library), joining molecules with reaction
> smarts is much (10x?) slower than using ReplaceSubstructs (with
> renumbering of atoms in the replacement).
>
Interesting. I'm not surprised that the reaction code is somewhat slower
(there's plenty of room for optimization there), but it's suprising that
the difference would be that large.
-greg
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