On 03/04/2021 00:03, Andrew Dalke wrote:
Hi Ling,
On Apr 2, 2021, at 16:23, Ling Chan <lingtrek...@gmail.com> wrote:
Thank you Francois, I took a look at your code and borrowed parts of
it to rejoin two molecules. It seems like my problem is solved. I
eventually arrived at something like example 4 in
https://www.programcreek.com/python/example/123334/rdkit.Chem.CombineMols
(which I discovered a bit late).
Still, I am not sure if the code is safe. In particular, I wonder if
the following conditions are always valid.
• Chem.CombineMols simply concatenates the atomic indices from the
input molecules.
• The Chem.EditableMol constructor preserves atom ordering from the
input.
• RemoveAtom in EditableMol results in all indices above the deleted
to decrease by one, i.e. atom ordering is preserved.
I've found that it's very hard to work with molecular graphs and
preserve stereochemistry.
Consider F/C=C/Cl breaking on the first bond, and the code I pointed
you to.
FragmentOnBonds() using '9' as the labels gives: [9*]/C=C/Cl.[9*]F
My "smiles_weld" code converts that to: CC\%99=C/Cl.F%99 which can be
re-canonicalized to the original: F/C=C/Cl .
Or, with F[C@H](Cl)Br again, breaking on the first bond.
FragmentOnBonds() gives [9*]F.[9*][C@H](Cl)Br
smiles_weld converts that to F%99.[C@@H]%99(Cl)Br which is
re-canonicalized as F[C@H](Cl)Br
Handling this correctly in the molecule API requires paying careful
attention to the bond direction, and bond attachment order around the
atom, which changes with RemoveAtom() calls. I didn't see
stereochemistry support in Francois's "bind_molecules()" nor in the
connect_mols() at
After discussing with an organic chemist, we decided that fragmenting
(on the computer) molecules
on bonds which are involved in stereochemistry (stereo bond or linked to
a stereo center)
is not desirable.
I.e. if the molecules being fragmented have stereochemistry assigned, we
don't touch around it.
https://github.com/molecularsets/moses/blob/master/moses/baselines/combinatorial.py
(one of the examples from the programcreek.com link you gave).
If you don't need to support or preserve stereochemistry, then of
course there's no problem.
Cheers,
Andrew
da...@dalkescientific.com
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