On 04/02/2021 00:35, Brian Peterson wrote:
Hello RDKit people,
Is it possible to modify the properties of elements in the periodic
table or to create new ones? Use case: Suppose one had some molecules
defined in terms of functional groups or united atoms or some other
entities that are not pure elemental atoms. Could one map these things
on to unused elements (e.g. my_functional_group --> U) and fix up the
properties of U so that it had the appropriate valence etc. and could
be present both in a molecule and in SMARTS patterns so that one could
do substructure matches within RDKit?
Maybe you can use the isotope number to encode some special meaning
for an atom.
Cf. http://www.rdkit.org/docs/GettingStartedInPython.html
"Other fragmentation approaches"
[...] attachment points are labelled (using isotopes) [...]
Those are preserved in the output SMILES.
Thanks,
Brian
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