Re: [Rdkit-discuss] non-element elements

[Francois B. <ml...@li...>]

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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