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Improve SMILES translation for surface adsorbates #2701

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Improve SMILES translation for surface adsorbates #2701

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Commits on Aug 2, 2024

  1. Conversion to RDKitMol can use 0 for surface sites X 

    You can use a * to represent a surface site in a SMILES string when
reading it via RDKit, and RDKit turns this into a dummy atom
with atomic number 0.

By doing the reverse (telling RDKit that our surface sites have
atomic number 0) we can use RDKit to *generate* SMILES strings
in the same format, enabling a round trip.

But for other things like InChIs it seems more robust to use
an atom like Platinum (78). This allows both, with default 0,
but 78 used in InChI conversion.
    @rwest
    rwest committed Aug 2, 2024
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  2. Unit test for conversion to/from RDKit with some adsorbate SMILES. 

    Using the new syntax with * for a surface site.
    @rwest
    rwest committed Aug 2, 2024
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  3. New unit tests for SMILES conversions of Adsorbates. 

    Unfortunately going from a molecule TO a smiles uses
OpenBabel if you have Nitrogen in the molecule, which 
then uses [Pt] in place of *.
But you can still READ smiles with * and N in. 
That means you don't get a round trip. 
In [9]: Molecule(smiles='CNC*').to_smiles()
Out[9]: 'CNC[Pt]'

Still, this is better than it was. (I think).
    @rwest
    rwest committed Aug 2, 2024
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  4. SMILES from OpenBabel now replace [Pt] with * 

    This means they can be parsed in a round trip by RDKit
(the default SMILES reader). 
This is handy because OpenBabel is the default SMILES
*writer* for things with an N atom, but not everything.
Now it's more consistent, outputting a * for a surface site.

I added a unit test for round-trip conversion to and from 
SMILES a few times for various adsorbates including some with N.
    @rwest
    rwest committed Aug 2, 2024
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