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Make surface molecules from smiles using Argon workaround #2607

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Make surface molecules from smiles using Argon workaround #2607

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sevyharris
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@sevyharris sevyharris commented Feb 7, 2024 •
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Motivation or Problem

The issue is described here, #2603, but basically RDKit complains when you try to make a surface molecule using smiles.

Description of Changes

This PR adds a workaround where you initialize the molecule using Ar as a replacement for X to get the adjacency list and then remove the extra pairs of electrons and change Ar back to X to get the originally intended molecule.

Testing

Run this code to test out instantiating all the species in the Surface family training reactions:
NOTE TO SELF -- DON'T FORGET TO REBUILD!

import os
import glob
import rmgpy
import rmgpy.chemkin
import rmgpy.molecule

# Get all of the surface training reactions
search_str = os.path.join(rmgpy.settings['database.directory'], 'kinetics', 'families', 'Surface_*', 'training', 'dictionary.txt')
species_dict_files = glob.glob(search_str)

# Test on all the species in surface training reactions
for dict_file in species_dict_files:
    species_dict = rmgpy.chemkin.load_species_dictionary(dict_file)
    for key in species_dict.keys():
        sp = species_dict[key]
        
        test_smiles = sp.smiles.replace('Pt', 'X')
        test_sp = rmgpy.molecule.Molecule(smiles=test_smiles)
        
        assert(test_sp.is_isomorphic(sp.molecule[0]))

@sevyharris sevyharris self-assigned this Feb 7, 2024
@sevyharris sevyharris linked an issue Feb 7, 2024 that may be closed by this pull request
Can't construct surface rmgpy.molecule.Molecule() #2603
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rwest
rwest reviewed Mar 8, 2024
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This looks good. Could we have a couple unit tests? I think there are some templates to copy. Can we do a round-trip (i.e. generate SMILES-like strings with X in, that reproduce the original molecule on import)?

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github-actions bot commented Jun 7, 2024

This pull request is being automatically marked as stale because it has not received any interaction in the last 90 days. Please leave a comment if this is still a relevant pull request, otherwise it will automatically be closed in 30 days.

@github-actions github-actions bot added the stale stale issue/PR as determined by actions bot label Jun 7, 2024
@sevyharris sevyharris removed the stale stale issue/PR as determined by actions bot label Jun 7, 2024
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github-actions bot commented Sep 6, 2024

This pull request is being automatically marked as stale because it has not received any interaction in the last 90 days. Please leave a comment if this is still a relevant pull request, otherwise it will automatically be closed in 30 days.

@github-actions github-actions bot added the stale stale issue/PR as determined by actions bot label Sep 6, 2024
@sevyharris sevyharris removed the stale stale issue/PR as determined by actions bot label Sep 6, 2024
@sevyharris sevyharris force-pushed the surface_smiles_to_molecule branch from 2b17b3c to 4732aa1 Compare October 18, 2024 19:21
@sevyharris
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This is working with the test code described above, so now I just need to put that into an actual unit test and it'll be ready to go.

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Unit tests added, but don't work yet because the SMILES string from the rdkit translator's to_smiles() uses 'Pt' instead of 'X'. Need to figure out where is the most appropriate place to make this final translation, but then it should be ready

@sevyharris
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Some mission creep: RMG molecule had no way to distinguish between specific Pt atom and more general surface X atom.

I wanted rmgpy.molecule.Molecule(smiles="[Pt]").to_smiles() to return '[Pt]' and rmgpy.molecule.Molecule(smiles="[X]").to_smiles() to return '[X]', but there was no good way to do this since the internal RMG molecule adjacency list always converted Pt to X and then converted all X's back to Pt in the to_smiles() function.

So, I added a specific Pt atom type with the intention of being able to add other metals later on.

It passes my simple test cases, but now I need to clean up the PR and look for other places this might cause problems for RMG-cat.

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Richard's working on a related PR: #2701. The rdkit * might be a more elegant way of doing this than the Ar workaround

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Can't construct surface rmgpy.molecule.Molecule()
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