Converting SMILES to Kekule Format

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For adding molecular structures to slides/papers, SMILEs can be converted into Kekule format with the following command:

    /nfs/soft/jchem/current/bin/molconvert smiles:-a {INPUT_SMILES.smi} > {OUTPUT_SMILES.smi}

The SMILES in the {OUTPUT_SMILES.smi} file will now be de-aromatized, and can be pasted into ChemDraw.


To run this command while also maintaining the IDs from the {INPUT_SMILES.smi} file, run this:

    python ~rstein/zzz.scripts/LSD_processing_scripts/kekule_smiles.py {INPUT_SMILES.smi}

The output will be "kekule_{INPUT_SMILES.smi}".