Converting SMILES to Kekule Format: Difference between revisions
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For adding molecular structures to slides/papers, SMILEs can be converted into Kekule format with the following command: | 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}". | |||
Latest revision as of 19:39, 30 October 2019
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}".