How to re-create smiles from molString('smiles') field?

User 677b9c22ff

13-10-2008 20:03:13


I created a new column with the chemical term molString('smiles').

However I was not able to re-create the same SMILES when exporting with any option like +a-H +a-H -a+H +a+H using the export function or

molconvert. Is there an underlying special function, or which parameters are called? I though its dearomatize (thats what the SMILES look like in Mview) and dehydrogenize (remove H) because otherwise SMILES become very long.

What would be the correct option for molconvert?

This is Instant-JChem 3.2.1

Thank you!


ChemAxon fa971619eb

14-10-2008 14:13:31

Chemical terms expressions are generated from the standardized form of the structure. That is why the smiles chemical terms column shows the structures in aromatic form (e.g. small c rather than big C for aromatic carbons). This assumes you have aromatization defined in your standardizer configuration, or no standardizer set in which case aromatization is part of the default standardization rules that will be used.

In contrast export works on the original form of the structure, which may well be in non-aromatic form. To convert this to aromatic form so that it matches the chem terms expression you will almost certainly need to use the "a-H" argunment, which means convert to aromatic from and remove hydrogens.


User 677b9c22ff

14-10-2008 19:26:32

Hi Tim,

"a-H" seems to do the job.

Thank you