JChemManager misinterprets cis-trans isomerism SMILES

Hi there,

when trying to import the following SMILES into a MySQL database by means of JChemManager

Cc1c(c2ccccc2[nH]1)/C=c/3\c(=O)n4c5ccccc5nc4s3

it confuses the cis-trans isomerism information with a markush structure:

"edu.emory.mathcs.backport.java.util.concurrent.ExecutionException:
chemaxon.jchem.db.UpdateHandlerException: Inserting a query or Markush
structure is not allowed for table: "molecules""

As the name already suggests, the table type is "Molecules". I could
figure out that it's definitely only due to the lowercased c in "c/3",
as I can import this structure when turning the letter into uppercased
- which I of course don't want to.

Any help or suggestions how to fix this?

 

And another one: I have to run JChemManager in commandline mode. In
the GUI you can tell the program NOT to hold if an error occurs. Is it
possible to invoke this command also via the commandline?

 

Thanks in advance!

Benny

Hello,

 

Could please tell us the verion number of your JChem. I tried to import the structure you mentioned (see attahed), but there was no error. Could you please attach the file you wanted to import?

You could also try the followings:

Open the file in msketch - does this work correctly?

Save the file in mrv format, can you import that?

I'm checking the option as well.

Bye,

Robert

Hi Robert,

thanks for the reply! I'm using JChem 5.1.4, s maybe it's due to that outdated version. Nevertheless, loading the file (attached) into MarvinSketch works fine.

The trouble is that the database was maintained by a former colleague so far, so I even don't have the possibility to make an update at the moment. I'll get back here as soon as I have managed to do so.

Cheers,

Benny

P.S.: Trying to load your attached file produces the same error message...

Hi Benny,

The current version also loads the second file without error.

Let us know if upgrading helps.

 

Alternatively, you could use the "Any structures" table type, which will allows any structures to be registered. See: https://www.chemaxon.com/jchem/doc/guide/dbconcepts/index.html#tabletypes

 

Best regards,

Szabolcs

Hi Szabolcs,

so it really seems that an update would solve my problem. Anyway, thanks for your "workaround-suggestion" and for your prompt help in general! I'll keep you posted.

 

Cheers,

Benny