Standardizer log output?

Hi,

 

We're trying to use command-line standardizer to process an sdf file.  We're using the following command line, but it generates an empty log file and no other stdout/stderr other than the total processing time.  Are we doing something incorrectly?

 

/ChemAxon/JChem/bin/standardize makeup.sdf -c st.xml --empty-mol-on-error -v --loglevel info --logfile st.log -f sdf -o makeup_post.sdf

 

/ChemAxon/JChem/bin/standardize -h

 

Standardizer 5.3.3, (C) 1999-2010 ChemAxon Ltd.

Molecule standardizer.

 

Any help would be appreciated.

 

Thanks.

 

Andrew

Hi Andrew,

This is normal. If there is no error (or anything important user should know about) during standardization, then the created log file will be empty even on the info level.

There are some lower log levels ("config", "fine", etc.) which are quite verbose and are used only for debugging. Please try one of these logging levels to see if logging works.

Example:

/ChemAxon/JChem/bin/standardize makeup.sdf -c st.xml --empty-mol-on-error -v --loglevel config --logfile st.log -f sdf -o makeup_post.sdf

At "config" level input molecules are also written to log file, so it should not be empty.

Please let us know if there is something you would like to see in the log file.

Regards,
Zsolt

Hi,

Thanks for the quick reply.  "config" does indeed create a non-empty log file.

We would find it useful to include in the log file whatever standardizer actions were found to apply to each structure.  For example:

"Explicit hydrogens found and removed in compound #13"

Would such log information be possible?

Thanks.

The main purpose of Standardizer is automatic structure canonicalization in database tables. However, there is a new validation tool called Structure Checker: http://www.chemaxon.com/marvin/help/structurechecker/checker.html

The upcoming 5.4 version will contain new and improved checkers, command line and wizard application for batch processing with automatic and manual operation modes and logging capabilites. Here is the lates presentation from our US UGM where a recorded video of the talk and demo will be available soon:

http://www.chemaxon.com/library/ugm-presentations/2010-usugm/restoration-of-molecular-artifacts-the-new-structure-checker-framework-of-standardizer-2/

Thanks for the reply .. yes, we are eagerly awaiting this .. smile.

Hi,

Is there a way in the 5.4 API to understand in how many places Standardizer has operated?  That is, after I do the following:

Standardizer standardizer = new Standardizer("O=N=O>>O=[N+]-[O-]");

standardizer.standardize(mol);

I'd like to know how many NO2 groups were found that needed to be altered.

Or do I have to check and count manually before running Standardizer (searching for O=N=O's)?

Thanks for any information.

Andrew

Well, it equals to the number of the neutral nitro groups in your compound. You can count them externally in various ways, for example by calling the matchCount function of evaluator. From command line it is:
evaluate -e 'matchCount("O=N=O")' in.mol

You can use the evaluator API, or molsearch API as well.

Thanks very much for the quick response .. I just wanted to make sure the functionality didn't already exist as a one-line call .. smile.