problem with standardizer removeexplicitH parameter

Hello everyone!

I'm having a problem with standardizer - it doesn't seem to work right.

input structure is withHydrogens.mol. According to
http://www.chemaxon.com/jchem/doc/user/Standardizer_files/examples/Exampl
es.html#05 parameter "removeexplicitH" should remove hydrogen atoms from
the molecule graph, but we still see them in the output
removeExplicit.svg
these are the parameters we use
jc_standardize(structure, 'config:removeexplicitH..clean:full')

Hi Alena,

Aren't those hydrogenes on the picture implicite ones? Did you specify the H_off option when converting to SVG?

Peter

Hi Alena,

 

This is a very basic and frequently used function, but we will check it.

(meanwhile you might also double-check your code)

Could you let us know the JChem Version you are using ? (this is needed for all support requests)

For the cartridge it's easiest to obtain it via:

select jchem_core_pkg.getenvironment() from dual;

Best regards,

Szilard

Here is our version information:

Oracle environment:
Oracle Database 10g Enterprise Edition Release 10.2.0.5.0 - 64bi
PL/SQL Release 10.2.0.5.0 - Production
CORE 10.2.0.5.0 Production
TNS for Linux: Version 10.2.0.5.0 - Production
NLSRTL Version 10.2.0.5.0 - Production

JChem owner: JCHEM
JChem Server environment:
Java VM vendor: Sun Microsystems Inc.
Java version: 1.6.0_23
Java VM version: 19.0-b09
JChem version: 5.6.0.2
JChem Index version: 5060000
JDBC driver version: 11.1.0.7.0-Production

 And, yes, I forgot to mention that we do use H_off option in SVG generation.

Hi,

As a quick test I have tested standardizer from command-line:

standardize -c "removeexplicitH..clean:full" ../../struc/withHydrogens.mol -f mol -o out.mol

The result is as expected, the explicit hydrogen atoms are removed properly (attached).

Though not impossible, but extremely unlikely that jc_standardize would work differently.

I suggest to forget about image generation for now, and concentrate the first step, standardization.

Could you send us the result of your jc_standardize call ? (the resulting molecule source)

Could it be possible that you are passing on the original (non-standardazied) structure later on for image generation by accident ? Could you share more of the relevant code part ?

 

Best regards,

 

Szilard

Hi again,

 

We could reproduce the problem, no further action is needed on your part.

After all it turned out that the Standardizer is called slightly differently in the cartridge.

So far it seems all structures are treated as queries by mistake, and in that case we specifically disable removing H atoms - so removeexplicitH is currently ineffective indeed.

All other actions should work fine - this is the only difference.

My colleague will let you know when the fix for H removal will be available.

 

Best regards,

 

Szilard 

Hi, Szilard!

Thanks a lot for your answer. 

We will be waiting for further information.

Hi Alenka,

This will be fixed in JChem version 5.7 scheduled for release in about 2 weeks.

Peter

Thanks again, Peter

Hi Alena,

JChem version 5.7 has been released with the fix.

Peter