another problem with standardizer

Hi again)

I have this structure of Gonadotropine Releasing Hormone analogue - GRH_analogue.mol

I can understand that it's rather complex structure, but anyways the result of 

jc_standardize(structure, 'config:clean:full') isn't very satisfying - check strange_clean.svg.

Maybe you could recommend some additional parameters to make it look better that don't affect the look of the other structures. Without clean it looks okay, but the problem is that we use batch standardization of all our structures.

our environment is the following:

 

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

Hi Alena,

Would template-based cleaning an acceptable solution here? (Please, see cleaningTemplate option of the jc_standardizer operator.)

Thanks

Peter

Hi, Peter!

I need to discuss it with our chemists, but it seems rather unlikely. It's simplier to keep it out of standardizing I guess.

My question actually is if you do think that the result of the particular clean will change somewhere in the future or we need to devise our own way around it - either with template-based cleaning or simply turning it off for certain structures (I think we have another examples of unsatisfying clean, do you need them?)

Hi Alena,

I moved this topic to the forum where cleaning-related issues are discussed.

Best regards,

Peter

Hi Alena,

My question actually is if you do think that the result of the particular 

clean will change somewhere in the future or we need to devise our own 

way around it - either with template-based cleaning or simply turning it

 off for certain structures (I think we have another examples of 

unsatisfying clean, do you need them?)

Thank you for the report. I have created a bugfix issue. As far as I see we will not have time to fix this in this year, but we will definitely want to improve our 2D celaning algorithm.

Thanks for your answer, volfi

We'll keep tracking changes

Hi, volfi!

Here are just few more examples of unsatisfying work of cleaning algorithm

Thank you for the examples.

We will start to work on the improvement soon.