Standardization in Synthesizer

Hi,


I am using the program synthesizer.So i have in cluded the <standardisation> tag in the synthesizer xml file.For some action of standaerdizer is working, some are not.





For e.g, Clean 3D , tautomerize etc are not working.


I have run with ur test data for synthesizer, i am attaching the xml file.





regards


Achuz

achuz wrote:

I am using the program synthesizer.So i have in cluded the <standardisation> tag in the synthesizer xml file.For some action of standaerdizer is working, some are not. For e.g, Clean 3D , tautomerize etc are not working. I have run with ur test data for synthesizer, i am attaching the xml file.

Hi,





Please attach your input and result files, and specify the exact command line call you have used. Specify also what do you expect to get as result.





Please read the following part of the Synthesizer documentation: http://www.chemaxon.com/jchem/doc/user/Synthesizer.html#config





"Standardizer configuration: this section specifies the standardization procedure that is performed on both the targets and the queries before performing substructure search to find the reaction centers."





The standardization steps specified in the <Standardizer> section are used for controlling the reaction. If you want to generate e.g. output molecules in 3D, then run the Standardizer on the output structures you get.





Best regards,


Zsolt