Printing SDF seperately

Dear All,





I would like to print the SDF separately for two of the given below standardizations rules.





rules:


<AbsoluteStereo Act="Set"/>


<Removal Method="keepLargest" Measure="atomCount"/>





i would like to know for which molecule the Removal method is applied in one SDF and the rest in another SDF as output.





Thanks in advance





Anil

Hi,





Standardizer can not do this, but you can use our jcsearch utility to filter molecules with more than one fragment.





Here is the command line expression (jcsearch call) which can filter molecules with more than one fragment (only molecules with multiple fragments will be returned):

Code:

jcsearch -e 'connectedGraph() == "false"' <filename>

Using the pipelining capabilities of Unix/Linux systems you can pipe the output to Standardizer:

Code:

jcsearch -e 'connectedGraph() == "false"' <filename> | standardize -c <config.xml>

In this way only molecules with multiple fragments will "go through" standardization.





<filename> : the name of the input file


<config.xml> : Standardizer config XML file (or action string)





Best regards,


Zsolt