seperated outout in structurecheck

Hello,

Is there a way to separate the output of structurecheck into two files of fixed and unfixed structures?

This option is available in the GUI (StructureChecker) but I couldn't find anything equivalent in the command-line tool.

I would like to filter a set of molecules through the checker and identify/throw-away the ones that did not pass.

 

Thanks,

Izhar

Unfortunately command line structure checker does not support this feature yet. We are working on this, it will be supported soon. Cannot you use the GUI until that?

Evaluate command line application can be used for filtering molecules having errors.

Filter molecules which are valid (does not have the specified errors):

evaluate -e 'isValid("ringstrainerror..pseudoatom")' -x sdf nci100.smiles 

Filter molecules which have the specified errors:

evaluate -e '!isValid("ringstrainerror..pseudoatom")' -x sdf nci100.smiles

You migtht also try to use jcsearch command line with an empty query and a chemical terms filter using the isvalid function.

 

jcsearch -q "" input.sdf -e '!isValid("ringstrainerror..pseudoatom")' -f sdf -o badmolecules.sdf

Thanks!

As a workaround I'm using the log file to get the indexes of the success/failure molecules.

 

-

Izhar