SIMONAPreprocessor
Automated Generation of Jobs

If you have a big amount of structures to convert from PDB to XML (think Decoy set), there is an automated conversion utility.


First you will need to generate a run exactly like in the other tutorials, but do not close your preprocessor after.

  1. Instead click Run->SaveParameters and specify a filename like myfile.sml
  2. Now locate the Script SIMGenerateIdenticalRun.py in the python folder and start it with
    1 python ./SIMGenerateIdenticalRun.py
  3. It will give the error message:
    1 Use with python SIMGenerateIdenticalRun.py parameter.sml(.gz) structure_file output.xml(.gz)
  4. Locate the PDB file and your yml file and do
    1 python SIMGenerateIdenticalRun.py myfile.sml mypdbfile.pdb myoutfile.xml
  5. Now a run exactly like the one before, but with a different structure file is generated.