Backwards Compatability of Standardizer

Hi,

I have a standardizer configuration file, generated using an old version of ChemAxon (3.2.1), which I have included as an attachment.

 

I am working with JChem 5.1.3. (On Windows XP, 32 bit). In so far as I can tell from the documentation:

file:file:///C:/Program%20Files/ChemAxon/JChem/index.html (from the JChem README), this old configuration file should still work (i.e. add explicit hydrogens and clean up 2D co-ordinates etc.) when using the 'standardize' command line tool.

I've tried processing SDF files using this script, and I don't get any error messages.

However, I would appreciate knowing if any of the actions described in the file shouldn't work with JChem 5.1.3. (For instance, I believe Dehydrogenize is now superseded?)

Many thanks for any clarification.

 

Richard

Hi,

Yes, it will work, backward compatibility is maintained.

There is an error in you config file, in this line:

<Removal ID="removal" Method="keepLargest" Measure="keepLargest"/>

The Measure shoud be "atomCount" or "molMass", see the documentation.

After correction:

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

you can open the config file with the Standardizer GUI application (see the attached screenshot) and edit/save it.

Zsolt