Error with Standardizer

Hi





I tried Stanardizer for the first time and it has produced an error. I have an SD file containing approx 20,000 structures. I chose the Remove Fragment option and set the output file to also be an SD file. About half way through the file the following error was produced:

Quote:

java.lang.ArrayIndexOutOfBoundsException: -1 at java.util.ArrayList.get(Unknown Source) at chemaxon.struc.Molecule.addChildSgroupClonesRecursively(Molecule.java:978) at chemaxon.struc.Molecule.clonecopySgroups(Molecule.java:1070) at chemaxon.struc.Molecule.clonecopy(Molecule.java:940) at chemaxon.struc.Molecule.cloneMolecule(Molecule.java:1128) at chemaxon.alchemist.standardizer.StandardizerAlchemistTask.calculate(Unknown Source) at chemaxon.alchemist.AlchemistTask$ActualTask.<init>(Unknown Source) at chemaxon.alchemist.AlchemistTask$3.construct(Unknown Source) at chemaxon.alchemist.utils.SwingWorker$2.run(Unknown Source) at java.lang.Thread.run(Unknown Source)

Seems odd because I can load the SD file of structures into a JChem enabled table without any problems. I will not be able to show the structure on this forum, but let me know if you need me to send you it directly. Any ideas...?

Hi,





Standardizer application in "Step 4 - Standardize" step displays the standardization progress and molecules before and after standardization if "Show samples (may reduce performance)" check box is checked. The code that threw the exception is used only for displaying the original (not standardized) molecules, that's why the standardized molecules are OK and can be loaded into JChem table without any problems.





Regards,


Zsolt

Even with the check box unticked, so I am not viewing the structures, I get an error when it reaches a particular structure:

Code:

java.lang.ArrayIndexOutOfBoundsException: -1    at java.util.ArrayList.get(Unknown Source)    at chemaxon.struc.Molecule.addChildSgroupClonesRecursively(Molecule.java:982)    at chemaxon.struc.Molecule.addSgroupClone(Molecule.java:1140)    at chemaxon.struc.Molecule.clonecopySgroups(Molecule.java:1117)    at chemaxon.struc.Molecule.clonecopy(Molecule.java:944)    at chemaxon.struc.Molecule.cloneMolecule(Molecule.java:1190)    at chemaxon.alchemist.standardizer.StandardizerAlchemistTask.calculate(Unknown Source)    at chemaxon.alchemist.AlchemistTask$ActualTask.<init>(Unknown Source)    at chemaxon.alchemist.AlchemistTask$3.construct(Unknown Source)    at chemaxon.alchemist.utils.SwingWorker$2.run(Unknown Source)    at java.lang.Thread.run(Unknown Source)

I think the structure contains S Groups to represent brackets around components of a mixture. It causes the Standardizer to crash so I cannot run this particular SD File through the application to remove salt fragments.





Is there no way to allow the Standardizer to ignore structures that might cause it to error?

Hi,





Until we fix this error in Standardizer GUI please use the Standardizer command line application.





Usage:

Code:

standardize -c config.xml in.sdf -f sdf -o out.sdf

This command line call will standardize the molecules stored in the file "in.sdf" and write the output to "out.sdf" file in "sdf" format. The "-c" command line option is used for specifying the configuration file (config.xml in this case).


The configuration file created with the Standardizer GUI can be saved in the "Step 2 - Create configuration" step using he "Save configuration" button (see screenshot), and can be used with the command line tool.





For more see Standardizer User's Guide.





I hope this helps.





Regards,


Zsolt