Same input file as ouput file in Standardizer problem

Hi,


using the same input file as output file in Standardizer GUI kills the file and


makes is zero length. From a programmers perspective I


can understand it, from a users perspective not because


I would expect that it reads (probably millions) of molecules


and then performs the reaction and writes it back under the same name.


Reactor is bit more clever and warns me.





Quick question: is the -z option (perform full reaction on all


reaction centers also available in the GUI)?





Thank you.


Tobias











no line to put back





chemaxon.marvin.io.PositionedInputStream.putBackLine(PositionedInputStream.java:497)


chemaxon.marvin.modules.SmilesImport.initMolImport(SmilesImport.java:437)


chemaxon.formats.MolImporter.initMolImportIfNeeded(MolImporter.java:506)


chemaxon.formats.MolImporter.createMol(MolImporter.java:588)


chemaxon.formats.MolImporter.read(MolImporter.java:606)


chemaxon.formats.MolImporter.read(MolImporter.java:574)


chemaxon.alchemist.standardizer.StandardizerAlchemistTask.calculate(StandardizerAlchemistTask.java:152)


chemaxon.alchemist.AlchemistTask$ActualTask.<init>(AlchemistTask.java:200)


chemaxon.alchemist.AlchemistTask$3.construct(AlchemistTask.java:97)


chemaxon.alchemist.utils.SwingWorker$2.run(SwingWorker.java:107)


java.lang.Thread.run(Thread.java:595)

You cannot overwrite your input with the ouptut, since Standardizer reads the input while converting the molecules. This method saves the memory. Imagine a million molecule input file, it would not be a good idea to load the entire file into the memory. Anyway, you are right with the warning, we should warn the users to avoid doing such a thing.





I assume, that your other question is related to Reactor not Standardizer. The -z option does not appear on the GUI and will be removed from the react command line tool as well in the future, because it breaks the synthetic feasibility calculations.

Thanks