Standardizer 5.1 NPE

Hi,


I tried the following molecule as part of a larger lib,


SMILES: O=C1Oc2ccc(cc2C=C1)N(=O)=O





Standardizer 5.0.1 GUI


with the following commands:

Code:

<?xml version="1.0" encoding="UTF-8"?> <!--This file is created with ChemAxon's Configuration Builder--> <!--This is a configuration file for ChemAxon's Standardizer--> <StandardizerConfiguration>   <Actions>     <ClearStereo ID="ClearStereo"/>     <WedgeClean ID="WedgeClean"/>     <Transformation ID="Transform" Structure="[*,#1]-[*,#1]&gt;&gt;[*,#1]-[*,#1] |(-8.31,2.26,;-6.97,3.03,;5.51,2.86,;4.17,2.09,)|"/>   </Actions> </StandardizerConfiguration>

NPE error:

Code:

java.lang.NullPointerException    at chemaxon.struc.MoleculeGraph.getStereo2(MoleculeGraph.java:2481)    at chemaxon.reaction.Standardizer.clearDoubleBondStereo(Standardizer.java:1251)    at chemaxon.reaction.Standardizer.performClearStereo(Standardizer.java:1223)    at chemaxon.reaction.Standardizer.standardizeComponent(Standardizer.java:1952)    at chemaxon.reaction.Standardizer.standardize(Standardizer.java:2061)    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)

For whatever reason the complete stereo removal does not work,


or I could not figure out how to do it. The transformation reaction


was actually written to all stereo, but this transformation did not work.





The XML file works for many other structures, but not for one of the examples from above. Error still exists without the transforms.





Another problem is that the error messages contain no information


on the molecule number where the error occoured so its hard to check


for problems.

Code:

#60: null #61: null #62: null #63: null #64: null #65: null #66: null    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)

The numbers are just the number of failures or Null pointer exceptions,


but not the actual molecule number. Maybe this is possible without GUI?





BTW, this error also kills the -g (ignore error) from the commandline.





Tobias

We are investigating this issue, sorry for the delay.

Dear Tobias,





I have just fixed this bug few days ago.


Zsolt is just testing it.


He will write you about the progress.





Andras

Thank you,


I need to check that with some diverse molecule DBs,


because many of the general problems came from nitro compounds, compounds with charges or radicals and metal and organometal compounds, in principle all the difficult species.


Tobias

volfi wrote:

I have just fixed this bug few days ago. Zsolt is just testing it. He will write you about the progress.

The fix will be included in JChem 5.1.1.

TobiasKind wrote:

Another problem is that the error messages contain no information on the molecule number where the error occurred so its hard to check for problems.

We will improve the error message in a future version.

TobiasKind wrote:

BTW, this error also kills the -g (ignore error) from the commandline.

The "-g" option ignores only import and export errors, processing errors are not ignored. This will be also improved in a future release.





Zsolt