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Standardizer 5.1 NPE
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Reply to topic    Home -> Forums -> Support -> Structure manipulation: Canonicalization / standardization -> Standardizer 5.1 NPE

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TobiasKind
Joined: 26 Jan 2005
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Post subject: Standardizer 5.1 NPE
Link to postPosted: Sat Aug 16, 2008 2:58 am  Reply with quote
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

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Gyuri
Joined: 21 May 2004
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Post subject:
Link to postPosted: Wed Aug 20, 2008 3:17 pm  Reply with quote
We are investigating this issue, sorry for the delay.
volfi
Joined: 07 Jun 2004
Posts: 396
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Post subject:
Link to postPosted: Tue Aug 26, 2008 6:43 pm  Reply with quote
Dear Tobias,

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

Andras
TobiasKind
Joined: 26 Jan 2005
Posts: 424


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Post subject:
Link to postPosted: Tue Aug 26, 2008 11:19 pm  Reply with quote
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
Zsolt
Joined: 11 Jan 2006
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Post subject:
Link to postPosted: Wed Aug 27, 2008 7:48 pm  Reply with quote
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
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