User 677b9c22ff
30-08-2008 03:59:06
Hi,
I got the following NPE in the Reactor GUI v5.1.0 (WIN32), unfortunately there is no indictator which molecule threw the error. This would be helpful for future possible errors. Otherwise its really cumbersome, because I have to check for every single molecule and split lists etc.
Could you please implement such an indicator with the last successful molecule or erroneous molecule ID and SMILES? Thank you!
After hundreds of trials I found out, that its the still faulty Standardizer option ClearStereo, because if I remove the ClearStereo it works. Well looking at the error later helps too :-)
To my knowledge this error exist since one year. Many other molecules
from PubChem also create such errors
Should I cross-post this error to the Standardizer section? Probably not.
Cheers
Tobias
Reaction: [#1,#6][C:1]([#1,#6])=[O:2]>[H]S[#7]>[H]S\[N:3]=[C:1](/[#1,#6])[#1,#6]
Standardizer:
<StandardizerConfiguration>
<Actions>
<AddExplicitH ID="AddExplicitH" Groups="reactant1"/>
<Aromatize ID="Aromatize" Groups="reactant1,reactant1,reactant1,reactant1" Type="general"/>
<ClearStereo ID="ClearStereo" Groups="reactant1,reactant1,reactant1,reactant1"/>
<Mesomerize ID="Mesomerize" Groups="reactant1"/>
<Tautomerize ID="Tautomerize" Groups="reactant1"/>
<Clean ID="Clean2D" Groups="reactant1,reactant1,reactant1,reactant1" Dim="2" Type="Partial"/>
</Actions>
</StandardizerConfiguration>
Tobias
I got the following NPE in the Reactor GUI v5.1.0 (WIN32), unfortunately there is no indictator which molecule threw the error. This would be helpful for future possible errors. Otherwise its really cumbersome, because I have to check for every single molecule and split lists etc.
Could you please implement such an indicator with the last successful molecule or erroneous molecule ID and SMILES? Thank you!
After hundreds of trials I found out, that its the still faulty Standardizer option ClearStereo, because if I remove the ClearStereo it works. Well looking at the error later helps too :-)
To my knowledge this error exist since one year. Many other molecules
from PubChem also create such errors
Should I cross-post this error to the Standardizer section? Probably not.
Cheers
Tobias
| 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.reaction.Reactor.standardizeReactant(Reactor.java:708) at chemaxon.reaction.Reactor.setReactants(Reactor.java:1519) at chemaxon.alchemist.reactor.ReactorAlchemistTask.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) |
Reaction: [#1,#6][C:1]([#1,#6])=[O:2]>[H]S[#7]>[H]S\[N:3]=[C:1](/[#1,#6])[#1,#6]
Standardizer:
<StandardizerConfiguration>
<Actions>
<AddExplicitH ID="AddExplicitH" Groups="reactant1"/>
<Aromatize ID="Aromatize" Groups="reactant1,reactant1,reactant1,reactant1" Type="general"/>
<ClearStereo ID="ClearStereo" Groups="reactant1,reactant1,reactant1,reactant1"/>
<Mesomerize ID="Mesomerize" Groups="reactant1"/>
<Tautomerize ID="Tautomerize" Groups="reactant1"/>
<Clean ID="Clean2D" Groups="reactant1,reactant1,reactant1,reactant1" Dim="2" Type="Partial"/>
</Actions>
</StandardizerConfiguration>
Tobias