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IUPACNamer$Error: The structure could not be dearomatized
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Enrique

Joined: 16 Sep 2014
Posts: 6

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Link to postPosted: Wed Apr 06, 2016 1:31 pmPost subject: IUPACNamer$Error: The structure could not be dearomatized Reply with quote

Hello,

I have several structures that fail with the Naming menu command.Here's one in Smiles format and the error message is below.


All explicit hydrogens have been specified.

Any ideas?

Thanks!

Enrique Frio

=======================

[H]OC1=C(O[H])C2=C(C([H])=C1[H])[C@]1([H])C([H])([H])OC3=C(C([H])=C4C(=C3[H])C(=O)C3=C(c5c(c([H])c(O[H])c([H])c5=O)C([H])([H])[C@]3([H])C(=O)N([H])[H])C4([H])[H])[C@]1([H])O2

=======================
ERROR:
Cannot run plugin: Naming
chemaxon.marvin.io.formats.name.nameexport.IUPACNamer$Error: The structure could not be dearomatized

STACK TRACE:
chemaxon.marvin.io.formats.name.nameexport.IUPACNamer$Error: The structure could not be dearomatized
    at chemaxon.marvin.io.formats.name.nameexport.NamingCentral.getNameCore(NamingCentral.java:271)
    at chemaxon.marvin.io.formats.name.nameexport.NamingCentral.getName(NamingCentral.java:222)
    at chemaxon.marvin.io.formats.name.nameexport.S2NTask.call(S2NTask.java:146)
    at chemaxon.marvin.io.formats.name.nameexport.S2NTask.call(S2NTask.java:30)
    at java.util.concurrent.FutureTask.run(FutureTask.java:262)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.RuntimeException: The structure could not be dearomatized
    at chemaxon.marvin.io.formats.name.nameexport.Modifiers.addBond(Modifiers.java:86)
    at chemaxon.marvin.io.formats.name.nameexport.SaturationAnalyser.findBonds(SaturationAnalyser.java:164)
    at chemaxon.marvin.io.formats.name.nameexport.SaturationAnalyser.analyse(SaturationAnalyser.java:36)
    at chemaxon.marvin.io.formats.name.nameexport.SimplePart.analyseSaturation(SimplePart.java:262)
    at chemaxon.marvin.io.formats.name.nameexport.SimplePart.<init>(SimplePart.java:26)
    at chemaxon.marvin.io.formats.name.nameexport.CarbonBridgedRingSystem.<init>(CarbonBridgedRingSystem.java:29)
    at chemaxon.marvin.io.formats.name.nameexport.RingSystem.create(RingSystem.java:56)
    at chemaxon.marvin.io.formats.name.nameexport.RingSystemRecognizer$RingTree.getPart(RingSystemRecognizer.java:173)
    at chemaxon.marvin.io.formats.name.nameexport.RingSystemRecognizer.separateRingsSystems(RingSystemRecognizer.java:50)
    at chemaxon.marvin.io.formats.name.nameexport.TopologyAnalyser.analyse(TopologyAnalyser.java:46)
    at chemaxon.marvin.io.formats.name.nameexport.NamingCentral.analyse(NamingCentral.java:338)
    at chemaxon.marvin.io.formats.name.nameexport.NamingCentral.getNameCore(NamingCentral.java:248)
    ... 7 more

kniesz
ChemAxon personnel
Joined: 11 Jan 2012
Posts: 269

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Link to postPosted: Wed Apr 06, 2016 3:17 pmPost subject: Reply with quote

Hello Enrique,

This structure contains an aromatised benzene ring with a double bonded O connected to one of the C atoms, hence there should be a valence error thrown right away. We are investigating it why it is not the case. 

Best,

Daniel
ChemAxon personnel
Joined: 22 Jan 2012
Posts: 315

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Link to postPosted: Thu Apr 07, 2016 10:10 amPost subject: Reply with quote

Hi, 

We managed to reproduce this bug in Marvin. We will fix it as soon as possible. 

Best regards, 

Daniel

Daniel
ChemAxon personnel
Joined: 22 Jan 2012
Posts: 315

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Link to postPosted: Wed Apr 20, 2016 10:05 amPost subject: Reply with quote

Hi, 

The reason for this issue is that the molecule has an aromatic valence error in it. I attach a picture showing the molecule after running the Structure Checker on it. The red rings holds the valence error. 

You should correct the valence error in order to get a UIPAC name. 

I hope this helps, 

Daniel

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