Alchemist 3.2.11 error (-2)

Hi,


Standardizer 3.2.11 under WIN XP and JAVA 1.6 (i think) failed.


These guys


C#[N]C=Cc1c[nH]c2ccccc12


C#[N]\C=C/c1c[nH]c2ccccc12


C#[N]\C=C/C1=CNC2=C1C=CC=C2


make the problems.





The correct structure of the isocyanides is something like


[C-]#[N+]\C=C\c1c[nH]c2ccccc12





I didn't have time to write a standardizer or reactor ttemplate to get rid


of that. I guess its something like SMARTS reaction (remove bastard isonitriles):


----------------------------------------------------------


Added (later): I need to point out that the SMARTS reaction


C#N>>[C-]#[N+] in Reactor alone transforms the groups


correctly, the problem is that if several/many bastard isonitrile groups


are included in one single molecule the reaction must be done completely,


so far I did no see that option in Reactor GUI and Standardizer GUI, but I remember that there was such an option.





The following doesnt work in Standardizer as


group transform reaction added, together with the


added XML at the bottom


---------------------------------------------------------








*~[N]#C>>*~[N+]#[C-] (doesn't work)





[C]=NC=Cc1c[nH]c2ccccc12


[C]=NC=Cc1c[nH]c2ccccc12


[C]=NC=Cc1c[nH]c2ccccc12


[C]=NC=Cc1c[nH]c2ccccc12








*[N]#C>>*[N+]#[C-] (doesn't work either)





[C]=NC=Cc1c[nH]c2ccccc12


[C]=NC=Cc1c[nH]c2ccccc12


[C]=NC=Cc1c[nH]c2ccccc12


[C]=NC=Cc1c[nH]c2ccccc12








*[N]#C>>[C-]#[N+]* (doesn't work either)








C#[N]\C*>>*C[N+]#[C-] (doesn't work either, but I guess it should in Reactor)








**[N]#C>>**[N+]#[C-] (doesn't work either)





Now I Just read about the non-existing SMILES radical support.


Well thats the hate-love with SMILES.





Can anybody help to get rid of the bastard IsoNitriles


with a SMARTS reaction? Otherwise I could use the good old regexps,


they never let me down, and if they don't work I always feel I am


not SMART enough - this is not the case when working with smarts...











Tobias


----





Alchemist error,


standardizer failed.


-2





chemaxon.struc.CGraph.getEdge(CGraph.java:343)


chemaxon.struc.MoleculeGraph.getBond(MoleculeGraph.java:1239)


chemaxon.calculations.HMO.isKetene(HMO.java:1632)


chemaxon.calculations.HMO.setSigmaSceleton(HMO.java:1506)


chemaxon.calculations.HMO.initCalc(HMO.java:250)


chemaxon.calculations.HMO.calcHMO(HMO.java:1142)


chemaxon.calculations.Charge.calcHMO(Charge.java:1737)


chemaxon.calculations.Charge.setInitialCharge(Charge.java:1829)


chemaxon.calculations.Charge.calcCharges(Charge.java:678)


chemaxon.calculations.CanonicResonant.setResonantScore(CanonicResonant.java:468)


chemaxon.calculations.CanonicResonant.calcCanonicalResonant(CanonicResonant.java:167)


chemaxon.marvin.calculations.MultiformPlugin.calcCanonicResonant(MultiformPlugin.java:318)


chemaxon.marvin.calculations.MultiformPlugin.run(MultiformPlugin.java:292)


chemaxon.reaction.Standardizer.performMesomerize(Standardizer.java:1607)


chemaxon.reaction.Standardizer.standardizeComponent(Standardizer.java:1777)


chemaxon.reaction.Standardizer.standardize(Standardizer.java:1850)


chemaxon.alchemist.standardizer.StandardizerAlchemistTask.calculate(StandardizerAlchemistTask.java:155)


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(Unknown Source)





-----------------------------------------------------------------------------------


<?xml version="1.0" encoding="UTF-8"?>


<!-- Standardizer configuration file -->


<!-- This configuration file is created with ChemAxon Config Builder -->





<StandardizerConfiguration Version ="0.1">


<Actions>


<Aromatize ID="aromatize" Type="general"/>


<RemoveExplicitH ID="removeexplicith" Lonely="true" Groups="target"/>


<Removal ID="removal" Method="keepLargest" Measure="keepLargest"/>


<Tautomerize ID="tautomerize"/>


<Mesomerize ID="mesomerize"/>


<AbsoluteStereo ID="clearstereo" Act="Clear"/>


</Actions>


</StandardizerConfiguration>


-----------------------------------------------------------------------------------





Tobias

Thanks Tobias for the report, I could reproduce the isonitrile problem. My collegues are examining it and we will get back to you soon with their results.





The second exception is not reproducable. I used the same radical isonitriles as input and your XML configuration. What version of JChem are you using?

Hi,


Thanks. which second exception? I only got one and added the xml.


I am currently using JChem Version 3.2.11


Tobias

I assumed, that the first problem was: How to make a transform for isonitriles. The second one was an exception raised the mesomerise function during resonant form calculation.

The error raised during the isonitrile conversion has been fixed and will appear in the next Marvin version.