Alchemist 3.2.11 error (-2)

User 677b9c22ff

19-10-2007 01:24:24

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

ChemAxon d76e6e95eb

19-10-2007 07:02:27

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?

User 677b9c22ff

19-10-2007 18:45:25

Hi,


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


I am currently using JChem Version 3.2.11


Tobias

ChemAxon d76e6e95eb

19-10-2007 20:57:25

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.

ChemAxon d76e6e95eb

24-10-2007 14:03:09

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