NMR Hose code java.lang.IllegalArgumentException

User 677b9c22ff

01-09-2013 18:02:54

Hi,


HNMR and CNMR with leads to the error below, I use the integrated NMR version in MSketch 5.11,


so maybe that is solved in the newer versions.


InChI=1S/C27H30O15/c1-7-17(32)21(36)23(38)27(40-7)16-20(35)15(26-24(39)22(37)18(33)13(6-28)42-26)19(34)14-11(31)5-12(41-25(14)16)8-2-3-9(29)10(30)4-8/h2-5,7,13,17-18,21-24,26-30,32-39H,6H2,1H3/t7-,13-,17-,18+,21+,22-,23-,24+,26-,27-/m0/s1
AuxInfo=1/0/N:37,14,15,18,8,41,31,13,16,17,7,9,25,4,2,6,30,20,3,1,35,21,34,22,5,23,33,42,19,40,11,36,26,12,28,39,27,38,29,32,10,24/it:im/rA:72CCCCCCCCCOOOCCCCCCOC.eC.eC.oC.eOC.eOOOOC.eC.eOC.oC.oC.oOCOOOC.eOHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH/rB:s1;d-2;s3;d-4;d-1s5;s4;s7;d-8;s5s9;d7;s3;s9;d+13;s14;d-15;s16;s13d-17;s16;;s20;s21;s2s22;s23;s20s24;s20;s21;s1;s22;;s30;s31;s6s32;s33;s30s34;s30;s31;s34;s35;s17;s25;s41;s8;s12;s14;s15;s18;s19;s20;s21;s22;s23;s25;s26;s27;s28;s29;s30;s31;s33;s34;s35;s36;s37;s37;s37;s38;s39;s40;s41;s41;s42;/rC:-1.1388,1.7362,4.6066;.144,1.2844,4.1973;1.1842,2.2382,4.0683;.9625,3.6041,4.3699;-.3618,4.034,4.6696;-1.4528,3.1222,4.7242;2.0081,4.5693,4.4003;1.7524,5.9104,4.7339;.4353,6.3083,5.0026;-.5417,5.3578,4.9463;3.2037,4.2836,4.1531;2.4157,1.8162,3.6653;.0863,7.6294,5.3571;-.8586,8.3379,4.5816;-1.2614,9.6435,5.0427;-.7307,10.229,6.2386;.2328,9.4883,6.954;.6499,8.2202,6.5095;-1.0779,11.4752,6.7706;2.057,-2.1768,2.4918;.7076,-1.7552,1.8531;.3363,-.312,2.2794;.3823,-.1547,3.8323;1.6378,-.6238,4.3849;2.0567,-1.9657,4.0378;2.3895,-3.5188,2.1363;.7913,-1.8359,.4302;-2.11,.8166,4.8833;-.9559,.019,1.7705;-4.0962,4.2705,2.259;-3.7087,2.8181,2.6735;-3.7809,2.6539,4.1123;-2.9146,3.5045,4.9125;-3.4827,4.9419,4.6499;-3.3684,5.3231,3.146;-3.7885,4.4944,.8831;-4.6259,1.7295,2.067;-3.0125,5.9508,5.5391;-3.9192,6.619,2.9122;.7726,9.9709,8.104;1.287,-3.0382,4.8545;1.3765,-2.7438,6.2439;2.5152,6.5922,4.7815;2.7209,2.4686,3.0012;-1.2081,7.8383,3.6939;-1.9513,10.1647,4.5027;1.3578,7.7145,7.0494;-1.6972,11.863,6.1202;2.8437,-1.5423,2.071;-.0794,-2.4437,2.17;1.0551,.3712,1.8173;-.3993,-.784,4.2612;3.0977,-2.0352,4.3622;1.6434,-4.07,2.4513;1.4813,-1.188,.1744;-2.1329,.2071,4.1171;-1.0654,.9743,1.9655;-5.1753,4.4025,2.3793;-2.6914,2.6143,2.3251;-3.1477,3.266,5.9538;-4.5518,4.9027,4.8855;-2.3143,5.3662,2.8656;-2.8258,4.3251,.8003;-4.2878,.7431,2.3954;-4.5955,1.7598,.9768;-5.6576,1.868,2.3976;-2.3603,6.4658,5.025;-4.8695,6.5416,3.1422;.124,10.6176,8.4528;1.7264,-4.0235,4.6895;.2347,-3.0788,4.5722;.9094,-3.4832,6.6829;
 


xception in thread "Thread-8" java.lang.IllegalArgumentException: Comparison method violates its general contract!
at java.util.TimSort.mergeLo(Unknown Source)
at java.util.TimSort.mergeAt(Unknown Source)
at java.util.TimSort.mergeCollapse(Unknown Source)
at java.util.TimSort.sort(Unknown Source)
at java.util.TimSort.sort(Unknown Source)
at java.util.Arrays.sort(Unknown Source)
at java.util.Collections.sort(Unknown Source)
at chemaxon.calculations.nmr.hose.CanonicalLabeler.sortArrayList(CanonicalLabeler.java:187)
at chemaxon.calculations.nmr.hose.CanonicalLabeler.step3(CanonicalLabeler.java:94)
at chemaxon.calculations.nmr.hose.CanonicalLabeler.step2(CanonicalLabeler.java:87)
at chemaxon.calculations.nmr.hose.CanonicalLabeler.step3(CanonicalLabeler.java:102)
at chemaxon.calculations.nmr.hose.CanonicalLabeler.step2(CanonicalLabeler.java:87)
at chemaxon.calculations.nmr.hose.CanonicalLabeler.step3(CanonicalLabeler.java:97)
at chemaxon.calculations.nmr.hose.CanonicalLabeler.step2(CanonicalLabeler.java:87)
at chemaxon.calculations.nmr.hose.CanonicalLabeler.step3(CanonicalLabeler.java:102)
at chemaxon.calculations.nmr.hose.CanonicalLabeler.step2(CanonicalLabeler.java:87)
at chemaxon.calculations.nmr.hose.CanonicalLabeler.step3(CanonicalLabeler.java:97)
at chemaxon.calculations.nmr.hose.CanonicalLabeler.step2(CanonicalLabeler.java:87)
at chemaxon.calculations.nmr.hose.CanonicalLabeler.step3(CanonicalLabeler.java:102)
at chemaxon.calculations.nmr.hose.CanonicalLabeler.step2(CanonicalLabeler.java:87)
at chemaxon.calculations.nmr.hose.CanonicalLabeler.step3(CanonicalLabeler.java:97)
at chemaxon.calculations.nmr.hose.CanonicalLabeler.step2(CanonicalLabeler.java:87)
at chemaxon.calculations.nmr.hose.CanonicalLabeler.step3(CanonicalLabeler.java:97)
at chemaxon.calculations.nmr.hose.CanonicalLabeler.step2(CanonicalLabeler.java:87)
at chemaxon.calculations.nmr.hose.CanonicalLabeler.step3(CanonicalLabeler.java:97)
at chemaxon.calculations.nmr.hose.CanonicalLabeler.step2(CanonicalLabeler.java:87)
at chemaxon.calculations.nmr.hose.CanonicalLabeler.step3(CanonicalLabeler.java:97)
at chemaxon.calculations.nmr.hose.CanonicalLabeler.step2(CanonicalLabeler.java:87)
at chemaxon.calculations.nmr.hose.CanonicalLabeler.step3(CanonicalLabeler.java:97)
at chemaxon.calculations.nmr.hose.CanonicalLabeler.step2(CanonicalLabeler.java:87)
at chemaxon.calculations.nmr.hose.CanonicalLabeler.step3(CanonicalLabeler.java:97)
at chemaxon.calculations.nmr.hose.CanonicalLabeler.step2(CanonicalLabeler.java:87)
at chemaxon.calculations.nmr.hose.CanonicalLabeler.step3(CanonicalLabeler.java:97)
at chemaxon.calculations.nmr.hose.CanonicalLabeler.step2(CanonicalLabeler.java:87)
at chemaxon.calculations.nmr.hose.CanonicalLabeler.step3(CanonicalLabeler.java:97)
at chemaxon.calculations.nmr.hose.CanonicalLabeler.canonLabel(CanonicalLabeler.java:79)
at chemaxon.calculations.nmr.hose.HoseCodeGenerator.getHOSECode(HoseCodeGenerator.java:198)
at chemaxon.calculations.nmr.hose.HoseCodeGenerator.getHOSECode(HoseCodeGenerator.java:172)
at chemaxon.calculations.nmr.hose.HoseShiftPredictor.predict(HoseShiftPredictor.java:91)
at chemaxon.calculations.nmr.MixedNMRPredictor.predictWithReport(MixedNMRPredictor.java:112)
at chemaxon.calculations.nmr.NMRCalculator.calculate(NMRCalculator.java:473)
at chemaxon.calculations.ui.nmr.NMRCalculatorDisplay.calculate(NMRCalculatorDisplay.java:319)
at chemaxon.calculations.ui.nmr.NMRCalculatorDisplay.access$000(NMRCalculatorDisplay.java:46)
at chemaxon.calculations.ui.nmr.NMRCalculatorDisplay$1.run(NMRCalculatorDisplay.java:116)
at java.lang.Thread.run(Unknown Source)





As usual, I recommend to download the whole PubChem database and run at least 1 million random molecules,


ftp://ftp.ncbi.nih.gov/pubchem


 


Also a link to some validation molecules would be nice to get a glimpse on the errors, is it 1ppm, 5ppm?


Cheers


Tobias

ChemAxon 5fc3e8d7d0

02-09-2013 12:43:01

Dear Tobias,

Yes, in the newer versions this bug was fixed. Please update Marvin to 6.0.5.
Thanks for your comments. We will consider your suggestion.

BR,
Laszlo