User 6b1e802ce9
13-07-2012 19:14:07
The sdf file is an export from IJC. I am using PP to import the export from IJC.
In lame language what does it mean Sgroup already added
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Error report:
Fri Jul 13 15:04:10 EDT 2012
Sgroup already added
JChem version : 5.4.1.0
Component collection version : 1.8.1_j54
JVM: Sun Microsystems Inc. Java HotSpot(TM) 64-Bit Server VM 1.6.0_01
Memory: 455.0 MB maximum 194.0 MB total 158.0 MB free
OS: amd64 Linux 2.6.18-92.1.18.el5
Exception ID: E55310104
Current input structure:
c12c(cccc1)[nH]cc2CC(C(=O)NC(CCC[NH+]=C(N)N)C(=O)NC(CS(=O)(=O)[O-])C(=O)NC3C(C)C(=O)CN(C)C(=O)C(C(O)C)NC(C(CC(=O)N)NC(=O)C(CC(C)C)NC(=O)C(CCC(=O)N)N(C)C3=O)=O)NC(=O)C(C(C)(C)C)NC(=O)C(C(C)(C)C)NC(=O)C4CCCN4C(=O)C(NC(=O)C(C)NC=O)Cc5ccccc5
Stack trace:
chemaxon.formats.MolFormatException: Sgroup already added
at chemaxon.marvin.io.MRecordImporter.readStructure(Unknown Source)
at chemaxon.marvin.io.MRecordImporter.readMol(Unknown Source)
at chemaxon.marvin.io.MRecordImporter.readMol(Unknown Source)
at chemaxon.marvin.io.MRecordImporter.readMol0(Unknown Source)
at chemaxon.marvin.io.MRecordImporter.readMol(Unknown Source)
at chemaxon.formats.MolImporter.readMol(Unknown Source)
at chemaxon.formats.MolImporter.read(Unknown Source)
at chemaxon.formats.MolImporter.read(Unknown Source)
at chemaxon.util.MolHandler.importMol(MolHandler.java:657)
at chemaxon.util.MolHandler.setMolecule(MolHandler.java:148)
at chemaxon.util.MolHandler.<init>(MolHandler.java:83)
at chemaxon.pp.util.Converter.sciMol2cxnMol(Converter.java:57)
at chemaxon.pp.util.Converter.getMoleculeFromDataRecord(Converter.java:32)
at chemaxon.pp.ChemAxonJChemBaseInsert.onProcessBody(ChemAxonJChemBaseInsert.java:89)
at chemaxon.pp.ChemAxonComponent.onProcess(ChemAxonComponent.java:50)
at com.scitegic.pilot.Pilot.callOnProcess(Pilot.java:300)
Caused by: java.lang.IllegalArgumentException: Sgroup already added
at chemaxon.struc.Sgroup.addChildSgroup(Unknown Source)
at chemaxon.marvin.io.formats.mdl.MolImport.readPropertiesBlockV2(Unknown Source)
at chemaxon.marvin.io.formats.mdl.MolImport.readCtab(Unknown Source)
at chemaxon.marvin.io.formats.mdl.MolImport.readMol0(Unknown Source)
at chemaxon.marvin.io.formats.mdl.MolImport.readMol(Unknown Source)
... 16 more
CTAB of current structure:
DISCODERMIN-A
SciTegic07131215042D
119123 0 0 0 0 999 V2000
-3.3942 -1.9767 0.0000 C 0 0
-3.3312 -1.1510 0.0000 C 0 0
-2.6360 -2.2898 0.0000 C 0 0
-4.0491 -2.4739 0.0000 C 0 0
-4.0414 -0.7543 0.0000 C 0 0
-2.5283 -0.9715 0.0000 C 0 0
-2.1000 -1.6756 0.0000 N 0 0
-2.5326 -3.1071 0.0000 C 0 0
-3.9457 -3.2983 0.0000 C 0 0
-4.0548 0.0774 0.0000 C 0 0
-3.1875 -3.6044 0.0000 C 0 0
-4.7033 0.5510 0.0000 N 0 0
-3.3720 0.5473 0.0000 C 0 0
-5.5283 0.5517 0.0000 C 0 0
-2.5470 0.5435 0.0000 N 0 0
-3.3783 1.3723 0.0000 O 0 0
-7.6845 0.5512 0.0000 C 0 0
-0.3839 0.5518 0.0000 N 0 0
0.2678 0.0803 0.0000 C 0 0
0.9472 0.5379 0.0000 C 0 0
0.2678 -0.7515 0.0000 C 0 0
-9.8408 0.5478 0.0000 C 0 0
2.2578 0.4478 0.0000 N 0 0
0.9542 1.3631 0.0000 O 0 0
0.9820 -1.1675 0.0000 S 0 0
2.9094 0.9262 0.0000 C 0 0
1.8001 -1.5558 0.0000 O 0 5
1.6268 -0.5368 0.0000 O 0 0
0.3510 -1.8123 0.0000 O 0 0
3.5888 0.4617 0.0000 C 0 0
2.9094 1.7514 0.0000 C 0 0
-11.9971 0.5476 0.0000 C 0 0
3.8926 1.5832 0.0000 N 0 0
3.5959 -0.3633 0.0000 O 0 0
3.5607 2.8448 0.0000 C 0 0
2.1952 2.1674 0.0000 C 0 0
-14.1534 0.5552 0.0000 C 0 0
6.2022 -0.6195 0.0000 N 0 0
6.7698 4.4420 0.0000 C 0 0
-16.3027 0.5697 0.0000 C 0 0
8.1478 0.8349 0.0000 N 0 0
-16.7603 1.3601 0.0000 O 0 0
8.0212 2.1602 0.0000 C 0 0
8.5487 1.5259 0.0000 C 0 0
7.2006 2.0732 0.0000 O 0 0
9.3760 1.6136 0.0000 C 0 0
9.7074 2.3669 0.0000 C 0 0
9.2254 3.0338 0.0000 N 0 0
10.5280 2.4540 0.0000 O 0 0
-12.6730 0.0848 0.0000 C 0 0
-11.9967 1.3797 0.0000 O 0 0
-12.6666 -0.7470 0.0000 C 0 0
-13.3284 0.5513 0.0000 N 0 0
-11.9563 -1.1507 0.0000 C 0 0
-11.9500 -1.9757 0.0000 C 0 0
-11.2453 -0.7361 0.0000 C 0 0
-11.2327 -2.3794 0.0000 C 0 0
-10.5282 -1.1398 0.0000 C 0 0
-10.5219 -1.9647 0.0000 C 0 0
4.4821 1.0301 0.0000 C 0 0
3.9938 2.4789 0.0000 C 0 0
5.2123 1.4096 0.0000 C 0 0
4.3830 0.2108 0.0000 C 0 0
5.3184 2.2277 0.0000 O 0 0
5.0429 -0.2809 0.0000 C 0 0
4.9438 -1.1001 0.0000 C 0 0
4.1857 -1.4204 0.0000 N 0 0
5.5968 -1.5911 0.0000 O 0 0
3.9783 3.5540 0.0000 C 0 0
3.9049 2.0950 0.0000 O 0 0
4.7715 3.3979 0.0000 N 0 0
5.1609 2.5849 0.0000 C 0 0
-10.5158 1.0191 0.0000 C 0 0
-9.8421 -0.2773 0.0000 O 0 0
-11.1721 0.5470 0.0000 N 0 0
-10.5145 1.8441 0.0000 C 0 0
-11.8037 1.1841 0.0000 C 0 0
-11.4007 1.9845 0.0000 C 0 0
-8.3655 0.0855 0.0000 C 0 0
-7.6949 1.4386 0.0000 O 0 0
-9.0158 0.5494 0.0000 N 0 0
-8.3557 -0.7462 0.0000 C 0 0
-7.6299 -1.1469 0.0000 C 0 0
-9.0650 -1.1638 0.0000 C 0 0
-8.5612 -1.5461 0.0000 C 0 0
-14.8322 1.0242 0.0000 C 0 0
-14.1673 -0.2767 0.0000 O 0 0
-15.4777 0.5633 0.0000 N 0 0
-14.8183 1.8561 0.0000 C 0 0
-1.8909 1.0162 0.0000 C 0 0
-1.2088 0.5455 0.0000 C 0 0
-1.8836 1.8412 0.0000 C 0 0
-1.2162 -0.2795 0.0000 O 0 0
-1.1660 2.2440 0.0000 C 0 0
-1.1587 3.0689 0.0000 C 0 0
-0.4481 3.4509 0.0000 N 0 3
-0.4268 4.2896 0.0000 C 0 0
-1.1230 4.7327 0.0000 N 0 0
0.2979 4.6714 0.0000 N 0 0
6.9290 -0.2882 0.0000 C 0 0
7.5087 -0.8753 0.0000 C 0 0
7.0974 0.5266 0.0000 C 0 0
7.3403 -1.6901 0.0000 O 0 0
7.8782 0.7759 0.0000 C 0 0
8.0465 1.5907 0.0000 C 0 0
8.4932 0.2240 0.0000 C 0 0
7.2348 3.7676 0.0000 C 0 0
7.0650 5.2123 0.0000 O 0 0
8.0139 3.9681 0.0000 N 0 0
6.9306 2.9932 0.0000 C 0 0
7.4458 2.3514 0.0000 C 0 0
6.1229 2.8711 0.0000 O 0 0
-6.2099 1.0165 0.0000 C 0 0
-5.5370 -0.2803 0.0000 O 0 0
-6.8595 0.5518 0.0000 N 0 0
-6.1942 1.8484 0.0000 C 0 0
-5.4757 2.2498 0.0000 C 0 0
-6.9108 2.2719 0.0000 C 0 0
-6.4007 2.6478 0.0000 C 0 0
12 14 1 0
13 15 1 0
115 17 1 0
91 18 1 0
18 19 1 0
19 20 1 0
19 21 1 0
81 22 1 0
20 23 1 0
20 24 2 0
21 25 1 0
23 26 1 0
25 27 1 0
25 28 2 0
25 29 2 0
26 30 1 0
26 31 1 0
75 32 1 0
30 33 1 0
30 34 2 0
31 35 1 0
31 36 1 0
53 37 1 0
62 38 1 0
71 39 1 0
88 40 1 0
101 41 1 0
109 43 1 0
40 42 2 0
41 44 1 0
43 45 2 0
44 46 1 0
46 47 1 0
47 48 1 0
47 49 2 0
43 44 1 0
32 50 1 0
32 51 2 0
50 52 1 0
50 53 1 0
52 54 1 0
54 55 2 0
54 56 1 0
55 57 1 0
56 58 2 0
57 59 2 0
58 59 1 0
33 60 1 0
33 61 1 0
60 62 1 0
60 63 1 0
62 64 2 0
63 65 1 0
65 66 1 0
66 67 1 0
66 68 2 0
35 69 1 0
35 70 2 0
69 71 1 0
71 72 1 0
73 22 1 0
22 74 2 0
73 75 1 0
73 76 1 0
75 77 1 0
76 78 1 0
77 78 1 0
17 79 1 0
17 80 2 0
79 81 1 0
79 82 1 0
82 83 1 0
82 84 1 0
82 85 1 0
37 86 1 0
37 87 2 0
86 88 1 0
86 89 1 0
1 2 1 0
1 3 2 0
1 4 1 0
2 5 1 0
2 6 2 0
3 7 1 0
3 8 1 0
4 9 2 0
10 5 1 0
8 11 2 0
10 12 1 0
10 13 1 0
13 16 2 0
6 7 1 0
9 11 1 0
15 90 1 0
90 91 1 0
90 92 1 0
91 93 2 0
92 94 1 0
94 95 1 0
95 96 1 0
96 97 2 0
97 98 1 0
97 99 1 0
38100 1 0
100101 1 0
100102 1 0
101103 2 0
102104 1 0
104105 1 0
104106 1 0
107 39 1 0
39108 2 0
107109 1 0
107110 1 0
110111 1 0
110112 1 0
14113 1 0
14114 2 0
113115 1 0
113116 1 0
116117 1 0
116118 1 0
116119 1 0
M CHG 2 27 -1 96 1
M STY 8 1 SUP 2 SUP 3 SUP 4 SUP 5 SUP 6 SUP 7 SUP 8 SUP
M STY 7 9 SUP 10 SUP 11 SUP 12 SUP 13 SUP 14 SUP 15 SUP
M SLB 8 1 1 2 2 3 3 4 4 5 5 6 6 7 7 8 8
M SLB 7 9 9 10 10 11 11 12 12 13 13 14 14 15 15
M SDS EXP 3 3 4 5
M SPL 8 1 4 2 4 3 4 5 4 6 4 7 4 8 4 9 4
M SPL 6 1 4 2 4 3 4 5 4 6 4 7 4 8 4 9 4
M SAL 1 11 32 50 51 52 53 54 55 56 57 58 59
M SBL 1 2 18 23
M SMT 1 Phe
M SCL 1 CXN
M SAP 1 1 32 0
M SAP 1 1 53 0
M SAL 2 8 41 43 44 45 46 47 48 49
M SBL 2 2 27 28
M SMT 2 Asn
M SCL 2 CXN
M SAP 2 1 41 0
M SAP 2 1 43 0
M SAL 3 6 23 26 30 31 34 36
M SBL 3 3 19 9 21
M SMT 3 Thr*
M SCL 3 CXN
M SAP 3 1 23 0 2
M SAP 3 1 30 0 2
M SAL 4 15 18 19 20 21 23 24 25 26 27 28 29 30 31 34 36
M SAL 4 15 40 42 41 43 44 45 46 47 48 49 32 50 51 52 53
M SAL 4 15 54 55 56 57 58 59 33 60 61 62 63 64 65 66 67
M SAL 4 15 68 35 69 70 71 72 22 73 74 75 76 77 78 17 79
M SAL 4 15 80 81 82 83 84 85 37 86 87 88 89 1 2 3 4
M SAL 4 15 5 6 7 8 9 10 11 12 13 16 15 90 91 92 93
M SAL 4 15 94 95 96 97 98 99 38 100 101 102 103 104 105 106 39
M SAL 4 14 107 108 109 110 111 112 14 113 114 115 116 117 118 119
M SMT 4 OH
M SCL 4 CXN
M SAP 4 1 18 0 10
M SAP 4 1 20 0 10
M SAP 4 1 23 0 10
M SAP 4 1 30 0 10
M SAP 4 1 41 0 10
M SAP 4 1 43 0 10
M SAP 4 1 32 0 10
M SAP 4 1 53 0 10
M SAP 4 1 33 0 10
M SAP 4 1 62 0 10
M SAP 4 1 35 0 10
M SAP 4 1 71 0 10
M SAP 4 1 22 0 10
M SAP 4 1 75 0 10
M SAP 4 1 17 0 10
M SAP 4 1 81 0 10
M SAP 4 1 37 0 10
M SAP 4 1 88 0 10
M SAP 4 1 12 0 10
M SAP 4 1 13 0 10
M SAP 4 1 15 0 10
M SAP 4 1 91 0 10
M SAP 4 1 38 0 10
M SAP 4 1 101 0 10
M SAP 4 1 39 0 10
M SAP 4 1 109 0 10
M SAP 4 1 14 0 10
M SAP 4 1 115 0 10
M SAL 5 9 18 19 20 21 24 25 27 28 29
M SBL 5 2 4 9
M SMT 5 DCys*
M SCL 5 CXN
M SAP 5 1 18 0
M SAP 5 1 20 0
M SAL 6 10 33 60 61 62 63 64 65 66 67 68
M SBL 6 2 19 24
M SMT 6 MeGln
M SCL 6 CXN
M SAP 6 1 33 0
M SAP 6 1 62 0
M SAL 7 5 35 69 70 71 72
M SBL 7 2 21 25
M SMT 7 Sar
M SCL 7 CXN
M SAP 7 1 35 0
M SAP 7 1 71 0
M SAL 8 7 22 73 74 75 76 77 78
M SBL 8 2 8 18
M SMT 8 DPro
M SCL 8 CXN
M SAP 8 1 22 0
M SAP 8 1 75 0
M SAL 9 8 17 79 80 81 82 83 84 85
M SBL 9 2 3 8
M SMT 9 DTle
M SCL 9 CXN
M SAP 9 1 17 0
M SAP 9 1 81 0
M SAL 10 5 37 86 87 88 89
M SBL 10 2 23 26
M SMT 10 DAla
M SCL 10 CXN
M SAP 10 1 37 0
M SAP 10 1 88 0
M SAL 11 14 1 2 3 4 5 6 7 8 9 10 11 12 13 16
M SBL 11 2 1 2
M SMT 11 DTrp
M SCL 11 CXN
M SAP 11 1 12 0
M SAP 11 1 13 0
M SAL 12 11 15 90 91 92 93 94 95 96 97 98 99
M SBL 12 2 2 4
M SMT 12 Arg
M SCL 12 CXN
M SAP 12 1 15 0
M SAP 12 1 91 0
M SAL 13 8 38 100 101 102 103 104 105 106
M SBL 13 2 24 27
M SMT 13 DLeu
M SCL 13 CXN
M SAP 13 1 38 0
M SAP 13 1 101 0
M SAL 14 7 39 107 108 109 110 111 112
M SBL 14 2 25 28
M SMT 14 Thr
M SCL 14 CXN
M SAP 14 1 39 0
M SAP 14 1 109 0
M SAL 15 8 14 113 114 115 116 117 118 119
M SBL 15 2 1 3
M SMT 15 Tle
M SCL 15 CXN
M SAP 15 1 14 0
M SAP 15 1 115 0
M END
$$$$
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