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Trying to read this corrupted smart rxn I have the following error is there a workaround ?
There are 9 cases like this in USPTO 1M dataset.
one example: 'C([O:4][CH2:5][C@@:6]12[C@@H:23]3[C@H:14]([C@H:15]4[C@@:19]([CH2:21][CH2:22]3)([CH3:20])[C:18](=[O:24])[CH2:17][CH2:16]4)CCC1=CC(=O)[CH2:8][CH2:7]2)(=O)C>[Br-].C[P+](C1C=CC=CC=1)(C1C=CC=CC=1)C1C=CC=CC=1.CCOCC.C([Li])CCC.CCCCCC>[CH2:8]=[C:7]1[CH2:8][CH2:7][C@@:6]2([CH2:5][OH:4])[C:23]([CH2:22][CH2:21][C@@H:22]3[C@@H:23]2[CH2:14][CH2:15][C@@:19]2([CH3:20])[C@H:21]3[CH2:16][CH2:17][C:18]2=[O:24])=[CH:6]1 |f:1.2|'
return error:
ERROR:root:Error processing structure: C([O:4][CH2:5][C@@:6]12[C@@H:23]3[C@H:14]([C@H:15]4[C@@:19]([CH2:21][CH2:22]3)([CH3:20])[C:18](=[O:24])[CH2:17][CH2:16]4)CCC1=CC(=O)[CH2:8][CH2:7]2)(=O)C>[Br-].C[P+](C1C=CC=CC=1)(C1C=CC=CC=1)C1C=CC=CC=1.CCOCC.C([Li])CCC.CCCCCC>[CH2:8]=[C:7]1[CH2:8][CH2:7][C@@:6]2([CH2:5][OH:4])[C:23]([CH2:22][CH2:21][C@@H:22]3[C@@H:23]2[CH2:14][CH2:15][C@@:19]2([CH3:20])[C@H:21]3[CH2:16][CH2:17][C:18]2=[O:24])=[CH:6]1 |f:1.2| | Error: Invariant Violation
could not find probe element
Violation occurred on line 71 in file Code[/RDGeneral/utils.h](http://localhost:8889/RDGeneral/utils.h)
Failed Expression: foundIt
RDKIT: 2024.03.1pre
BOOST: 1_82
Describe the bug
Trying to read this corrupted smart rxn I have the following error is there a workaround ?
There are 9 cases like this in USPTO 1M dataset.
one example:
'C([O:4][CH2:5][C@@:6]12[C@@H:23]3[C@H:14]([C@H:15]4[C@@:19]([CH2:21][CH2:22]3)([CH3:20])[C:18](=[O:24])[CH2:17][CH2:16]4)CCC1=CC(=O)[CH2:8][CH2:7]2)(=O)C>[Br-].C[P+](C1C=CC=CC=1)(C1C=CC=CC=1)C1C=CC=CC=1.CCOCC.C([Li])CCC.CCCCCC>[CH2:8]=[C:7]1[CH2:8][CH2:7][C@@:6]2([CH2:5][OH:4])[C:23]([CH2:22][CH2:21][C@@H:22]3[C@@H:23]2[CH2:14][CH2:15][C@@:19]2([CH3:20])[C@H:21]3[CH2:16][CH2:17][C:18]2=[O:24])=[CH:6]1 |f:1.2|'
return error:
To Reproduce
Expected behavior
My goal is to remove the atommaps. Or at least have an explanation of the root cause.
Configuration (please complete the following information):
Additional context
Add any other context about the problem here.
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