Table 2 Checker total number of the different penalty scores output from subjecting the ChEMBL Literature set, the SureChEMBL set and the PubChem Set to the Checker process
From: An open source chemical structure curation pipeline using RDKit
Penalty score | Penalty explanation | SureChEMBL | ChEMBL Literature | PubChem |
|---|---|---|---|---|
7 | Error-9986 (Cannot process aromatic bonds) | 4 | 0 | 0 |
Illegal input | 0 | 1 | 0 | |
InChI: Unknown element(s) | 3 | 0 | 1355 | |
6 | All atoms have zero coordinates | 0 | 0 | 12 |
InChI: Accepted unusual valence(s) | 73 | 1 | 2155 | |
InChI: Empty structure | 0 | 1 | 5824 | |
Molecule has 3D coordinates | 0 | 1 | 1024 | |
Molecule has a radical that is not found in the known list | 187 | 1 | 252 | |
Molecule has six (or more) atoms with exactly the same coordinates | 3 | 0 | 206 | |
Number of atoms less than 1 | 0 | 1 | 5824 | |
Polymer information in mol file | 2 | 0 | 0 | |
V3000 mol file | 594 | 0 | 0 | |
5 | InChI_RDKit/Mol stereo mismatch | 588 | 152 | 339 |
Mol/Inchi/RDKit stereo mismatch | 0 | 0 | 28 | |
RDKit_Mol/InChI stereo mismatch | 23 | 22 | 1479 | |
Molecule has a bond with an illegal stereo flag | 1054 | 0 | 0 | |
Molecule has a bond with an illegal type | 6 | 0 | 0 | |
Molecule has a crossed bond in a ring | 34 | 36 | 134 | |
Molecule has two (or more) atoms with exactly the same coordinates | 4 | 5 | 2367 | |
2 | InChI_Mol/RDKit stereo mismatch | 0 | 55 | 307 |
Molecule has a stereo bond in a ring | 2359 | 5763 | 7061 | |
Molecule has an atom with multiple stereo bonds | 1493 | 52 | 3660 | |
Molecule has a stereo bond to a stereocenter | 331 | 27 | 983 | |
Molecule has the 3D flag set for a 2D conformer | 0 | 0 | 5 | |
Other InChI Warnings | 20188 | 34052 | 170678 | |
No errors | 15015 | 111137 | 177815 |