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Table 1 Penalty scores and annotation that are output from the Checker module

From: An open source chemical structure curation pipeline using RDKit

Penalty score Penalty explanation
7 Error-9986 (Cannot process aromatic bonds)
Illegal input
InChI: Unknown element(s)
6 All atoms have zero coordinates
InChI: Accepted unusual valence(s)
InChI: Empty structure
Molecule has 3D coordinates
Molecule has a radical that is not found in the known list
Molecule has six (or more) atoms with exactly the same coordinates
Number of atoms less than 1
Polymer information in mol file
V3000 mol file
5 InChI_RDKit/Mol stereo mismatch
Mol/Inchi/RDKit stereo mismatch
RDKit_Mol/InChI stereo mismatch
Molecule has a bond with an illegal stereo flag
Molecule has a bond with an illegal type
Molecule has a crossed bond in a ring
Molecule has two (or more) atoms with exactly the same coordinates
2 InChI_Mol/RDKit stereo mismatch
Molecule has a stereo bond in a ring
Molecule has an atom with multiple stereo bonds
Molecule has a stereo bond to a stereocenter
Molecule has the 3D flag set for a 2D conformer
Other InChI Warnings
  1. 7 is the most serious penalty score and 2 the least important