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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