# Known bond order perception failures for the corpus in this directory.
#
# <path relative to data/bondorders>  <charged|neutral|both>  <fail|wrong|kekule>  <reason>
#
# charged: formal charges as stored in the file; neutral: all formal charges
# set to zero first. fail: perception reports failure (cleanly); wrong: it
# reports success with valences that differ from the file; kekule: valid
# valences but a different Kekule structure from the reference.
# Generated from a run of tests/io/bondorderscorpustest.cpp. Delete a line
# when perception starts passing the entry.
carbon/nanotube-10-0-open.mol both fail open-ended nanotube without H caps: each rim carbon has two bonds and needs two more
carbon/nanotube-5-5-defect-hcap.mol both fail odd number of sp2 carbons (a vacancy defect): no perfect matching exists
ccd/0HV.sdf both fail nitro or N-oxide N=O: needs hypervalent or charge-separated nitrogen
ccd/0RD.sdf both fail sulfonyl or sulfoxide S=O: sulfur valence 4 or 6 is not chosen
ccd/1HZ.sdf both fail sulfonyl or sulfoxide S=O: sulfur valence 4 or 6 is not chosen
ccd/2CX.sdf both fail sulfonyl or sulfoxide S=O: sulfur valence 4 or 6 is not chosen
ccd/3BA.sdf both kekule fused aromatic ring system: valid alternative Kekule structure, not the file's
ccd/3Z5.sdf both kekule fused aromatic ring system: valid alternative Kekule structure, not the file's
ccd/4SX.sdf both fail sulfonyl or sulfoxide S=O: sulfur valence 4 or 6 is not chosen
ccd/4TW.sdf both fail sulfonyl or sulfoxide S=O: sulfur valence 4 or 6 is not chosen
ccd/5NU.sdf both fail nitro or N-oxide N=O: needs hypervalent or charge-separated nitrogen
ccd/75D.sdf both fail sulfonyl or sulfoxide S=O: sulfur valence 4 or 6 is not chosen
ccd/7L3.sdf both fail sulfonyl or sulfoxide S=O: sulfur valence 4 or 6 is not chosen
ccd/87D.sdf both fail sulfonyl or sulfoxide S=O: sulfur valence 4 or 6 is not chosen
ccd/A1E3B.sdf both fail sulfonyl or sulfoxide S=O: sulfur valence 4 or 6 is not chosen
ccd/A1ECY.sdf both fail sulfonyl or sulfoxide S=O: sulfur valence 4 or 6 is not chosen
ccd/A1MIQ.sdf both fail unsatisfied: N(C1 N2 ) N(N-2 N2 ) N-(N2 )
ccd/ARG.sdf neutral fail formal charges stripped: C(N+2 N1 N1 )
ccd/B12.sdf both fail metal complex: how bonds to the metal count toward ligand valence is not modelled
ccd/B4W.sdf both kekule fused aromatic ring system: valid alternative Kekule structure, not the file's
ccd/BCB.sdf charged fail metal complex: how bonds to the metal count toward ligand valence is not modelled
ccd/BCB.sdf neutral wrong metal complex: how bonds to the metal count toward ligand valence is not modelled
ccd/BCL.sdf charged fail metal complex: how bonds to the metal count toward ligand valence is not modelled
ccd/BCL.sdf neutral wrong metal complex: how bonds to the metal count toward ligand valence is not modelled
ccd/CHL.sdf charged fail metal complex: how bonds to the metal count toward ligand valence is not modelled
ccd/CHL.sdf neutral wrong metal complex: how bonds to the metal count toward ligand valence is not modelled
ccd/CLA.sdf charged fail metal complex: how bonds to the metal count toward ligand valence is not modelled
ccd/CLA.sdf neutral wrong metal complex: how bonds to the metal count toward ligand valence is not modelled
ccd/DY5.sdf both fail nitro or N-oxide N=O: needs hypervalent or charge-separated nitrogen
ccd/E36.sdf both fail sulfonyl or sulfoxide S=O: sulfur valence 4 or 6 is not chosen
ccd/ERL.sdf both fail sulfonyl or sulfoxide S=O: sulfur valence 4 or 6 is not chosen
ccd/F43.sdf both fail metal complex: how bonds to the metal count toward ligand valence is not modelled
ccd/HE6.sdf both wrong metal complex: how bonds to the metal count toward ligand valence is not modelled
ccd/HEA.sdf both wrong metal complex: how bonds to the metal count toward ligand valence is not modelled
ccd/HEB.sdf both wrong metal complex: how bonds to the metal count toward ligand valence is not modelled
ccd/HEC.sdf both wrong metal complex: how bonds to the metal count toward ligand valence is not modelled
ccd/HEM.sdf charged fail metal complex: how bonds to the metal count toward ligand valence is not modelled
ccd/HEM.sdf neutral wrong metal complex: how bonds to the metal count toward ligand valence is not modelled
ccd/HIS.sdf neutral fail formal charges stripped: C(H1 N+2 N1 )
ccd/IMD.sdf neutral fail formal charges stripped: C(H1 N+2 N1 )
ccd/IRE.sdf both kekule fused aromatic ring system: valid alternative Kekule structure, not the file's
ccd/IYK.sdf both kekule fused aromatic ring system: valid alternative Kekule structure, not the file's
ccd/J4J.sdf both fail nitro or N-oxide N=O: needs hypervalent or charge-separated nitrogen
ccd/M57.sdf both fail sulfonyl or sulfoxide S=O: sulfur valence 4 or 6 is not chosen
ccd/M98.sdf both fail unsatisfied: C(C1 C1 C2 ) C(C1 C2 H1 ) C(C1 H1 N+2 ) C(C2 H1 N+1 ) N+(C1 C2 O1 ) O(N+1 )
ccd/MTX.sdf both kekule fused aromatic ring system: valid alternative Kekule structure, not the file's
ccd/NAD.sdf both fail phosphate P=O: phosphorus valence 5 with ambiguous terminal oxygens
ccd/NAP.sdf both fail phosphate P=O: phosphorus valence 5 with ambiguous terminal oxygens
ccd/NE7.sdf both fail sulfonyl or sulfoxide S=O: sulfur valence 4 or 6 is not chosen
ccd/R43.sdf both fail sulfonyl or sulfoxide S=O: sulfur valence 4 or 6 is not chosen
ccd/R9R.sdf both fail sulfonyl or sulfoxide S=O: sulfur valence 4 or 6 is not chosen
ccd/RRU.sdf both fail sulfonyl or sulfoxide S=O: sulfur valence 4 or 6 is not chosen
ccd/SAM.sdf both fail unsatisfied: C(C1 O1 O2 ) O(C1 ) O(C2 )
ccd/SKU.sdf both fail sulfonyl or sulfoxide S=O: sulfur valence 4 or 6 is not chosen
ccd/SRM.sdf charged fail metal complex: how bonds to the metal count toward ligand valence is not modelled
ccd/SRM.sdf neutral wrong metal complex: how bonds to the metal count toward ligand valence is not modelled
ccd/TAU.sdf both fail sulfonyl or sulfoxide S=O: sulfur valence 4 or 6 is not chosen
ccd/TPP.sdf neutral fail formal charges stripped: C(H1 N+2 S1 )
ccd/TRR.sdf neutral fail formal charges stripped: C(C1 C1 C2 ) C(C1 N1 N2 ) C(C2 H1 N+1 ) C(N+2 N1 N1 ) N(C1 C2 )
ccd/YKS.sdf both fail sulfonyl or sulfoxide S=O: sulfur valence 4 or 6 is not chosen
ccd/YUQ.sdf both fail sulfonyl or sulfoxide S=O: sulfur valence 4 or 6 is not chosen
hetero/acridine.mol both kekule fused aromatic ring system: valid alternative Kekule structure, not the file's
hetero/adenine-9H-heavy.mol both fail heavy atoms only: the missing hydrogens change every valence
hetero/imidazole-heavy.mol both wrong heavy atoms only: the missing hydrogens change every valence
hetero/indole-heavy.mol both fail heavy atoms only: the missing hydrogens change every valence
hetero/phenazine.mol both kekule fused aromatic ring system: valid alternative Kekule structure, not the file's
hetero/pteridine.mol both kekule fused aromatic ring system: valid alternative Kekule structure, not the file's
hetero/purine-9H-heavy.mol both fail heavy atoms only: the missing hydrogens change every valence
molecules/amino_acids/L-4-nitrophenylalanine.cjson both fail nitro group N=O: needs hypervalent or charge-separated nitrogen
molecules/aromatics/acridine.cjson both kekule fused aromatic ring system: valid alternative Kekule structure, not the file's
molecules/aromatics/anthracene.cjson both kekule fused aromatic ring system: valid alternative Kekule structure, not the file's
molecules/aromatics/naphthalene.cjson both kekule fused aromatic ring system: valid alternative Kekule structure, not the file's
molecules/aromatics/nitrobenzene.cjson both fail nitro group N=O: needs hypervalent or charge-separated nitrogen
molecules/coordination/5-square-pyramidal.cjson both fail hypervalent sulfur (5 bonds to F): sulfur valence 6 is not chosen
molecules/fullerenes/PC70BM.cjson both kekule fullerene derivative: valid alternative Kekule structure of the cage
molecules/ligands/Cp-cyclopentadienyl.cjson neutral fail formal charges stripped: cyclopentadienyl anion
molecules/macrocycles/phthalocyanine.cjson both kekule fused aromatic ring system: valid alternative Kekule structure, not the file's
pyrene.mol both kekule fused aromatic ring system: valid alternative Kekule structure, not the file's
