GreenGroup/RMG-Java — Issue #231: Fused C6-C5 system incorrectly recognized as aromatic
Author: gmagoon
Created: 2011-12-03 00:52:41+00:00
State: open

The following molecule is incorrectly recognized as aromatic:
InChI=1/C9H8/c1-2-5-9-7-3-6-8(9)4-1/h1-2,4-7H,3H2

1 C 0 {2,D} {9,S}
2 C 0 {1,D} {3,S}
3 C 0 {2,S} {4,D} {7,S}
4 C 0 {3,D} {5,S}
5 C 0 {4,S} {6,S}
6 C 0 {5,S} {7,D}
7 C 0 {6,D} {8,S} {3,S}
8 C 0 {7,S} {9,D}
9 C 0 {8,D} {1,S}

This causes the following error during aromaticity perception:

Exception in thread "main" jing.chemUtil.InvalidConnectivityException
at jing.chemUtil.Node.generateFgElement(Node.java:755)
at jing.chemUtil.Node.updateFgElement(Node.java:1430)
at jing.chem.ChemGraph.determineAromaticityAndWriteBBonds(ChemGraph.java:211)
at jing.chem.ChemGraph.(ChemGraph.java:142)
at jing.chem.ChemGraph.make(ChemGraph.java:2426)
at ThermoDataEstimator.readChemGraphsFromFile(ThermoDataEstimator.java:279)
at ThermoDataEstimator.main(ThermoDataEstimator.java:93)

I will probably need to unwind the "fixes" to get different naphthalene resonance forms recognized as aromatic (cf. issue #223).