GreenGroup/RMG-Java — pull request #219 by nickvandewiele (2011-10-25 16:48:16+00:00)
Title: Aromaticity perception algorithm of @mrharper added

Mike's aro perception algo was already created some time ago, but just not ready for use.

Because his algo was part of the branch heteroatom_aromatic that contains more than just this algorithm, I cherry-picked the single commit in which he created this.

The algorithm "ChemGraph.determineAromaticityAndWriteBBonds", contained in a single instance method of ChemGraph is added to the private constructor of ChemGraph so that each time a ChemGraph is created, the aro perception is performed.

After the perception, all aromatic bonds were assigned "B" labels.

Along with @gmagoon we figured out that atom types needed to be perceived again, in order
to produce correct thermochemistry. this is done by calling the Node.updateFgElement() instance method for each node in the perceived ChemGraph.

Aromatics will finally be perceived correctly. One small step for kinetic modelling, a giant leap for RMG!

All hail @mrharper