The download can be found here:
http://comp.chem.nottingham.ac.uk/download/tmacc/index.html
And part of the diff for Atom.java is:
+
+ // added by JLM 06-Mar 06
+ public ChiralityInfo getChiralityInfo();
+
+ public void setChiralityInfo(ChiralityInfo chiralityInfo);
+
+ public void updateChiralityInfo(Map<Integer, Integer> conversionTable);
+
+ public void reorderChiralityInfo(List<Integer> newIndexes);
+ public void assignChiralityInfo();
I think it would be good to talk to those guys in Nottingham and see if these patches can be applied 'upstream' too.