fromOldAdjacencyList: blank lone pairs on group interpreted as undefined (wildcard).

Previously, these were all ending up as -1. Now they are set to None, 
which is what the new fromAdjacencyList does.
Small tweak in Atom.isSpecificCaseOf; use list iterator instead of index, range, len, lookup etc.
TODO: lone pairs and charges are not compared when comparing Atoms or GroupAtoms

isSpceficiCaseOf etc is ignoring lone pairs and charges. Made a few notes as to where this should be fixed
Adjacency list I/O for groups better for Lone Pairs