This function gives the boolean of whether two LogicOr objects are
equivilant or not. I needed this for database checking

The function equivilant and isSpecificCaseOf for GroupAtom now checks the
list of charges and atom label

The function isIsomorphic was meant to compare molecules to groups,
therefore it respects wildcards (seeing as a molecule will never have an
atom named Cs or Ct). However, this makes the function isIsomorphic not
useful when tryint to compare two groups.

I've created a new function isIdentical which will not respect wildcards
and can tell if two groups are the same.

This function is used to check for malformed kinetic families. I have also
removed the function isWellFormed from base.py because it is deprecated by
this new function (and also didn't work due to the many changes we've been
making).

The new function checks for:
-rule labels that have group names which do not exist in groups.py
-rule adjLists that do not match with the corresponding adj list in
groups.py
-Each group must exist in the tree
-Each group adjList must actually be a more specific case of it's parent's adjList

Coded another check in checkWellFormed to see if each node is unique inside
of a family.