Added new test files to testing.
Fixed line ends.
Moving around files to support .itps included in files.
Defaults switched to micelle for now for ease of use.
varios changes:

1) made it possible to incldue the itps in the same directory
as the top and gro files. Before, it only looked at the directory
the program was run in.

2) there appear to be issues with the way atomstypes are read into

             if len(split) == 3:
                               # Searching for matching bondtype to pull values from
-                            tempType = AbstractBondType(split[0], split[1], split[2])
+                            # Can't be this hard?
+                            atomtype1 = currentMolecule._atoms[int(split[0])-1].getAtomType()[0]
+                            atomtype2 = currentMolecule._atoms[int(split[1])-1].getAtomType()[0]
+                            tempType = AbstractBondType(atomtype1, atomtype2, split[2])
                             bondType = self.bondtypes.get(tempType)

Also, changes like this, explaining where bondType info comes frmo.

if isinstance(bondType, CubicBondType):
-                                split.append(length)
-                                split.append(C2)
-                                split.append(C3)
+                                split.append(bondType.length)
+                                split.append(bondType.C2)
+                                split.append(bondType.C3)

Finally,  there's apparently a dihedal format that justa gives the middle
atoms with wildcards assume on the edge, this currently isn't
supported.   And will need to be  supported, but isn't right noe.