patch to fix UIT for single atom query

I've got a fix for bug 2888845 (https://sourceforge.net/tracker/?func=detail&aid=2888845&group_id=20024&atid=120024) that updates getIsomorphMaps to directly match single atom
queries. The return value is the same as usual but in this case, RMap
refers to atom indices rather than bond indices - thus there is no need to
call makeAtomsMapsOfBondsMaps. However, in the interests of generality,
makeAtomsMapsOfBondsMaps is also modified to account for single atom
queries. Thus the return value is the appropriate atom-atom mapping
(basically, just return the input mapping). This way code for multi-atom
queries is the same as for single-atom queries. Unit tests and Javadocs are
updated in the patch. Needs review. For cdk-1.2.x