fixed a typo/bug in getStructureChainIDs.
changed permittedRelations so the restricted permission gets higher
priority, also added a translateToPATO hashtable so restricted relations
get translated back to PATO when their parent class from PATO is wanted.
in SSP, corrected the code so candidates modifier characters are not
directly post-composed to keyentities when their own entity are not
found--they are used as plain characters for keyentities instead.
added isEquivalentClass in ELKReasoner.
corrected two lower case 'score' to 'Score' in EQEvaluation code.