Fixed and New JUnit Failures

Tests fixed since Rev fcb05b29d8b601c8b7053e502639038abb058c1b New failures in Rev 29dc71957334b8410cc38bcd9fb67c8ab976ecd5
t66 testFindMatchingAtomType_IAtomContainer(org.openscience.cdk.atomtype.StructGenMatcherTest)t
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