if params.setParseCAOnly(true) and params.setCreateAtomBonds(true) are
set, some bonds specified in LINK records or SSBOND records cannot be
set (atoms are not there). In these cases StructureException should not
be thrown.
Merge pull request #87 from pwrose/master

if params.setParseCAOnly(true) and params.setCreateAtomBonds(true) are