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Resolve "Processing MOF data problems"

Dinga Wonanke requested to merge 1665-processing-mof-data-problems into develop

There was an error in the manner in which the code handled layer systems. This issue has now been fixed such that the code can effective parse layered COFs or MOFs. In addition the code could not deconstruct sulfide bonds functional groups connected to metal. This issue has also been resolved.

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