Version 1.56 of SketchEl adds in MDL MOL reading/writing extensions that preserve hydrogen counts and zero-order bonds. The writing algorithm uses a charge separation algorithm for improving interoperability with legacy software that understands only the obsolete core feature set of the format.
For more information, see:
"Accurate Specification of Molecular Structures: The Case for Zero-Order Bonds and Explicit Hydrogen Counting"
Alex M. Clark, Journal of Chemical Information and Modeling, vol. 51, pp. 3149-3157 (2011)
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