On the myth of chemical structure format conversion

Cheminformatics 2.0

There has been a lot of work, many products, and plenty said on the topic of converting chemical structures from one format to another, and a number of well used and highly regarded packages (e.g. OpenBabel) that specialise in providing this capability. Less well discussed, it would seem, is that when it comes to connection-table formats used to encode chemists’ sketches of molecules, there are no software packages and no two formats for which a round trip conversion can be reliably carried out without losing information, even if the chemical entities being expressed fall within the applicable domain of both formats.

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