From the chair and boat representations of six-membered rings to Fischer and Haworth projections to pseudo-3D perspective drawings, chemists have been drawing 2D versions of 3D molecules for over a century and a quarter. Humans are able to accurately interpret the implicit 3D information of these 2D chemical structure representations, but the interpretation by computer software has been less accurate. The explosion of chemical structures in electronic format has heightened this problem.
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To address the issue, chemical information scientists have used software-based “standardization” of chemical structures. This includes the conversion of Haworth projections and chair and boat representations to regular hexagons with wedge and hashed bonds, sometimes removing or misinterpreting the implicit stereochemistry of the original representation. The alternative to software-based standardization is software-based interpretation, that is, software that accurately interprets the original 3D intent of the 2D drawing in exactly the same way that a chemist would. Case studies of misinterpretation resulting from software-based standardization will be discussed and will be contrasted with software-based interpretation of the same cases.
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