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The OpenEye oedepict package (part of OpenEye's ogham product)
includes functionality for generating and rendering 2D co-ordinates of
chemical structures.
OpenEye's depiction algorithm assigns 2D co-ordinates to a given molbase, which need not be a single connected structure, using both pattern matching of ring templates, and algorithmic rules for laying out simple ring systems, ring attachments and acyclic chains and functional groups. The depiction algorithm attempts to resolve any clashes in this initial "rule-based" structure using a variety of heuristics.
OpenEye's rendering functionality can display or generate graphical file formats from either the co-ordinates calculated above, or from user provided co-ordinates. Numerous options are available to control the display of atom and bond color, aromaticity, dative bonds, super atoms, etc... in the final image.
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