Grapheme TK 1.1.0

New features

• Added the following to visualize color forcefields:

  • OEColorForceFieldDisplay

  • OEColorForceFieldLegendDisplayOptions

  • OEDrawColorForceFieldLegend

• Added the following to visualize the reference molecule of a color and shape overlap:

  • OEShapeOverlapDisplay

  • OEShapeOverlapDisplayOptions

  • OERenderShapeQuery

• Added the following to visualize shape and color overlaps:

  • OEShapeOverlapDisplay

  • OEShapeOverlapDisplayOptions

  • OERenderShapeOverlap

  • OEColorOverlapDisplayOptions

  • OERenderColorOverlap

Note

A valid shape license is required to use any of these new shape or color APIs.

• Added the OEDepictionFrom3DOptions class that allows more advanced customization of the generation of 2D coordinates driven by the 3D conformation when calling the OEPrepareDepictionFrom3D function. By default, OEPrepareDepictionFrom3D is tuned for generating 2D coordinates for representing 3D overlays in 2D. This class allows the 2D coordinate generation to choose a set of 2D coordinates that are much closer to how the molecule would look in a 3D viewer.

• Added the following to render user-defined labels when depicting color gradients:

  • OEColorGradientDisplayOptions.AddLabel

  • OEColorGradientDisplayOptions.ClearLabels

  • OEColorGradientDisplayOptions.GetLabels

• Added OEColorGradientDisplayOptions.ClearBoxRange method to remove the box range previously set to a color gradient.

• Added OEGet2DSurfaceArcs function to return the arcs of the molecule surface of a specific atom with the given radius. Varying radii can be passed to generate multiple surfaces in the range specified by the OESurfaceArcScale namespace. OEGetMoleculeSurfaceScale can be used to determine the appropriate scale for the molecule with the specified radius.

• Implemented the ShapeOverlap2PDF.java Java Grapheme TK example.

• Rewriting the ViewShapeMatch.java Java Grapheme TK example using the new classes and functions designed to depict shape and color overlaps.

Major bug fixes

• Molecule surface arcs inside macrocycles are no longer returned. See the effect of this change in Table: Example of depicting molecule surface.

  Example of depicting molecule surface

  Grapheme TK 1.0.6 (2013 Jun)	Grapheme TK 1.1.0 (2013 Oct)

Documentation changes

• All images were automatically regenerated to reflect the changes made since the previous release.