Grapheme TK 1.3.0¶
Due to the deprecation of OEFragmentNetwork and related classes in OEBio, Grapheme TK has introduced the following overloads:
- OEPrepareActiveSiteDepiction function has been overloaded. The new version takes an OEInteractionHintContainer object.
- OE2DActiveSiteDisplay class now should be constructed with an OEInteractionHintContainer object.
All functions and methods using OEFragmentNetwork are deprecated in Grapheme TK and will throw a warning when called. Active site depictions generated with the deprecated API will have a “deprecated” watermark (see the example below).
using the deprecated OEFragmentNetwork class using the new OEInteractionHintContainer class
In order to avoid the “deprecated” watermark from appearing in the image, use
OEInteractionHintContainer asite = new OEInteractionHintContainer(protein, ligand);
OEFragmentNetwork asite = new OEFragmentNetwork(protein, ligand);
For more details about the deprecated classes and functions, see the Deprecated OEFragmentNetwork and related API section.
OE2DActiveSiteDisplay now can visualize salt-bridge and aromatic ring stacking interactions.
The color scheme used to visualize different interaction types when depicting protein-ligand interaction has been changed to accommodate the new types (Pi- and T-stacking and salt-bridge).
2016.Feb color scheme 2016.Jun color scheme
OEShapeOverlapDisplayStyle.PropertyCloud style has been added to visualize shape overlays along with the following APIs:
- OEShapeOverlapDisplayStyle namespace
- OEShapeOverlapDisplayOptions.SetOverlapDisplayStyle and OEShapeOverlapDisplayOptions.SetOverlapDisplayStyle methods
Using this new style can result in a 10-times performance increase when generating shape overlay images; the generated images will also be significantly smaller (PNG 50%, SVG 60-times, PDF 9-times).
The following APIs have been added to identify ligand atoms and bonds, along with residues of an OE2DActiveSiteDisplay object that are close to a given 2D display coordinate: