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(protein, ligand);
OEFragmentNetwork asite(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: