Grapheme TK 1.3.0

New features

• 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);
  

  instead of

  OEFragmentNetwork asite(protein, ligand);
  

  See also

  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

• OE2DActiveSiteDisplay::GetDisplayedLigand and OE2DActiveSiteDisplay::GetDisplayedResidues methods have been added.

• OEAddLigandHighlighting and OEAddResidueHighlighting functions have been added to allow highlighting in active site depiction. See the example below.

  

  Example of ligand highlighting

• OEShapeOverlapDisplayStyle::PropertyCloud style has been added to visualize shape overlays along with the following APIs:

  • OEShapeOverlapDisplayStyle namespace

  • OEShapeOverlapDisplayOptions::SetOverlapDisplayStyle and OEShapeOverlapDisplayOptions::SetOverlapDisplayStyle methods

  

  Example of visualizing shape overlaps with PropertyCloud style

  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:

  • OEGetNearestAtom and OEGetNearbyAtom functions

  • OEGetNearestBond and OEGetNearbyBond functions

  • OEGetNearestResidue and OEGetNearbyResidue functions along with the OENearestResidue class

Documentation changes

• All images in the Grapheme TK documentation were automatically regenerated to reflect the changes made since the previous release.

• The example in Depicting Active Site Interactions has been updated to use the new OEInteractionHintContainer class instead of the deprecated OEFragmentNetwork.