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

  asite = OEInteractionHintContainer(protein, ligand)
  

  instead of

  asite = OEFragmentNetwork(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.