OEDepict TK 2.0.4

New features

Major bug fixes

  • The following molecule depiction defaults have been changed:

    • The background color is now pure white instead of a very light grey.
    • The bond width is now 2.0 instead of 1.0.

    See the effect of these changes in Table: Example of default molecule depictions.

    Example of default molecule depictions
    OEDepict TK 2.0.3 OEDepict TK 2.0.4
    ../../_images/DepictMolSimple-toolkits2012_Jun.png ../../_images/DepictMolSimple-toolkits2012_Oct.png

Minor bug fixes

  • Adding the depiction of R-groups for molecules that have not been initialized from a MDL query file. See the example the in the Table: Example of depicting R-Groups.

    Example of depicting R-Groups
    OEDepict TK 2.0.3 OEDepict TK 2.0.4
    ../../_images/RGroupFromSmiles-toolkits2012_Jun.png ../../_images/RGroupFromSmiles-toolkits2012_Oct.png
  • Fixed a bug that would erroneously hide the following types of hydrogens in a depiction:

    • isolated hydrogens
    • charged hydrogens
    • hydrogen isotopes
  • Fused ring system templates added for 29 different types of complex depiction cases.

  • OE2DAtomDisplay::SetHCount method will now place the hydrogen position correctly as returned by OE2DAtomDisplay::GetHPosition, i.e., the position relative to the heavy atom. An incorrect position was possible when generating 2D coordinates with OEPrepareDepiction with the parameter suppressH set to false.

  • The stipple factor of a line in now based on the line width instead of the scaling factor of the molecule display.

    Example of line width affecting the stipple factor
    OEDepict TK 2.0.3 OEDepict TK 2.0.4
    ../../_images/MoleculeAromaticDash-toolkits2012_Jun.png ../../_images/MoleculeAromaticDash-toolkits2012_Oct.png
  • Atom stereo depiction improved:

    See the effect of these improvements in Table: Example of depicting atom stereo.

    Example of depicting atom stereo
    OEDepict TK 2.0.3 OEDepict TK 2.0.4
    ../../_images/StereoBond-toolkits2012_Jun.png ../../_images/StereoBond-toolkits2012_Oct.png
  • OEBondDisplayType::Any bond type will now properly set the stipple factor for the end pen of that bond.

  • Fixing the problem when the default atom label colors were not updated after atom color style change. For example when setting the atom color style to OEAtomColorStyle::WhiteMonochrome the super atoms remained pink rather than changed to black. See the effect of fix in Table: Example of using the ‘WhiteMonochrome’ atom color style.

    Example of using the ‘WhiteMonochrome’ atom color style
    OEDepict TK 2.0.3 OEDepict TK 2.0.4
    ../../_images/WhiteMonochrome-toolkits2012_Jun.png ../../_images/WhiteMonochrome-toolkits2012_Oct.png

Documentation changes

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