OEDepict TK 2.2.5

New features

Major bug fixes

  • OEPrepareDepiction now automatically regenerates 2D coordinates when the current 2D coordinates are not in the XY plane. OEPrepareDepiction now clears coordinates when any of the following conditions are true:

    This protects against corrupted coordinate states that may be caused by file formats not normally used for depiction, such as PDB.

  • PNG images generated on Linux will now have properly filled objects and will no longer look different than those generated on OSX or Windows, as shown in the following images:

    Example of drawing filled objects with Cairo
    OEDepict TK 2.2.4 OEDepict TK 2.2.5
    ../../_images/DrawObjectsForReleaseNote-toolkits2014_Oct.png ../../_images/DrawObjectsForReleaseNote-toolkits2015_Feb.png
  • The cubic and quadratic curves drawn on OSX PNG images are no longer closed and are now consistent with PNG images generated on other platforms.

    Example of drawing cubic and quadratic curves on OSX
    OEDepict TK 2.2.4 OEDepict TK 2.2.5
    ../../_images/DrawCubicBezier-osx-toolkits2014_Oct.png ../../_images/DrawCubicBezier-osx-toolkits2015_Feb.png
    ../../_images/DrawQuadraticBezier-osx-toolkits2014_Oct.png ../../_images/DrawQuadraticBezier-osx-toolkits2015_Feb.png
  • PDF files should no longer cause the following warning message when read into Adobe Acrobat:

    The font "Times" contains a bad/BBox.
    

Minor bug fixes

  • A new OE2DMolDisplay::IsValid method has been added. A molecule display is considered valid only if it was initialized with a non-empty molecule with either 2D or 3D coordinates. An invalid molecule display cannot be rendered by the OERenderMolecule or the OERenderMoleculeToString functions.
  • The OEHydrogenStyle::Hidden style will no longer show any hydrogen labels, even if the hydrogen has a charge, isotopic mass, or is a radical.
  • The OEAnnotateDepictionProblems function now displays E/Z CIP bond labels rather than C/T in cases where double bonds are not correctly depicted according to their cis/trans stereo specifications.

Documentation changes

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

  • The documentation of all deprecated Ogham classes, functions, and namespaces has been removed:

    Deprecated Ogham classes:

    • OE8BitImage
    • OEAtomStyle
    • OEBondStyle
    • OEDepictBase
    • OEDepictColor
    • OEDepictView
    • OEPSImage
    • OEPoly
    • OEPolyF
    • OESVGImage
    • OEVert
    • OEVertF

    Deprecated Ogham functions:

    • OEWriteBMP
    • OEWriteEPS
    • OEWriteGIF
    • OEWritePPM
    • OEWriteRGB
    • OEWriteXPM

    Deprecated Ogham namespace:

    • OENamedColor
  • Minor changes have been made to the documentation and examples for consistency and/or spelling errors.

  • More C# examples have been added.

C++-specific changes

Python-specific changes

  • OEDepict TK no longer provides Python wrapping for the following methods of the deprecated OEDepictView class:
    • GetViewCoords
    • GetForeColor and SetForeColor
    • GetBackColor and SetBackColor