OEDepict TK 2.0.2

New features

• Adding a scaling factor that can be used to increase or decrease the size of the fonts used to depict atom properties. (OE2DMolDisplayOptions.SetAtomPropLabelFontScale)

• Adding a scaling factor that can be used to increase or decrease the size of the fonts used to depict bond properties. (OE2DMolDisplayOptions.SetBondPropLabelFontScale)

• Adding the following examples:

  • Depict.java

  • Match2Img.java

  • MCSAlign2D.java

  • MDLQuery2Img.java

  • MDLReaction2Img.java

  • Mol2Img.java

  • Mols2Img.java

• The constructor of the OEImage class now takes a background color that is used to clear the image upon construction. A .png image with transparent background can be generated by using the OETransparentColor color as a background color when constructing an OEImage object.

• Fixing the run-time initialization of the color that is used to depict super atoms.

Major bug fixes

• The cairo graphics library (http://cairographics.org) used to draw .png images on Linux has a bug where it is not thread safe when rendering text. OEDepict TK now performs its own mutual exclusion when calling into the cairo graphics library for text rendering to ensure thread safety.

• Improving the depiction of super atoms (See examples in the OESuperAtomStyle namespace)

Minor bug fixes

• OERenderMolecule called with an image and a molecule now uses the width and height of the image being passed.

• Fixing a problem where isolated atoms were not highlighted when using the OEHighlightStyle.Color and OEHighlightStyle.Stick highlighting styles.

• OEDepictCoordinates throws a warning when trying to generate 2D coordinates for a two member ring, for example, C1N1. The function will then fall back to trying to generate coordinates for those atoms as a chain.

• The OEDisassembleExpressions function tags atoms and bonds of the query molecule that can later be used by the OE2DMolDisplay constructor when creating atom and bond displays.

• Throwing a warning when attempting to draw a line or an arc with the OEStipple.NoLine pen property. Throwing a warning when attempting to draw a rectangle, circle, triangle or a polygon with OEStipple.NoLine and OEFill.Off pen properties.

• Making sure that no radical dots are displayed for a query atom that has implicit hydrogen count information.

• Before registering an aromatic ring for the OEAromaticStyle.Circle style, a check is performed to ensure that the detected ring is not a fused ring of two smaller rings.

• Making the background color consistent for the monochrome atom color styles. (See: OEAtomColorStyle.WhiteMonochrome and OEAtomColorStyle.BlackMonochrome)

• When two molecules are aligned by calling the OEPrepareAlignedDepiction function, the fit molecule is scaled by the average bond length of the reference molecule.

Deprecated Ogham

• Deprecating the OEDepictFixedCoordinates function. For molecule alignment, please use the OEPrepareAlignedDepiction function.

Documentation changes

• Renaming the Application chapter to OEDepict Examples Summary and inserting the source code of the examples into the Examples chapter.

• Adding code snippets for the OEAddHighlighting function.

• Describing the layout of a depicted atom in the OE2DAtomDisplay class.

• All images in this manual are now automatically generated as part of the release process and tested against benchmark images on all supported platforms.