Grapheme TK 1.2.2

New features

• OEDrawROCSScores function has been added to visualize scores.

  

• OEAlignedDepictionFrom3DOptions has been added to allow more customization of the OEPrepareAlignedDepictionFrom3D function.

• OEShapeQueryDisplayOptions::GetDepictOrientation and OEShapeQueryDisplayOptions::SetDepictOrientation methods have been added to allow the shape query to orient horizontal, vertical, or square.

• OEShapeQueryDisplay::GetTitle and OEShapeOverlapDisplay::GetTitle methods were added to access the title of the objects.

• OEShapeQueryDisplay::IsValid and OEShapeOverlapDisplay::IsValid methods were added to determine whether the objects have been initialized correctly.

• OERenderShapeOverlap function has been overloaded to enable rendering of shape overlap into two images: one image containing the fit molecule with transparent background and the other image showing the property map of the shape overlap. By superimposing the two images (molecule image on top), the result would be similar to visualizing the shape overlay in one image.

• OE2DActiveSiteDisplay class was rewritten to use the new implementation of the OEBio::OEFragmentNetwork class.

Major bug fixes

• OEPrepareDepictionFrom3D function has been improved to use a better scoring function in cases of atom clashes.

Minor bug fixes

• The default parameter for the maximum number of bond rotations of the OEDepictionFrom3DOptions class is now \(2^{16} = 65536\). This means that by default only the first 16 single bonds of molecule will be rotated to find the “closest” 2D layout from the original 3D conformation when invoking the OEPrepareDepictionFrom3D function.

• OEShapeOverlapDisplay now limits the maximum number of bond rotations to \(2^{14} = 16384\) when calling the OEPrepareAlignedDepictionFrom3D function to generate 2D coordinates aligned to the query molecule. This limit provides a reasonable trade-off between speed and the quality of the alignments.

• OEPrepareDepictionFrom3D and OEPrepareAlignedDepictionFrom3D have been optimized to be 10% faster on average. The algorithms were also revised to reduce the accumulation of floating point errors.

• Constructing OEShapeQueryDisplay and OEShapeOverlapDisplay objects is now significantly faster due to code optimization and constraining the 2D layout generations.

• OERenderActiveSite function was fixed to depict the OEResidueIndex::I residue with the DNA/RNA style.

• OEShapeOverlapDisplay and OEShapeOverlapDisplay now can handle queries without any color atoms.

• OERenderShapeQuery and OERenderColorOverlap now scale the line width of the pens used to render the circles representing color atom matches.

• OEPrepareDepictionFrom3D can now handle molecules containing atoms with an unknown atomic number (PDB examples: 1S9R, 3KXA, 1I1W).

• OEGetMoleculeSurfaceScale has been improved to capitalize on the molecule layout enhancements done in OEDepict TK in this release.

• OERenderColorOverlap was fixed to render the molecule surface of the query molecule as OERenderShapeOverlap does.

Documentation changes

• The Depicting Shape and Color Atom Overlaps example has been updated to visualize shape and color atom scores.

• The Depicting Active Site Interactions and Depicting BFactor examples have been updated to perceive residues in cases when it is not done by the molecule reader (for example, in the case of mol2).

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