Minor internal improvements have been made.
Shape TK 3.5.1¶
The following new methods have been added to OEOverlayOptions to improve flexibility in defining parameters:
A new overload for the method CreateGrid has been added that takes a transform object as an additional argument that is applied after the grid is generated.
Major bug fixes¶
Default forcefields in OEFlexiOverlapOptions now ignore electrostatic interactions, as electrostatics appear to have negligible effects on optimized overlaid structures. Ignoring the electrostatic interactions also improves efficiency of optimization for the corresponding OEFlexiOverlapFunc.
The default for OEOverlapFunc in OEFlexiOverlayOptions now consists of
Shapeonly and no
Color. The default
Shape scoreused is Overlap.
Minor bug fixes¶
A mismatch between the Hermite grid and the input molecule has been fixed.
The maximum value on the Hermite resolution parameter has been increased from 30 to 100.
The following C++ and Python examples have been added to demonstrate how to use new preliminary APIs:
Two new C++ and Python examples have been added to the Flexible Overlay with Shape, Color, and Forcefield section that show flexible overlay optimization of the fit molecules against a single reference molecule conformer.
When using BestOverlay, only one conformer that has the highest Tanimoto-combo similarity to the reference molecule is returned.