Shape TK 3.9.0

New Features

  • The SetupRef method in OEOverlay now accepts molecules containing only color atoms. Accordingly, any molecule containing only color atoms or an OEShapeQuery containing only color Gaussians can now be used as a reference for overlay optimization.

  • The SetupRef method in OEOverlapFunc now accepts molecules and OEShapeQuery containing just color components.

  • A new class, OEHermiteOverlay, and a corresponding options class, OEHermiteOverlayOptions, are introduced, enabling overlays using the Hermite expansion approach. Three types of reference and database molecule representations are supported: Hermite vector, molecule, and scalar grid. Consequently, grid/grid overlays are enabled by using these classes.

  • The grid-to-Gaussians fit algorithm, to add Gaussians in an OEShapeQuery using AddShapeGaussians and AddColorGaussians, has been improved for better representation of the grid by the generated Gaussians. With the introduction of the modified algorithm, some of the associated options in OEShapeQueryOptions are no longer relevant and have been removed from the class API. The following functions have been removed:

    • GetDuplicateDistance and SetDuplicateDistance

    • GetMaxNumGaussians and SetMaxNumGaussians

  • A new overload has been added for Transform that enables transformation of a scalar grid by the rigid transformation in OEBestOverlayScore.

  • A new overload has been added for Setup that enables setting up OEStarts with known fit symmetry.

  • The following new methods have been added to OEHermite to enhance usability:

Minor Bug Fixes

  • An issue related to Init was causing intermittent slowdown in some API calls, especially in CUDA-enabled builds. This has been fixed.