Shape TK 1.8.0

New features

• Added new functions that will cache the self shape score on a molecule. Analogous to the caching of self color, introduced in 1.7.2, this can speed up repeat shape calculations on the same molecule by not recalculating the self terms.

  • OESetCachedSelfShape

  • OEHasCachedSelfShape

  • OEGetCachedSelfShape

  • OEClearCachedSelfShape

• Updated the functions that cache self color to store work with multi-conformer molecules, storing a self color for each conformer.

• Added two new color force fields, ImplicitMillsDeanNoRings and ExplicitMillsDeanNoRings. These are identical to the existing similarly named force fields, but with no “rings” atom types or interactions.

• Added Has and Delete functions to the API for dealing with compressed color atoms.

• Several of the examples have been updated to count the output better and to use a better sort functor when color is included.

• Add new methods to OEBestOverlayScore to allow access to the transform.

  • OEBestOverlayScore.GetRotMatrix

  • OEBestOverlayScore.GetTranslation

Bug fixes

• Added OEGetColorAtoms and OEGetColorParents to Python, Java and C#.

• Fixed a bug where non-deterministic results could sometime occur when using OEBestOverlay and a highly symmetric molecule.

• Fixed calculation of multipoles. Previous versions used a non-irreducible representation of multipoles that is nonstandard. This method now calculates standard multipoles and allow better comparison between the values of two molecules.

• Fixed a missing type in ImplicitMillsDean to match an aldehyde acceptor with or without the explicit proton.

• Fixed a bug where OECalcVolume could crash using a molecule with deleted atoms.