ROCS 3.10.0

Minor internal improvements have been made.

Related Toolkit Information

When using the Overlay method in OEOverlay for overlay optimization, any of the inertial start methods now automatically trigger an additional as-is start if the optimization results in similarity measures less than the original similarity. This improves the default behavior of Overlay for some calculations.
The following modifications have been made to OEOverlapPrepOptions to provide more flexibility in assigning color atoms during the Prep process in OEOverlapPrep:
- Two new methods, SetRemoveColor and GetRemoveColor, have been added to enable removal or reassignment of color atoms.
- The new methods AddDuplicateSmarts, GetDuplicateSmarts, and ClearDuplicateSmarts have been added to enable duplicate color atom removal based on provided SMARTS patterns.
- Duplicate color atom removal is now more robust in keeping the central atoms instead of the first atom that it encounters and in placing the remaining atoms appropriately (at the center of corresponding clusters).
- Defaults for SetRemoveDuplicate and SetDuplicateDistance have been changed from False and 0.001 to True and 0.0, respectively. This improves robustness but keeps the default behavior unchanged.
A new method, SetupFrame, has been added to OEStarts that simplifies setting up a reference frame for calculating the starts.

The overlay optimization in OEHermiteOverlay with the OEAsIsStarts start option has been updated to use Hermite expansions around the center of mass to prevent inconsistent overlaps when objects are far from the origin.
Overlay optimization with the Overlay method in OEOverlay now captures the fit conformer self-overlap and color scores more accurately during the optimization.