A new distance geometry-based, conformational space-sampling method has been added to Omega TK as a preliminary API. This approach opens up a new avenue for exploring conformer ensembles in Omega TK. Although the distance geometry-based sampling is slower than the traditional torsion driving-based approach, it works substantially better for ensemble generation of macrocyclic molecules. This sampling method can also be applied to linear and small ring-containing molecules.
FastROCS TK previously had been available only in Python. This release extends support to C++ and Java. All classes, functions, and constants are wrapped and available for use. Several example scripts now have C++ and Java versions to showcase FastROCS TK functionalities. Additionally, users running FastROCS TK on Tesla GPUs will see a 10-30% speed-up over the previous version depending on the system.
This release adds several improvements to the tautomer functionality in Quacpac TK. Tautomer handling in molecular modeling and cheminformatics usually includes three important functions:
This release provides new API to cover each of these use-cases. The algorithm has also been improved to handle memory usage when a large number of possible tautomeric forms are present.
The following APIs have been added to generate consistent legend layouts:
The following APIs have been added to depict common protective groups:
|default depiction||using OEProtectiveGroupStyle.Fmoc style|
The following APIs have been added to mark up the bonds in SVG images generated by the OERenderMolecule functions:
A new OEDrawHighlighting function has been added to enable rendering molecule highlights into a separate image rather than into the molecule display.
New OEAddWatermark functions has been added that render a light gray watermark onto an image or a molecule display.
A new OEImageBase.GetSVGGroups method has been added to return the SVG groups associated with the image.
A new OEAddSVGHover function has been added that takes two target SVG groups to create a “hover” effect.
Java and C++ FastROCS TK API points are currently intended to be used only for toolkit functionality and not client-server functionality. The Python API should be used if client-server utilities are needed.
A new OEShapeDatabasePrep function has been added to provide the same functionality as the shapedatabaseprep example, except as a multi-threaded function. This should improve performance when prepping databases on systems with multiple cores. This function is non-deterministic, so molecules will not appear in the same order as the input file.
Two new methods, OEColorGradientDisplayOptions.GetColorStopVisibility and OEColorGradientDisplayOptions.SetColorStopVisibility, have been added to customize color gradient depiction.
A new OERenderActiveSiteMaps function has been added that generates an interactive image of protein-ligand maps.
The following new preliminary APIs have been added for macrocycle functionality in the Omega TK:
The following new preliminary APIs have been added to enhance small molecule conformer generation functionality in the Omega TK:
New additions and modifications have been made to existing APIs to enhance small molecule conformer generation functionality in Omega TK:
The following C++ and Python examples have been added to demonstrate using the new preliminary APIs:
Spruce TK now requires a specific license. For information on Spruce TK licensing, please contact firstname.lastname@example.org.