OEToolkits 2018.Oct

Omega TK: Macrocycle

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.


Conformer ensemble subset for geldanamycin (PDB: 1YET) generated using the macrocycle method

FastROCS TK: C++ and Java Support

Previously, FastROCS TK was 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.

Quacpac TK: Tautomers

This release adds several improvements to the tautomer functionality in Quacpac TK. Tautomer handling in molecular modeling and cheminformatics usually includes three important functions:

  • Generating a canonical protomer representation for duplicate-free storage

  • Generating a single tautomer suitable for visualization by chemists and modelers

  • Generating an ensemble of aqueous-phase tautomers suitable for molecular modeling


Example of generating an ensemble of biologically relevant tautomers

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.

General Notices

  • The release cycle of OpenEye Toolkits has been changed. See the Release Cycle section for more information.

  • This is the last release to support GCC 4.4 on RHEL6. For future toolkit releases, GCC 4.8 will be the oldest targeted compiler.

  • This is the last release to support OS X 10.11. Full support for macOS 10.14 will be added in the next release.

  • This release adds support for Ubuntu 18 and will be the last release to support Ubuntu 14.

  • This release adds support for Python 3.7 on macOS and Linux. On Windows, Python 3.7 will be supported in the next release that will also drop support for Python 3.5.

  • FastROCS TK no longer supports Nvidia Tesla, GeForce, and Quadro cards with a compute capability of less than 3.0. This includes all GPUs with Fermi architecture (e.g., Tesla C2050 and GeForce GTX 430). Users running one of these older GPUs who cannot upgrade their hardware should not update to this version of FastROCS TK.

  • Spruce TK now requires a specific license. For information on Spruce TK licensing, please visit https://www.eyesopen.com/contact.

  • Improvements have been made to the Python 3 toolkits with regard to wrapping optimization. This results in Python 3 performance being comparable to Python 2.