OpenEye is pleased to announce the release of OpenEye Toolkits v2019.Apr. These libraries include the usual support for C++, Python, C#, and Java.
- FastROCS TK now calculates color on GPU, resulting in a 2x performance improvement.
- OEChem TK now includes a compressed binary format with the OEZ extension.
- OEGrapheme TK can now depict interactive Ramachandran plots.
FastROCS TK: color calculation on GPU
Changes to the FastROCS algorithm, including porting the static color calculation to GPU, have resulted in a more than 2x performance improvement of FastROCS on some GPU systems. Benchmarking was carried out on AWS GPU instances and compared to the 2018.Oct version of FastROCS TK:
Performance comparison between the 2018.Oct release and the 2019.Apr release using OpenEye’s standard benchmark dataset of 14M conformers on AWS
For some systems, the standard benchmark dataset of 14M conformers is not large enough to fully saturate the GPUs. To demonstrate the potential performance of larger databases, a 2 billion conformer subset of Enamine was searched on suitable AWS instances. FastROCS searched the 2 billion conformer database on an AWS P3 instance with 8x Nvidia Tesla V100 GPUs at a rate of over 44 million overlays per second:
Performance of a 2 billion conformer subset of Enamine on suitable AWS instances
OEChem TK: OEZ compressed file format
A new compressed file format with the extension OEZ has been added to OEChem TK. This format uses the Zstandard algorithm to efficiently compress individual multi-conformer molecules, making it well-suited to work with OEMolDatabase for fast read-only random access to molecules. See more details in the Compressed Input and Output section of the OEChem TK documentation.
Note: This new file format is not backwards compatible. OpenEye applications and toolkits released before April 2019 will not be able to read or write this file format.
OEGrapheme TK: Ramachandran plot
Following our tradition of providing easily comprehensible visualization of complex data, OEGrapheme TK can now depict Ramachandran plots. These plots provide an easy way to examine the distribution of backbone dihedral angles in a particular protein. For instance, structure quality can be assessed by identifying residues whose backbone ϕ and ψ angles are outside energetically accessible regions. Grapheme TK uses the data and classifications available in OEBio TK, which were extracted from the open-source Computational Crystallography Toolbox.
Examples of visualizing the Ramachandran plots of various residue types in Grapheme TK (PDB: 2ROX)
- OpenEye currently uses OpenJDK8 to build its Java packages.
- The following prerequisites have been introduced so that OpenEye can implement algorithms in a more modern and efficient C++11 style:
- GCC 4.8 is now the oldest targeted compiler for toolkits. RHEL6 with the default GCC 4.4 compiler is no longer supported.
- The minimum recommended GNU binutils version is 2.26 for the C++ single build Linux packages.
- The minimum CMake version required to build the C++ examples is now 3.1.3 on all platforms.
- This release adds support for Visual Studio 2017 for C++ and C#. This is the last release to support Visual Studio 2013, as well as 32-bit Windows for C++ and C#.
- This release adds full support for Python 3.7. Python 3.5 for Windows is no longer supported.
- This release skips Java support for macOS. For Java support on RHEL6, please contact firstname.lastname@example.org.
- This release adds support for macOS 10.14. macOS 10.11 is no longer supported.
- This release adds support for Ubuntu 18. Ubuntu 14 is no longer supported.
See the Release Notes for full and specific details on improvements and fixes.
About OpenEye Scientific
OpenEye Scientific is a privately held company headquartered in Santa Fe, New Mexico, with offices in Boston, Cologne, and Tokyo. It was founded in 1997 to develop large-scale molecular modeling applications and toolkits. Primarily aimed towards drug discovery and design, areas of application include:
- Structure Generation
- Shape Comparison
- Fragment Replacement
The software is designed for scientific rigor as well as speed, scalability, and platform independence. OpenEye makes most of its technology available as toolkits—programming libraries suitable for custom development. OpenEye software typically is distributable across multiple processors and runs on Linux, Windows, and macOS.
For additional information