OEToolkits 2020.2

Release Highlights 2020.2

Omega TK: New fragment library

A new enhanced fragment library has been created for use in Omega TK. The new fragment library consists of more than 500,000 fragments that have been generated using the MMFF force field.

This new library is designed to reduce the run time of large-scale conformer generation, and therefore is not built in to Omega TK but is available as a separate download. To run Omega TK with the enhanced library, simply use the OEOmega method OEOmega.AddFragLib.

The fragments have been collated from commonly used electronic databases, such as Enamine Building Blocks. Consequently, dramatic runtime performance improvements can be seen for the Enamine Real dataset, among others, since less time is spent building fragments on the fly. Runtime performance improvements can be seen for all datasets; the Platinum and Enamine Real sets show particular improvement and run ~50% faster (benchmarks run on Ubuntu 16 with Intel(R) Xeon(R) Gold 6128 CPU 3.40GHz and NVIDIA Tesla V100 GPU).

../../_images/Omega_FragLib_Runtime_Perf.png

GPU-OMEGA runtime performance using the built-in fragment library compared to the new enhanced fragment library. Benchmark datasets are a filtered set of 2359 molecules of the Platinum dataset and 10,000 randomly chosen molecules of the Enamine Real, Mcule and WuXi databases.

The enhanced fragment library generates the same high-quality conformers as the built-in library, as shown by the minimum RMSDs of the filtered Platinum dataset.

../../_images/Omega_FragLib_Plat_Div_Perf.png

Box plots showing minimum RMSDs of a filtered set of 2359 molecules of the Platinum dataset with the built-in fragment library and the new enhanced fragment library.

Datasets can be downloaded from:

We are eager to get your feedback on the new enhanced fragment library. Please share your experience with us at support@eyesopen.com.

OEDocking TK: Improved receptors

Receptors used in OEDocking TK classes, including FRED, HYBRID, and POSIT, have been improved to take advantage of properly prepared structures from SPRUCE. A new OEReceptor object has been introduced and is created and contained within an OEDesignUnit. Since an OEReceptor is now an integral part of an OEDesignUnit, it is saved into an OEDU file along with a design unit. There is no separate I/O for the receptors.

../../_images/2IKO_receptor.png

OEDocking receptor, along with the target structure and the bound ligand, for the 2IKO Human Renin Complexed with Inhibitor.

Having the receptors as part of the design unit with properly prepped structures makes it easier for the docked and posed structures to be used in further downstream modeling, which is especially necessary when working with protein force fields like FF14SB. The new receptors with properly prepped protein also enabled use of modern force fields like FF14SB and Parsley for structure optimization in flexible OEPosit.

Szybki TK: A new protein force field

The AMBER FF14SB protein force field has been implemented in OEFF TK. This new force field has also been made available in SZYBKI for optimizing both protein and protein-ligand complexes.

FF14SB is the most widely used protein force field for molecular dynamics or any other force field-based calculations. It is also used in Orion molecular dynamics package, and is the community gold standard for such calculations.

Supported Platforms

Package Versions Linux Windows macOS
Python 3.6, 3.7, 3.8 RHEL7/8, Ubuntu18/20 Win10 10.13, 10.14, 10.15
C++   RHEL7/8, Ubuntu18/20 Win10 (VS2017, VS2019) 10.13, 10.14, 10.15
Java 1.8, 11 RHEL7/8, Ubuntu18/20 Win10 10.13, 10.14, 10.15
C#     Win10 (VS2015, VS2017, VS2019)  

General Notices

  • Support for Ubuntu20 has been added. Ubuntu16 is no longer supported.
  • C++ CUDA-enabled toolkits and features are now supported on RHEL8 and Ubuntu18.
  • This is the last release to support GCC 4.x and GCC 5.x. GCC 7.4 will be the minimum GCC supported in the next release.
  • This is the last release to support Python 3.6.
  • This is the last release to support VS2015.

Detailed Release Notes 2020.2

Version 3.1.0

OEChem TK 3.1.0

Fall 2020

New features

Minor bug fixes

  • An issue that occurred when a change in the aromaticity model perception would result in double bonds that should have lost their cis/trans parity assignments has been fixed. The bond stereo parities had been incorrectly being retained on aromatic atom endpoints.
  • An issue with parsing SMILES with ExtBond couplings that were not honoring the convention that a specified bond order takes precedence over an implicit one, similar to ring closures, has been fixed.
  • Extra processing has been added to ensure that a common header corruption for SDF format files throws a warning to indicate a format problem. In general, attempts to skip individual corrupted records in a multi-record file format are employed to ensure that as much of the valid input as possible can be processed. Depending on the type of corruption as well as the specific file format, there is no guarantee that a warning will be emitted for all corrupted records.
  • An issue that caused OECopyPDBData and OECopySDData to avoid the copy activity if the source and destination molecules are the same molecule instance, which can cause a crash, has been fixed. The status return will be false, just like a general failure for the copy activity.
  • An issue in OEPDBOrderAtoms that caused bad behavior when atoms in a molecule do not have any residue information has been fixed.

OEBio TK 3.1.0

Fall 2020

New features

Major bug fixes

Minor bug fixes

  • A bug in OEPlaceHydrogens that resulted in histidine residues being in an unoptimized state, depending on the input state, has been fixed.

OESystem TK 3.1.0

Fall 2020

New features

Minor bug fixes

  • Behavior of the field metadata on OERecord has been fixed to ensure that at most one field on a record can have the ID flag.
  • An issue that caused corruption when reusing an OERecord in a loop has been fixed.

OEPlatform TK 3.1.0

Fall 2020

New features

  • OEOnce has been deprecated. See the OEPlatform TK documentation for alternatives.

OEGrid TK 3.1.0

Fall 2020

Major bug fixes

  • A bug in the symmetry operators for the I121 space group has been fixed.

Minor bug fixes

  • An issue that caused the function OEReadGrid to incorrectly change the OEGridType of grids to the OEGridFileType, where it was being used to read an OEFizzGrid from a file, has been fixed. The OEGridType now remains the same through a round trip grid write and read.
  • An issue that caused the function OEReadMTZ to crash when it read large MTZ files and converted them to an OESkewGrid as well as computing the AMIN and AMAX statistics for the resulting OESkewGrid incorrectly has been fixed. The code has been corrected so that the crash no longer happens for large grids; the AMIN and AMAX calculations have also been corrected.
  • An issue that caused the script make_design_units.py to crash when reading PDB files using the function OEReadMolecule, when space group numbers that could not be recognized has been fixed. These space group numbers had been preventing the code from reading symmetry correctly from the PDB file. The code has been changed so that incorrect space group numbers result in a warning instead of a fatal crash.

OEMath TK 3.1.0

Fall 2020

New features

OEDepict TK 2.4.5

Fall 2020

New features

Minor bug fixes

OEDocking TK 4.0.0

Fall 2020

New features

Documentation changes

  • The OEHybrid class documentation has been modified to clarify that it is derived from OEDock.
  • Documentation for OEDocking::OEDockBase and OEDocking::OEScoreBase has been removed.
  • All the OEDocking TK examples have been reorganized to reflect the modified API behavior.

FastROCS TK 2.1.0

Fall 2020

New features

  • FastROCS TK now requires a minimum NVIDIA Driver version of 450.x. See NVIDIA Drivers for more details.
  • FastROCS TK now requires a minimum GPU compute capability of 3.5. See Supported GPUs for more details.
  • OEShapeQuery objects now have limited support for use as queries with the OEShapeDatabase.GetScores and OEShapeDatabase.GetSortedScores database searching methods.
  • Support has been dropped for database files that are gzipped (e.g. oeb.gz in the FastROCS TK examples). .oeb and .oez are still supported.
  • A new database type, OEShapeDatabaseType_Sitehopper, has been added that runs Sitehopper calculations using fastrocs. Note that a Sitehopper license is required to run a Sitehopper calculation. Please contact sales@eyesopen.com or your account manager for a license.

Major bug fixes

  • Previously, GPU memory limits were being reached for routine searches when using OEFastROCSOrientation_InertialAtHeavyAtoms with OEShapeDatabaseOptions.SetColorOptimization set to true, causing the color calculation to default to the CPU. The improved alternative starts algorithm handles any number of starts without reaching GPU memory limits.

    Warning

    Performance will be affected by using large numbers (> 10) of alternative starts.

  • Previously, the Shape Clustering example suffered some performance degradation. This has now been fixed thanks to a performance bug fix in OESelfShape. The script should now perform at its normal speed, ~10x that of the previous release.

Minor bug fixes

  • A warning is now thrown if users attempt to use a custom color forcefield that has either a non-Gaussian functional form or interactions between different color types.

Python specific changes

Java specific changes

C++ specific changes

Documentation changes

Grapheme TM TK 1.4.2

Fall 2020

New features

  • A new function, OEDrawResidues, has been added that visualizes residue information for peptides.

    hover mouse over any residue circles

    Example of using the OEDrawResidues function to generate an interactive SVG image

Minor bug fixes

  • A bug related to drawing interaction hints spanning multiple residues has been fixed.

GraphSim TK 2.5.1

Fall 2020

New features

Lexichem TK 2.7.2

Fall 2020

Minor bug fixes

  • An issue that caused the function OEParseIUPACName to incorrectly interpret elemental halogens as aromatic molecules due to their suffix “ine” has been fixed. Previously, the function failed to kekulize the halogens and therefore failed to parse them.
  • An issue that caused the function OEParseIUPACName to fail to parse non-IUPAC names of carboxamide derivatives, such as benzimidazole-5-carboxylic acid, due to a failure to kekulize the benzimidazole rings has been fixed. 1H hydrogen is now added by default to benzimidazole if a prefix is not included to specify hydrogen locations.
  • An issue that caused the function OEParseIUPACName to fail to parse names, such as carboxylic acid methyl amide, where methyl amide is used as a suffix has been fixed.

OEMedChem TK 1.1.3

Fall 2020

New features

Documentation changes

  • Examples of custom Bemis-Murcko fragmentation have been added to the fragmentation documentation in the Molecule Fragmentation chapter.
  • The BemisMurckoPerception example script has been modified to include examples of custom Bemis-Murcko fragmentation, using the flag -unsatHetero to include unsaturated bonds to hetero atoms on the framework and the flag -smartsSubstituents to include substituents specified by given SMARTS patterns.

MolProp TK 2.5.5

Fall 2020

  • Minor internal improvements have been made.

OEFF TK 2.3.0

Fall 2020

New features

Documentation changes

  • All the OEFF TK examples have been reorganized to reflect the modified API behavior.

Omega TK 4.1.0

Fall 2020

New features

  • GPU-Omega now requires a minimum NVIDIA Driver version of 450.x and a minimum GPU compute capability of 3.5. See NVIDIA Drivers and Supported GPUs for more details.
  • Conformer generation using dense mode now defaults to running on the CPU instead of the GPU. The other torsion-driving sampling modes (sparse, rocs, fastrocs, and pose) will still run on a GPU by default if one is available on a Linux platform. For details on how to run with dense mode sampling on a GPU, see the Usage section of the GPU-Omega docs.
  • A new class, OEFlipperOptions, has been added that defines parameters for specifying stereo centers and other options.
  • OEFlipper has been updated to take a molecule and an OEFlipperOptions. The old version of OEFlipper that takes five parameters has been deprecated.
  • A new function, OEFlipperStereoCenters, has been added added that returns a number of undefined stereo centers in a molecule as interpreted by OEFlipper.

Major bug fixes

  • A memory leak in GPU-Omega has been fixed.
  • An issue with generating conformers on the CPU using child processes with the same OEOmega object has been fixed.
  • GPU-Omega no longer throws an error when attempting to generate conformers with the same OEOmega object in child processes. Instead, it falls back to the CPU. To use GPU-Omega with child processes, each child must construct a new OEOmega object.

Minor bug fixes

  • OEOmega.ClearFragLibs now clears all fragment libraries. Previous releases did not clear the internal shared fragment library (a shared memory library of fragments accrued while generating conformers with the same OEOmega object).

Documentation changes

Quacpac TK 2.1.1

Fall 2020

New features

Shape TK 3.4.1

Fall 2020

New features

Major bug fixes

  • An issue that caused performance slowdown in OESelfShape has been fixed.
  • An issue that caused OEGridColorFunc to give incorrect results when used with a custom color force field containing a range value other than 1.0 has been fixed.

Minor bug fixes

  • The UserColor example has been updated to more robustly check return statuses. See Calculating Overlap.

Spicoli TK 1.5.1

Fall 2020

  • Minor internal improvements have been made.

Spruce TK 1.2.0

Fall 2020

New features

Major bug fixes

  • A bug that caused some modeled loops to be missing the backbone NH hydrogen where the modeled loops were attached has been fixed.
  • Fragment numbers for build loops have been fixed to be consistent with the anchor residues where the loops are inserted.
  • A bug in OEFixBackbone has been fixed to ensure that OXT atoms are always built on C-terminal residues.
  • An issue with atom order for built pieces like loops or caps has been fixed to ensure that these are sequential with the location they are built.
  • A bug in OEBuildLoops that in specific situations caused incorrect detection of gaps in protein structures has been fixed. Additionally, options have been exposed in OELoopBuilderOptions to allows users to control the underlying sequence alignment in the event of a failure.

Minor bug fixes

  • Improvements have been made to standard amino acid residue perception when preparing structures.
  • Site residues in OEMakeDesignUnits are now being checked against all the biological units so one can serve as a reference for the rest.
  • A bug in loop modeling that caused the function to create residues with identical residue numbers has been fixed. The function now properly builds using insertion codes.
  • A bug in loop modeling that caused problems for the underlying sequence alignment code and incorrect loops when a single residue was floating in space between two gaps has been fixed.
  • The chemical component dictionary used internally in OEMakeDesignUnits has been updated with the latest changes from the RCSB, including some fixes for incorrect entries in the source data based on rules and literature searches.

Szmap TK 1.6.1

Fall 2020

  • Minor internal improvements have been made.

Szybki TK 2.3.0

Fall 2020

New features

Minor bug fixes

  • Protein-ligand optimization with OpenFF/Parsley force fields using OESzybki no longer fails, even when the initial gradient norm is 1e^15 kcal/(mol A) or larger.

Zap TK 2.4.0

  • Minor internal improvements have been made.