Toolkit Version 2021.2

• Release Highlights 2021.2
  • SiteHopper: New Toolkit for Protein Binding Site Comparison
  • SZYBKI: OpenFF-Sage force field support
  • OEChem: MMCIF and CIF writers

Detailed Release Notes 2021.2

OEChem TK 3.2.0

Fall 2021

New features

• A new options class, OEUniMolecularRxnOptions, has been added to provide control arguments to the unimolecular reaction APIs OEUniMolecularRxn and OEGetUniMolecularRxnIter. The new options class adds support for enabling valence correction, as well as retrieval of altered atom information from the transform for post-processing of the transformed products.

• Small molecule crystal structures are now writeable as CIF files, see OEWriteCIFFile for details.

• Small molecule crystal structures are now writeable as CIF files, see OEWriteCIFFile for details.

• Macromolecule files are now writeable as MMCIF files, see OEWriteCIFFile for details.

• CIF and MMCIF files are now readable using oemolithread. This enables their use as OEMolDatabase as well.

• The gemmi library used to read and parse MMCIF files has been updated to version 0.4.8.

• New overloads of constructors for the OESimpleAppOptions and OERefInputAppOptions have been added to extend their abilities to be used when no sub-options are involved for an application or when custom file extensions are required.

• New overloads of constructors for the OEFileStringParameter and OEOutFileStringParameter have been added that accepts file extensions as arguments instead of predefined constants.

Major bug fixes

• An issue causing missing amide (peptide) bonds when reading protein structures from MMCIF files has been fixed.

• An issue related to incorrect hydrogen atom stripping from stereocenters that are asymmetric by virtue of hydrogen isotope substitutions has been fixed. Isomeric SMILES for structures containing hydrogen isotopes on stereogenic centers will now have the atom/bond parity information correctly preserved. A minor consequence of the fix is that a small number of isomeric SMILES with explicit (non-isotopic) hydrogens may have SMILES differences due to conversion to a fully hydrogen-suppressed SMILES form.

Minor bug fixes

• An issue that could cause a crash during reads of OEFormat_OEB format files has been fixed. The read and write of OEGroupBase information in OEB files is now more rigorously checked for invalid objects. Existing corrupted OEB files will return an error status when read.

• An issue that could cause overflow in the MDL molecule reader has been fixed.

• An issue that caused return of an incorrect default value for OEPredicateParameter when it was set to a non-default value has been fixed.

OEBio TK 3.2.0

New features

• The logic identifying aromatic nitrogen atoms has been updated in OEPlaceHydrogens, enabling improved hydrogen network optimization as well as the ability to properly distinguish and pick appropritate ligand tautomers in the protein binding site.

Minor bug fixes

• An issue causing the ligand density coverage (LaD) to change as a result of hydrogen placement in limited circumstances has been fixed.

• An issue causing the operator bool on OEAtomMatchResidue to return true even if no valid data was provided to the constructor has been fixed.

• An issue causing an OEDesignUnit attached as generic data on molecules to be lost during I/O has been fixed.

• An issue causing proper backbone verification to fail for capping groups has been fixed.

• An issue causing proper backbone verification to fail for non-standard amino acids has been fixed.

• An issue causing histidine residues to be in the charged state (HIS+ or HIP) when it clearly was not favorable has been fixed.

• The AspDyad mover rule in OEPlaceHydrogens has been refined.

• The class OEPlaceHydrogensOptions has been modified to derive from OEOptions.

OESystem TK 3.2.0

New features

• OEParameter classes that accept strings as input values now work with case-insensitive string inputs.

• A new overload of OEMultiParameter.SetValue has been added that accepts oeifstream as input.

Minor bug fixes

• An issue that could cause OEStringToNumber to crash has been fixed.

OEPlatform TK 3.2.0

• Minor internal improvements have been made.

OEGrid TK 3.2.0

• Minor internal improvements have been made.

OEMath TK 3.2.0

New features

• A new premilinary API class, OEKernelPLS, has been added that builds QSAR models from kernelized descriptors using partial least squares (PLS).

OEDepict TK 2.4.7

Fall 2021

• Minor internal improvements have been made.

OEDocking TK 4.1.1

Fall 2021

New features

• OEPosit can now generate poses using all the provided receptors. This can be controled via a new method SetBestReceptorPoseOnly. The default behavior remains posing with the best receptor only.

• A new premilinary API class, OEROCSQueryModelBuilder, has been added that builds an OEShapeQuery from structure-based data, and can be used as a query to perform an OEShapeOverlay or ROCS calculation.

• A new premilinary API class, OEROCSQueryModelOptions, has been added that provides choices for OEROCSQueryModelBuilder calculations.

Minor bug fixes

• An issue with redundat SD data after docking a multi conformer molecule using the OEDock.DockMultiConformerMolecule method has been fixed.

Documentation changes

• Two new examples have been added to the section, Using Multiple Receptors that handle multiple input receptors and generate single or multiple poses for each ligand.

• Example PoseMolsMultiReceptor has removed.

FastROCS TK 2.2.1

Fall 2021

• Minor internal improvements have been made.

Grapheme TK 1.4.4

Fall 2021

• Minor internal improvements have been made.

GraphSim TK 2.5.3

Fall 2021

• Minor internal improvements have been made.

Lexichem TK 2.7.4

Fall 2021

New features

• Support for common alkaloid name conversion to SMILES was added.

Major bug fixes

• A bug where isotopes were not labeled on certain ring substituents when naming molecules or SMILES has been fixed.

Minor bug fixes

• A bug where pyrazole ring substituents were not numbered correctly has been fixed.

• A bug where reaction input was incorrectly parsed into a single molecule has been fixed so that reaction input is now rejected as invalid in the name to molecule workflow.

• A bug where primary amines with non-IUPAC names, such as methylethylamine, were incorrectly parsed into SMILES has been fixed.

OEMedChem TK 1.1.5

Fall 2021

• Minor internal improvements have been made.

MolProp TK 2.5.7

Fall 2021

New Features

• A function, OEFilter.GetMessage, was added to the OEFilter class to be able to retrieve information on whether the filter passed a molecule, or why it failed a specific molecule.

• A function, OEFilter.SetErrorLevel, was added to the OEFilter class to add explicit control of warnings output by the filter class and the filter application.

• A combined OEFilterType_BlockBusterPAINS filter was added, which combines filtering criteria for the OEFilterType_BlockBuster and OEFilter_PAINS filters.

• Excess warning output that was causing large log files is now suppressed by default, and can be switched on using the new OEFilter.SetErrorLevel method. See OEFilterType.

OEFF TK 2.4.0

Fall 2021

New features

• The following new classes have been added to provide support for the OpenFF 2.0.0 Sage force field:

  • OESageParams

  • OEFF14SBSageParams

  • OESage

  • OEFF14SBSage

  • OEFF14SBSageComplex

• OEForceFieldParameter and OEComplexFFParameter now accept case-insensitive string input values.

Minor bug fixes

• A potential risk of vectors going out-of-bounds while working with OESmirnoff and related classes have been addressed.

Omega TK 4.1.2

Fall 2021

Minor bug fixes

• An issue with overwriting partial charges of atoms in input molecules has been fixed.

• The Generating Stereoisomers example has been modified to use OEFlipperOptions.

• An issue running OEOmega when both OETorDriveOptions.SetUseGPU and OEMolBuilderOptions.SetSampleHydrogens are set to True has been fixed by disabling OETorDriveOptions.SetUseGPU in these cases.

Quacpac TK 2.1.3

Fall 2021

New features

• OEChargeParameter now accepts case-insensitive string input values.

Shape TK 3.4.3

Fall 2021

New features

• A new method, OEMol2Query, has been added that creates an OEShapeQuery from an input OEMolBase.

• A new premilinary API class, OEColorFFParameter, has been added as part of the extended set of OEParameter classes. The new parameter class works with predefined color force fields using an OEColorForceField object.

Minor bug fixes

• OESetColorParents now errors out properly if the color atom and the parent atoms specified do not have the same parent molecule.

SiteHopper TK 2.0.0

Fall 2021

This is the initial release of the SiteHopper TK.

Spicoli TK 1.5.2

July 2021

Minor internal improvements have been made.

Spruce TK 1.4.0

Fall 2021

New features

• A new method, OECapBuilderOptions.SetForceCapping, has been added to enable capping even if it will result in a clash.

• Two new methods, OELoopBuilderOptions.SetBuildTails and OELoopBuilderOptions.GetBuildTails, have been added to set and get an option that controls whether to build tails when there is missing residues at the N- and C- termini.

• OESuperPoseOptions_SiteHopper is now a supported superposition method in OESuperpose, and can be set using SetMEthod.

• All Options classes have been modified to derive from OEOptions. This affects classes:

  • OEDesignUnitEnumerateSitesOptions

  • OEProtonateDesignUnitOptions

  • OEDesignUnitBuildOptions

  • OEDesignUnitPrepOptions

  • OEDesignUnitSplitOptions

  • OEBioUnitExtractionOptions

  • OEMakeDesignUnitOptions

  • OEPlaceHydrogensOptions

Major bug fixes

• An issue causing capping a non-standard residue to fail has been fixed.

• An issue causing covalent ligands to have their covalent bond broken when there were alternate locations in the structure, has been fixed.

• An issue causing side-chains to either not be built or being built in non-optimal configurations has been fixed.

• An issue with pockets identifying liganded sites in OEMakeDesignUnitFromPocket not generating a proper design unit with a ligand bound in the identified site has been fixed.

Minor bug fixes

• An issue causing the warning message ‘Truncated cap due to clash’ to appear when OECapBuilderOptions.SetAllowTruncate is False has been fixed.

• An issue caused by Heuristic score offset beeing added before comparing to original structure therefore unable to pick the more energy favorable conformation has been fixed.

• An issue causing the gap finding code to mis-identify gaps in the protein structure due to residues with missing backbone atoms has been fixed. The function now removes these residues prior to gap detection inside OEBuildLoops.

• An issue caused by malformed PDB Header data, specifically with regards to REMARK 300 sections, has been fixed.

Szmap TK 1.6.3

Fall 2021

• Minor internal improvements have been made.

Szybki TK 2.4.0

Fall 2021

New features

• A new function, OEGetFreeFormError, is provided that returns error messages corresponding to return codes defined in OEFreeFormReturnCode namespace.

• The latest version of the Open Force Field Initiative, Sage 2.0.0, has been added to OEForceFieldType as built-in force field OEForceFieldType_SAGE_OPENFF200.

• Freeform for estimating free energy of conformations in the ensemble, OEFreeFormConf, now defaults to using the most recent version of the Open Force Field (OESage). Previously it was using MMFF94S by default.

• Protein-ligand optimization classes OEFixedProteinLigandOptimizer and OEFlexProteinLigandOptimizer now defaults to using the OEFF14SBSageComplex force field.

Minor bug fixes

• OETorsionScanOptions.SetForceField now properly defaults to OEForceFieldType_MMFF94S.

Zap TK 2.4.2

Fall 2021

• Minor internal improvements have been made.

Recent Release History

• Release Highlights 2021.1
  • OEDocking TK: Receptors in Design Unit
  • OESiteHopper: Application Suite for Rapid Protein Binding Site Comparison
  • VIDA 5: Major Update and OEDesignUnit Support
  • Supported Platforms
  • Related TK Versions
  • General Notices
• Release Highlights 2020.2
  • OEToolkits 2020.2.2
  • Omega TK: New fragment library
  • OEDocking TK: Improved receptors
  • Szybki TK: A new protein force field
  • Supported Platforms
  • Related TK Versions
  • General Notices
• Release Highlights 2020.1
  • OEToolkits 2020.1.1
  • OEToolkits 2020.1
  • OEToolkits 2020.0
  • General Notices

Previous Release History

• OEToolkits 2019.Oct
• OEToolkits 2019.Apr
• OEToolkits 2018.Oct
• OEToolkits 2018.Feb
• OEToolkits 2017.Oct
• OEToolkits 2017.Jun
• OEToolkits 2017.Feb
• OEToolkits 2016.Oct
• OEToolkits 2016.Jun
• OEToolkits 2016.Feb
• OEToolkits 2015.Oct
• OEToolkits 2015.Jun
• OEToolkits 2015.Feb
• OEToolkits 2014.Oct
• OEToolkits 2014.Jun
• OEToolkits 2014.Feb
• OEToolkits 2013.Oct
• OEToolkits 2013.Jun
• OEToolkits 2013.Feb
• OEToolkits 2012.Oct
• OEToolkits 2012.Jun
• OEToolkits 2012.Feb
• OEToolkits 2011.Oct
• OEToolkits 2011.1
• OEToolkits 1.7.4
• OEToolkits 1.7.2
• OEToolkits 1.7.1
• OEToolkits 1.7.0