Toolkit Version 2023.2

Detailed Release Notes 2023.2

OEChem TK 4.0.0

New features

  • A new preliminary API that supports generation of atom–atom mapping information for an input reaction has been provided in C++ and Python. See details at OERxnAutomapperOptions, OERxnAutomapper, and OERxnAutomapStatus.

  • A new nondefault input flavor has been added to support the conversion of implicit enhanced stereogroups from a V2000 SD format input file into explicit stereogroups. This allows subsequent export of explicit enhanced stereogroups in formats that support that information, like SDF and CXSMILES. See details at SDF_ForceImp2ExpENHSTE.

  • The explicit chiral-off designation (r) in the CXSMILES appendix is now tolerated when parsing the CXSMILES appendix. This explicit designation is appearing more frequently in vendor structure sets.

  • New overloads of OESimpleAppOptions and OERefInputAppOptions have been added to support applications that do not produce an output file.

  • The MMCIF reader now runs on Gemmi version 0.6.2. It is able to parse and write more sections in MMCIF files.

  • The default OEIFlavor for PDB has been changed to include PDB_DATA by default.

  • The default OEIFlavor for MMCIF has been changed to not include MMCIF_ALTLOC by default, to match the PDB default behavior.

  • Two new OEIFlavor defaults have been added, PDB_SpruceDefault and MMCIF_SpruceDefault, that add ALTLOC in addition to the default flavors for those file formats. These are being used in both the SPRUCE and MakeReceptor applications.

  • OEHasAtomName has been extended to take a new optional argument called trimspaces (default=false) to more flexibly match atom names.

  • OEHasChainID has been changed to internally operate on strings instead of characters to support multicharacter chain IDs. The character-based constructor is still available.

Minor bug fixes

  • The SD data format specifies that blank lines are the delimiters between different SD data fields. If an SD file contains blanks within one or more SD data fields, the reader would previously complain about the format error. The reader has been augmented to be more tolerant of this case, but in the process it must strip blank lines from the input SD data to ensure that the SD output does not generate a noncompliant output file. If blank lines are detected in the SD data for a molecule being exported in SD format, a new write status is returned to indicate the blank lines were removed in order to generate a compliant SD output file, and the generated output file will have the noncompliant blank line(s) removed. See details at OEWriteMolReturnCode_InvalidSDData.

  • A minor issue that caused OEGetTorsion to crash if one or more of the atom arguments were null has been fixed.

  • A minor issue that generated an invalid read error from V3000 SD files with nonconsecutively ordered object indices has been fixed. Generally, object indices in V3000 format files can be arbitrarily ordered.

  • A defect that could result in a crash during MCS searching for targets containing single atom fragments has been fixed.

  • An issue that caused OEMolParameter to not be properly transmitted in MPI mode has been fixed.

  • An issue with the assignment operator for OEIsBridgeHead being incorrectly defined has been fixed.

  • New overloads of OESameResidue and OESameChain that take atoms instead of residues have been added. This will prevent the need to get copies of OEResidue objects in wrapped languages, instead of using const references internally.

OEBio TK 4.0.0

New features

  • Two new methods in OEReceptor, GetOuterContourVolume and GetInnerContourVolume, have been added as convenience functions to get the volume of the receptor grid at the set contour level.

  • The function OEUpdateDesignUnit will not fail and return false if passed an empty molecule to update with.

  • The function OEUpdateDesignUnit has been updated to take an optional listIndex parameter if an item in a list molecule needs to be updated (e.g., one of several cofactors).

  • The OEDesignUnit class has been extended with a method ClearComponent to remove or clear a component from a design unit; this method can also take an optional listIndex to remove a specific molecule in a list component (e.g., one of several cofactors).

OESystem TK 4.0.0

New features

  • A new overload of the OEGetColors function has been added that generates a custom color iterator for use in depictions by passing a vector of desired colors.

OEPlatform TK 4.0.0

Minor internal improvements have been made.

OEGrid TK 4.0.0

Minor internal improvements have been made.

OEDepict TK 2.5.3

Minor internal improvements have been made.

OEDocking TK 4.3.0

New features

Major bug fixes

  • An issue has been fixed where relaxation failed in OEPosit when the pose relaxation mode was set to either ALL or CLASHED.

  • An issue causing generation of bent ring structures and high strain poses when performing OEPosit has been fixed.

  • An issue has been fixed that caused flexible OEPosit with ALL relaxation mode to fail while generating nonclashing poses when NONE was successful.

Minor bug fixes

  • An issue where Dock passed too many conformers for flexible optimization with relaxation in OEPosit has been fixed. Now, OEShapeFit no longer passes too many conformers for flexible optimization that could occasionally cause a less accurate conformer to become the top predicted pose.

  • The Dock method with relaxation has been modified to be more aligned with other modes of failure when ligand charge assignments fail.

FastROCS TK 2.2.5

Minor internal improvements have been made.

Grapheme TK 1.5.0

Minor internal improvements have been made.

GraphSim TK 2.5.7

Minor internal improvements have been made.

Lexichem TK 2.9.0

Minor bug fixes

  • Custom polymer naming was added in the molecule-to-name workflow to avoid memory overflow when reading in large polymers.

  • Kekulization was added in the molecule-to-name workflow to ensure that the same aromatic structures produce the same names.

  • Support was added for some cases of complex (bis-, tris-, tetrakis-, etc.) multipliers in the molecule-to-name and name-to-molecule workflows.

OEMedChem TK 1.2.1

Minor internal improvements have been made.

MolProp TK 2.6.3

Minor internal improvements have been made.

OEFF TK 2.7.0

New features

Major bug fixes

  • The internal algorithms for VdW parameter assignment with OESmirnoffParams have been modified to improve performance in working with large molecules.

Minor bug fixes

  • The GetTitle method for OESmirnoff now properly returns the user set title of the force field.

Omega TK 5.0.0

New features

  • The default fragment library for OEOmega and OEMolBuilder has been updated. The new fragment library consists of over 580 K fragments, replacing the previous library with ~80 K fragments.

  • Three new force fields have been added and can be used with OEMolBuilder and OETorDriver in OEOmega:

  • The behavior of OEFlipperOptions has changed. New flags have been added to OEFlipperOptions, facilitating more complete decoupling of individual flags and more selective enumeration of specific stereocenter classes and environments than was previously possible.

  • A new option class, OEFlipperClassicOptions, has been added to allow a detailed comparison of the new flag behaviors with the previous OEFlipper enumeration behavior. This class will be deprecated in a future toolkit release.

  • The internal algorithm for storage and usage of torsion rules in OETorLib has been modified to improve performance when working with a library containing a large set of rules.

  • A new return code FailedCharges has been added to OEOmegaReturnCode to indicate failures due to partial charge assignment.

Minor bug fixes

  • The order of torsion rules in the default OETorLib has been changed to ensure that a specific rule is not ignored due to the presence of a more generic rule.

Quacpac TK 2.2.3

Minor internal improvements have been made.

Shape TK 3.6.1

Major bug fixes

  • Memory consumption when initiating an OEColorForceField has been reduced by moving instantiation of internal OESubSearch-based colorer objects to a lazy instantiation mode.

Sitehopper TK 2.0.4

Minor internal improvements have been made.

Spicoli TK 1.5.7

New features

  • A function was added to assign surface potentials based on a molecule’s OECalculateSurfacePotentials, using either atomic potentials or a potential based on formal charges of protein residues at the protein surface (GRASP) using Zap (license required).

  • A function was added to color a surface based on its stored potential OEColorSurfaceByPotential.

Spruce TK 1.5.3

New features

  • The chemical components dictionary was updated with latest data from the RCSB.

Major bug fixes

  • An issue that caused OESpruceFilter to segfault has been fixed and safeguarded.

Minor bug fixes

  • An issue has been fixed that caused incorrectly built loops when the protein structure contains nonstandard amino acids, particularly in the gap needing to be built or anchoring to it.

  • An issue with sequence mutation for cysteine residues, where an explicit hydrogen was left over after the mutation, has been fixed.

Szmap TK 1.6.7

Minor internal improvements have been made.

Szybki TK 2.7.0

New features

Major bug fixes

Minor bug fixes

  • Validation of user-selected torsion in torsion scan has been added. If a torsion passed to function OETorsionScan or method Scan does not exist, the torsion scan code stops with a message that the torsion does not exist in the input molecule.

Zap TK 2.4.6

New features

  • New overloads of GetArea have been added that return solvent accessible surface areas for specific residues.