Version 3.1.0.2

OEChem TK 3.1.0.2

March 2021

  • Additional metadata constants were added to the OEMetadata namespace for controlling the visibility of fields in the Orion user interface.

OEBio TK 3.1.0.2

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