Version 2.2.0

OEChem TK 2.2.0

New features

Major bug fixes

  • The number of cases where round-tripping to MDL file format results in stereo information loss has been significantly reduced.

Minor bug fixes

  • High-level SMILES readers such as OESmilesToMol and OEReadMolecule now clear cis/trans bond specifications on bonds in small rings (less than 7 members).

  • The and methods now correctly set the formats for gz filenames.

  • A bug that caused a crash when an invalid oemolostream is finalized has been fixed.

  • oemolistream.Setgz and oemolostream.Setgz methods are now a no-op if the state of the stream is unchanged.

  • An issue that caused the JSON writer to crash with user-specified cis/trans stereo has been fixed.

  • The MDL V3000 reader has been fixed and no longer marks “either” double bonds with cis/trans parity.

  • The MDL V2000 reader has been fixed and no longer adds “either” double marks to chiral but unspecified cis/trans double bonds.

  • OESubsetMol no longer crashes when breaking and adding multiple R-groups to the same atoms.

  • Cobalt ions are now assigned a formal charge when being read from the PDB file.

Python-specific changes

Documentation changes

OEBio TK 2.2.0

New features

  • A new OEIsCTerminalAtom predicate has been added to identify the C-terminal atom(s) in a protein structure.

  • A new OEIsNTerminalAtom predicate has been added to identify the N-terminal atom(s) in a protein structure.

  • A new OEAtomMatchResidue predicate has been added to identify residue atoms by RegEx.

  • New OEGetResidueAtom functions have been added to provide easy access for specific residue atoms.

  • The OEIsBackboneAtom predicate has been updated to take an optional argument to consider the terminal oxygen atom (OXT) as part of the backbone.

  • The OEIsWater predicate has been updated to take two optional arguments:

    • to match hydrogen atoms in water molecules

    • to match the water ions \(OH^{-}\) and \(H_{3}O^{+}\)

  • A new OEIsStandardProteinResidue overload that takes an atom has been added.

Minor bug fixes

Java-specific changes

Documentation changes

OESystem TK 2.2.0

Minor bug fixes

  • The OEMakeMolecularGaussianGrid function now returns false for an empty molecule.

  • New code snippets have been added to the OEThrow class to demonstrate how to redirect warning and error messages to a file.

OEPlatform TK 2.2.0

New features

Minor bug fixes

  • The OEAddLicenseFromHttp function available in the wrapped languages (Python, Java, and C#) now accepts HTTP responses with a text/plain; charset=utf-8 content type.

OEGrid TK 1.6.3

Minor bug fixes

  • The OEReadMTZ function has been updated to read CCP4 alternative space group numbers (e.g., 4005).

  • OEReadGrid no longer loses its title beyond the first blank space.

  • A potential memory corruption issue with Gaussian volume calculation has been fixed.