Version 2.2.0¶

OEChem TK 2.2.0¶

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 oemolistream.open and oemolostream.open 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.

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.

New features (Preliminary)¶

• The following preliminary APIs have been added to handle design units:

The above classes and functions are currently used by Spruce TK for protein handling.

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 OESystem_OEThrow class to demonstrate how to redirect warning and error messages to a file.

OEPlatform TK 2.2.0¶

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.