OEChem TK 3.3.0¶

Spring 2022

New features¶

Support for CXSMILES has been added as a new molecule I/O format, OEFormat.CXSMILES.
A new option flag, OESMILESFlag.EnhStereo has been added to the OESMILESFlag flags for controlling the output of CXSMILES enhanced stereo information.
New methods were added to the OEParseSmilesOptions class to control the consideration of CXSMILES appendices during the parse. See, GetCXSMILES and SetCXSMILES.
New methods were added to the OEInChIOptions class to control the SUU option during InChI generation. This will necessarily generate nonstandard InChIs when enabled. See, GetUndefinedStereo and SetUndefinedStereo.
New flavor flags were added to OEFileStringParameter and OEOutFileStringParameter to support file type selections. See the OEFileStringTypeFlavor namespace.
Overloads for OECalcPMI and OEGetRadiusOfGyration were added that accept OEMCMolBase and OEConfBase objects.

A minor bug related to uninitialized memory in OECalcPMI was fixed.
An issue disallowing the use of multiple options for OEIFlavor support with SDF, RDF, MDL formats has been fixed.
An issue affecting copy activities of OEGroupBase objects during conformer copy activities has been fixed.
The GetHasValue method now returns false for a non-zero input argument, as appropriate.

An issue with the assignment operator for OEDesignUnit has been fixed.
An issue with automated titles for OEDesignUnit has been fixed.
An issue with the default style on generated OEDesignUnit related to built residues has been fixed.
The algorithm for OEDesignUnit creating has been improved to better detect unnatural amino acids.

A new method, AddParameterPrefix, has been added for adding a prefix to all the command line parameter’s names.
a new method, GetPrettyLegalValues, has been added to get the list of the named legal values.

An issue causing list parameters to be not updated properly in UpdateValues has been fixed.

The ZSTD dependency has been updated to version 1.5.2, which should positively effect the OEFormat.OEZ format type in both compression level and encoding and decoding performance.
The ZLIB dependency has been updated to version 1.2.12 with latest security improvements.

The mrc file format is now recongized as a CPP4 grid file type in OEGridFileType.