The following API have been added to generate and use 2D ring dictionaries:
The following sections provide examples to generate and utilize user-defined 2D ring dictionaries:
ringdict2pdf example in OEDepict TK will generate a multi-page PDF report of a 2D ring dictionary.
221 new ring templates have been added to the built-in ring dictionary.
|Pure Carbon Skeleton Ring Templates||Ring Templates with Specified CIS/Trans Bonds|
OEIFlavor.MOL2.Forcefield flavor has been added to the MOL2 reader. This allows atom names in the MOL2 file to be interpreted as chemical elements while not using the second character if capitalized; for example, CA and CD are both carbon instead of calcium and cadmium. This will help reading OEFormat.MOL2 files that contain forcefield information like partial charges.
OEAddCustomFASTAResidue now provides the ability to customize OEFormat.FASTA input files with unnatural nucleic acids. OEIFlavor.FASTA.CustomResidues flavor is used to activate the new feature. OEIFlavor.FASTA.EmbeddedSMILES flavor has also been added to experiment with adding cyclizations to peptides using custom tethers. These features are currently considered experimental; please send feedback to email@example.com.
OEOFlavor.SDF.UnsetBad2DStereo and OEOFlavor.CDX.UnsetBad2DStereo, new output flavors for SDF and CDX output formats, have been added. These constants control behavior when generating 2D coordinates during output. When used, the writer will set the stereo to “undefined” for any misleading stereochemistry that may result from layout limitations.
OESubsetMol has a new overload that supports the use of OEAtomBondSet input. This can offer significant performance improvements over the predicate overloads since a full molecule iteration can be avoided.
OEMolBase.ClearCoords has been added to fully clear molecule coordinates, clear the dimension code, and reset perception flags.
OEMolDatabase.WriteMolecule has been added to automatically extract a molecule from the database and write it to the oemolostream. This function is optimized for performance to simply move bytes around if the input OEMolDatabase format and the output format match exactly.
OEMolDatabase.GetMoleculeString has been added to allow direct access to the molecular record data.
OEPRECompress and OESweepRotorCompressHydrogens have been added and documented to allow advanced users to start experimenting with perfect-rotor-encoding OEB files to achieve higher rates of conformer compression. This feature is currently only available to the C++ toolkits.
The following free functions have been added for handling dummy atoms in forcefield calculations in special circumstances:
Currently, dummy atoms are only allowed in Szybki TK for non-bonded interactions.
OEAssignRadii free function has been added to allow for a central entry point for any OpenEye Toolkit atomic radii assignment. This free function uses the OERadiiType namespace for choosing the type of radii to assign.
OEThrow.SetLevel and OEThrow.GetLevel race conditions should be largely alleviated now. OEErrorHandler.SetLevel and OEErrorHandler.GetLevel will now affect the error message level for the current thread only; all new threads launch with the default error level of OEErrorLevel.Default (Info or above).
Multi-threaded OpenEye Toolkit programs may need to be updated to allow the desired output to be sent to standard error. However, the previous behavior was race-condition prone and difficult to get correct.