OEBformat has been extended to support MDL enhanced stereogroup information.
OEBformat has been enhanced to support reaction atom-atom mapping and reaction component information.
The OEGroupBase API has been augmented to support reaction component information. In addition, new predicates have been added to loop over the new OEGroupBase collection types. See
OEGroupBase.GetGroupDefinition, OEHasGroupType, OEIsRxnComponentGroup, OEIsReactantGroup, OEIsProductGroup.
SDFreader is now more tolerant of molfile header lines that exceed the specification maximum of 80 characters. A warning is issued on read and the longer lines are truncated to 80 characters on write to prohibit generating files that do not meet the format specification.
New functions for computing weighted RMS deviation between pairs of Cartesian coordinates, molecules, and partial molecules have been added. See
Minor bug fixes¶
The tag used to identify style data in
OEBfiles has been changed. The old tag was not updated when the data structure was modified last year. As a result,
OEBfiles with style data that were generated before 2015.Jun cannot be read with more recent toolkits. Data with the old tag will be ignored. Since style data is only used internally, we do not anticipate any read problems with
OEBfiles generated by our customers.
Several problems with the internal implementation of
OEMolBaseType_OEMiniMolhave been fixed.
A problem in the
SDFreader where uninitialized memory was being accessed during the perception of V3000 reaction files has been fixed.
A problem in the
SDFwriter relating to relative stereochemistry has been fixed. Previously, the writer incorrectly exported an input V3000 format file as a V2000 format output, resulting in the incorrect promotion of racemic stereocollection information to absolute stereochemistry.
A problem with the
MOL2reader that limited input lines to 80 characters has been fixed. The reader now supports 512 character lines for this format.
New overloads of
OEChem::OEWriteMolToStringin C++ allow more efficient encoding of molecules to strings.
OEWriteMolToBytes takes advantage of the new overloaded versions of the
OEChem::OEWriteMolToStringC++ functions to improve encoding performance.
OEPlaceHydrogensis a new function that adds hydrogens to a molecule and builds hydrogen bonding networks, flipping amide and imidazole groups if necessary.
The following API has been added to customize and improve the perception of potential protein-ligand interactions:
A variant of the
OESplitMolComplexfunction enables a more efficient two-step process. The function
OEGetMolComplexFragmentsanalyzes a molecule and returns an OEAtomBondSet vector describing the role of each fragment. Functions
OEFilterMolComplexFragmentsthen use this information to create new subset molecules.
Minor bug fixes¶
OEClearMolComplexSDDatanow correctly identifies data by tag prefixes.
falseif the molecule has a default
CRYST1record. PDB format rules lead to these default records, which should be interpreted to mean the molecule has no symmetry record.
The description of the output parameters for the function
OEExpandCrystalSymmetryhas been improved.
OEGetAllocaThresholdhave been added to manage stack memory usage. Rather than keeping track of stack usage, which impacts performance, the new functions set/get the threshold for the largest single allocation from the stack. Above the threshold, memory is allocated from the heap. Although this only indirectly controls total stack usage, it is lightweight and can help mitigate stack memory problems.