The SDF reader 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 OEWeightedRMSD for details.
The tag used to identify style data in OEB
files has been changed. The old tag was not updated when the data structure
was modified last year. As a result,
OEB files 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
OEB files generated by our customers.
A problem in the SDF reader where
uninitialized memory was being accessed during the perception of V3000
reaction files has been fixed.
A problem in the SDF writer 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 MOL2 reader
that limited input lines to 80 characters has been fixed.
The reader now supports 512 character lines for this format.
The function OEHasCrystalSymmetry now returns false
if the molecule has a default CRYST1 record. PDB format rules lead to
these default records, which should be interpreted to mean the molecule has
no symmetry record.
Functions OESetAllocaThreshold and
OEGetAllocaThreshold have 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.