The performance of reading V2000 MDL MOL files has been significantly improved. See table Performance improvement of importing molecules from various file formats above.
The performance of 2D coordinate generation has been improved by as much as 33% in some cases.
Added new OESMILESFlag.AllBonds output Flavor for SMILES generation. When set all bonds will be explicit in the generated output SMILES.
A new OEIsSDDataFormat function that can return whether the given file format supports SD data information has been added.
213 new ring templates have been added to the built-in ring dictionary.
|Carbon Skeleton||Specified Cis/Trans|
The performance of reading OEFormat.CDX files has been improved.
The memory subsystem in the OpenEye Toolkits has been revamped to allow more types of objects to pass safely between operating system threads by default. The following objects are no longer affected by OESetMemPoolMode:
The upgrade fixes crashes observed in the OEMolProp TK and OEDocking TK in multi-threaded web servers. A more thorough description of what can and can’t be done with threads with the OpenEye Toolkits can be found in the recently updated Multi-Threading chapter.
Care was taken to ensure the same or better level of performance with the new system. However, if you experience a performance degradation when switching to the Toolkit 2015.Oct release, please do not hesitate to contact email@example.com.
OEMCMolBase.GetMCMolTitle will now be consistent when reading single-conformer file formats. Previously, reading SMILES and CDX files would set the title on the parent OEMCMolBase, but MOL2, CSV, SDF, and single-conformer OEB file formats would not. All these file formats will now initialize the parent OEMCMolBase title allowing more consistent behavior when annotating conformer titles (warting) across all file formats. The conformers can be warted, leaving the parent title intact as well.
OEChem::OEConfBase::operator bool will now conform better to the OEMolBase API by returning whether the molecule contains atoms. The previous behavior was odd and unused, returning the state of the coordinates in the conformer.
OEPerceiveResidues will no longer crash when a thread has a small stack size and the molecule is very large.
The following changes were made to improve the support for OEFormat.CDX file format:
OpenEye Toolkits header files should no longer contain the C++11 deprecated “register” keyword causing compilations with -Werror to fail.
oestream and derived classes will no longer allow implicit conversion to int and unsigned int. This avoids surprising behavior like the following from compiling:
oeisstream is1; oeisstream is2; bool what = (is1 == is2);