Version 1.7.4¶

OEChem 1.7.4¶

The substructure search algorithm was optimized resulting in a significant performance increase for certain queries.
Adding CIP (Cahn-Ingold-Prelog) atom and bond stereo perception.
See also
- OEPerceiveCIPStereo
- OESetCIPStereo
- CIP Stereo Perception section
Adding two new options to the OEMDLQueryOpts namespace.
- The OEMDLQueryOpts_MatchAtomStereo option allows R/S atom stereo configuration match.
- The OEMDLQueryOpts_MatchIsotope option allows isotope match.
The CDX file reader was extended to read superatoms. Superatoms such as (Me, OEt, Ph) are represented in CDX files as disconnected fragments with no coordinates. OEChem now reads superatoms correctly, although no coordinates are assigned for the fragments.

The default bfactor of OEResidues was changed to 20.0 from 0.0. This is to allow OEResidues written out of OEChem to play nicer with other software that doesn’t know what to do with a bfactor of 0.0.
OEDBMCMols would crash during copy construction if already compressed. Allowing OEDBMCMols to copy construct while compressed allows them to be directly used inside of STL containers.

Bug fixed in the MDL query interpretation (OEBuildMDLQueryExpressions) that occurred when a hydrogen atom occurred in a generic atom list of a ring query atom.
Bug fixed that occurred when “zero-level” parentheses are used in SMARTS to perform component queries. The (X).(Y) SMARTS means that the X and Y SMARTS pattern have to be located in separate components of the target structure. For example (CO).(C=O) has a match in CCO.CC=O but not in OCCC(=O).
Fixed bug that broke reading of any map idx greater than 9 from OEB files.
Fixed a rare crash when using DBMols from Python or Java.
Fixed a bug where MDL parity bits were ignored when reading a mol file with no dimension set.
Modified the coordinate handling in CDX to invert and scale coordinates correctly.

Many usability improvements and a new documentation chapter, Command Line Interface Definition, on using OEInterface for command line parsing.
Adding new OEColor constants such as OESystem_OEBrown and OESystem_OEViolet. For the full list see the OESystem namespace.
Adding the OEGeom3DMatrixTranspose and OECenter OEMath functions.
Major optimization to OEAnnotation.AddChild.

Fixed a bug where some operations on an oeigzstream (including molstreams on gzipped files) could result in an infinite loop when the associated gz file was prematurely truncated.

Fixed bug where grids were not written out when attached to molecules. This could only sometimes occur in a statically linked C++ application depending on what set of OEGrid functions were being used.