OEChem now supports the creation of InChI. OEChem produces the same InChI as the InChI library provided application for 99.77% of MDDR in the SDF format. The differences fall into two categories:
The inclusion of InChI support added the following:
In addition, oemolostream will automatically write InChI when using the .inchi file extension.
OEPrepareSearch added that perceives atom and bond properties of a molecule that are necessary to successfully execute a given substructure search. It is now highly recommended to run this function on a molecule before passing the molecule to any of OEChem’s graph matching algorithms.
Several Java API points that pass primitive arrays of doubles or floats were optimized with good results. The following API points that take these primitive array types were optimized: NewConf, SetCoords, and GetCoords.
It used to be possible to perform a substructure search for stereochemistry or hybridization on a molecule that did not yet have those properties perceived. This led to very subtle to detect problems where molecules would not match that were expected to match.
To combat this, the following OESubSearch methods now throw warnings in case some property that is necessary to successfully execute the substructure search has not been perceived yet:
These warnings can be suppressed by calling the OEPrepareSearch function on the molecule first.
It is now thread-safe to copy the same OEMol from multiple threads at the same time. This was caused by some OEMCMolBase methods not actually being const. The following methods were marked as const, but were not actually const, leading to subtle race conditions: