OEChem 1.4.2 is a bug fix release including dozens of minor and major bug
fixes. It also includes numerous new minor features, and also brings
significant practical changes. OEChem 1.4.2 is the first OEChem that is being
released along with all the other public OpenEye toolkits. This will be a
major step forward for inter-operability between different OpenEye toolkits and
will open the way for easier support of customer applications that span
multiple OpenEye toolkits.
OpenEye continues to be committed to maintaining a stable OEChem API and thus
any programs written with previous versions of OEChem should re-build with the
1.4.2 version of OEChem. However, as is the nature of C/C++ code, particularly
C++ template code, some of the bug fixes are in header files, so dependent
libraries such as most other OpenEye libraries may require a re-link.
OEChem 1.4.2 will be the first release in which OpenEye is beginning to move
toward synchronizing our library releases. This will remedy problems some
people have experienced with link-problems when combining three or more OpenEye
libraries into a single application.
Major bug fixes
- Added safeguards against stack over-runs in all molecule implementations.
- Fixed a major bug in rotor-offset compressed OEBinary file handling that
made these molecules fragile with respect to molecule copies.
- Fixed thread-safety of reading SMILES.
- Fixed crash-bug when OEPerceiveResidues was called on unusual
small-molecule peptide mimics such as O=CC(C)NC(C)C=O.
- Fixed dummy-atom handling in the CDX reader. Also improves
implicit-hydrogen handling, but limits the reader to reading a single
- Corrected failure to include Isotope information in OEBinary files.
- Fixed crash-bug from processing stereochemistry on MDL atoms with degree
three having hashes and wedges.
- A major oemolistream bug was fixed by fixing a stream bug (see
OEPlatform‘s Major bug fixes above).
- Fixed a bug where OELibraryGen failed to convert an aromatic ring
to aliphatic accurately.
Minor bug fixes
- Dramatic improvement in the search speed of disconnected SMARTS such as
- Speed optimizations were added to molecular geometry manipulations.
- Fixed very rare search-path bug in aromaticity perception.
- Allow support for C[N@H]O and C[N@@H]O in SMILES output.
- Fixed side-effects of OECanonicalOrderBonds on stereochemistry.
- Added BondIntType I/O in OEBinary format.
- Improve OEKekulize fall-backs to it fails gracefully.
- Add support for fully explicit Hydrogen flavor in SMILES (i.e. [CH4]).
- Fixed bug in the over-application of constraint for MCS searches.
- Added support for aromatic lead, aluminum, germanium and tin.
- Improved support for MDL’s V3000 format.
- Improved perception of cationic N.pl3 atoms with partial charge greater
- Added protection to SMILES writer for molecules with a terminal single
bond that has stereochemistry specified.
- Fixed initialization of OEBinaryHandlers.
- Added support for the aromaticity model being used to effect chirality
- Improved carbon dioxide, acetonitrile, cyanamide, cyanic acid and
thiocyanic acid fragment recognition in bond perception algorithms.
- Fixed rounding error in OENetCharge function.
- Fixed endian bug in CDX reader for OS X.
- Added protection from molecule titles >4K in length.
- Added proper support for comments in MOPAC files.
- Improved copy construction and assignment of OEQAtomBase and
- Added OEOFlavor.PDB.HETBONDS flavor to the PDB writer that
causes any bond to or from a HETATOM to be written explicitly.
The HETBONDS flavor now part of the default
- Added support for UNK atoms attached to a backbone and LIG atoms
that are covalently bound ligand or post-translational modifications to be
given the same chain ID and residue number as the residue to which they are
- Added OESymmetryNumber to calculate the symmetry number of a given
conformer within a user-defined threshold.
- Fixed bug that lost SD data attached to an OEMol (not its conformers)
when the molecule was written to OEB (Note, SD data is not generally stored on
the parent molecule).
- Fixed OrderConfs OS X memory bug.
- Fixed strip salts to only count heavy atoms in determining the fragment
with the largest size. This makes the behavior remain consistent with implicit
and explicit hydrogens.
- Added support for x in SMARTS as defined in v4.9 of Daylight’s toolkit.
- Prevent PDB writer from generating CONECT records that have the same
serial number for the source and destination.
- Fixed bug in automorphism calculations on molecules with hydrogen-defined
cis-trans bond stereo.
- Improved algorithm for perception of 3D bond stereo.
- Added support for stable serial numbers, alternate locations, insertion
codes and heteroatoms during calls to OEPerceiveResidues.
- Improved heuristics for residue perception in the presence of unusual