OEChem TK 2.1.5¶
OEPrepareSearchfunction now takes a parameter that determines whether to adjust the hydrogen of a target molecule based on the presence or absence of implicit and explicit hydrogens on the query molecule of the substructure search.
OEGetSmallestSubtreefunctions now take an optional max depth parameter that allows partial traversal of subtrees. For example, the parameter allows identification of the subtree of a proline residue without traversing back onto the main chain. Similarly, it is possible to get the subtree of a cysteine residue involved in a disulfide without traversing across the disulfide bond and back on the main chain.
Two new constants,
OEOFlavor.MDL.SuppressImp2ExpENHSTE, have been added with related MDL input and output formats (e.g., SDF, RDF) to allow suppression of explicit MDL stereogroup generation for implied stereocollection membership. By default, marked stereocenters not explicitly included in stereocollections are added to their implied stereocollection membership based on the chiral flag setting.
OEIsBridgeHeadfunctor has been added to identify bridge head atoms in a molecule.
OERingBondCountfunction has been added that returns the number of bonds connected to an atom that are part of a ring.
Major bug fixes¶
The FASTA reader has been fixed to support reading multiline FASTA strings.
Generic data attached to
OEGroupBaseis no longer lost when the molecule is copied.
Relative stereo (e.g., 1,4-disubstituted cyclohexanes) information is now preserved on input, ensuring that the conformers generated will respect the input stereochemistry. Previously, such relative stereocenters would be cleared during activities to clear other illegally marked stereochemistry.
The V3000 MDL format readers called by
OEReadMoleculenow support noncontiguous object indices. It previously had been assumed that such indices were contiguous, but recent third-party writers have demonstrated that this assumption is no longer valid.
Minor bug fixes¶
OEGenerate2DCoordinatesfunction now returns
falsewhen it fails to generate coordinates that are consistent with the atom/bond stereo of a molecule.
A memory corruption issue in the InChI generation code that previously required a check for hydrogen isotopes beyond
[3H]will no longer generate InChI for these unrealistic hydrogen isotopes.
Malformed SD bond lines that lacked both atom endpoints had previously been ignored.
OEReadMoleculenow fails for these types of format errors.
OEUniMolecularRxninternal validations have been relaxed to allow reaction transformations that create a bond between two separate fragments.
OEGetHybridizationhas been repaired to return
OEHybridization.sp3d2for high valence halogens. Previously, this function had only returned
OEHybridization.sp3for these cases.
OEUncolorMolhas been augmented to remove stereogroups when stripping atom stereochemistry. Additionally, a new option,
OEUncolorStrategy.RemoveGroupStereo, has been added to support the explicit stripping of stereogroups.
A new copy constructor and new assignment operator have been added to
Type comparisons between
OEBaseobjects have been fixed to ensure that an exception is longer thrown.
__str__()function has been added to
OEResidueto provide a convenient string representation.
OELibExtractor.GetTmpDirName()method has been added to return the temporary directory used for the extraction of native libraries from the JarFile and the extraction lock file. This directory location can potentially be used to clean up extraction locks that have been left behind due to inadvertent or explicit Java process kill activities.
OEBio TK 2.1.5¶
The following APIs have been added to perform Ramachandran analyses on protein structures:
The following atom predicates have been added to identify RNA atoms:
OESetRotameroverload has been added that takes a residue atom.
Minor bug fixes¶
It is now possible to set an alternative rotamer on proline residues.
OEBio TK now depends on OEGrid TK. As result, CMake files might need to be modified to reflect this library dependency.
OEPlatform TK 2.1.5¶
Minor internal improvements have been made.