Version 2.1.5

OEChem TK 2.1.5

New features

  • New OEHasExplicitHydrogenExpression and OEHasImplicitHydrogenExpression functions have been added.
  • The OEPrepareSearch function 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.
  • Both OEGetSubtree and OEGetSmallestSubtree functions 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, OEIFlavor::MDL::SuppressImp2ExpENHSTE and 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.
  • A new OEGroupType::UserDefined type has been added to OEGroupBase to support serialization and deserialization via the OEB format.
  • A new OEIsBridgeHead functor has been added to identify bridge head atoms in a molecule.
  • A new OERingBondCount function 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 OEGroupBase is no longer lost when the molecule is copied.
  • Generic data attached to OEGroupBase is no longer lost when the molecule is added to another molecule by invoking the OEAddMols function.
  • 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 OEReadMolecule now 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assumed that such indices were contiguous, but recent third-party writers have demonstrated that this assumption is no longer valid.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

  • The OEGenerate2DCoordinates function now returns false when 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. OEReadMolecule now fails for these types of format errors.
  • OEUniMolecularRxn internal validations have been relaxed to allow reaction transformations that create a bond between two separate fragments.
  • OEGetHybridization has been repaired to return OEHybridization::sp3d and OEHybridization::sp3d2 for high valence halogens. Previously, this function had only returned OEHybridization::sp3 for these cases.
  • OEUncolorMol has 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.
  • OEAnd and OEOr have been augmented to support using OEGroupBase types to allow a more complex selection of MDL stereogroup types via custom predicates.
  • A new copy constructor and new assignment operator have been added to OERotMatrix.

Python-specific changes

  • Type comparisons between OEBase and non-OEBase objects have been fixed to ensure that an exception is longer thrown.
  • A new __str__() function has been added to OEResidue to provide a convenient string representation.

Java-specific changes

  • A new 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.

Documentation changes

OEBio TK 2.1.5

New features

Minor bug fixes

  • It is now possible to set an alternative rotamer on proline residues.

C++-specific changes

  • OEBio TK now depends on OEGrid TK. As result, CMake files might need to be modified to reflect this library dependency.

Java-specific changes

C#-specific changes

OEPlatform TK 2.1.5

  • Minor internal improvements have been made.

OESystem TK 2.1.5

  • The OEWriteSettings function now takes a 4th argument that specifies the name of an optimized parameter set for OpenEye‘s applications.