Version 2.3.0

OEChem TK 2.3.0

New features (Preliminary)

New features

  • Two new classes, OEConfRMSDOptions and OEConfRMSD, have been added that set up OEConfRMSD calculations and provide fast RMSD calculation of conformers of the same molecule, respectively.
  • A new function, OEFastaToMol, has been added that converts a FASTA sequence into a molecule.
  • A new optional sorting argument has been added to the OEGetNearestNbrs function that allows returned atom pairs to be sorted based on distance.
  • OEIsAlphaCarbon has been deprecated. The OEIsCAlpha predicate should be used instead.
  • New OEUncolorMol overload functions have been added to OEMCMolBase. A new constant, OEUncolorStrategy::RemoveDimension, has been added that invalidates 3D coordinates and sets the dimension to 0 when uncoloring molecules.
  • Support has been added to OEReadMolecule that enables reading both CIF and mmCIF files.
  • Updates have been made to the OEFormat namespace to include new CIF and mmCIF formats. Corresponding updates have also been added to OEIFlavor and OEOFlavor.
  • Updates have been made to the OEResidueIndex namespace to include residue IDs for metals observed in PDB files.
  • The formal charge assignment for less common metals observed in PDB files has been expanded.
  • Updates have been made to the OEExprType namespace to allow for more fuzzy searches. For example, OEExprType::ElemMinHCount or OEExprType::ElemMinDegree can now be used to specify an atom’s minimum hydrogen count or minimum degree.
  • Changes have been made to the OEResidue class to support the mmCIF format. These changes include the following three new string member variables, with the appropriate getter and setter functions:
    • SequenceID captures the mmCIF field, label_seq_id, which is the sequential number of residues from 1.
    • ExtChainID captures the fact that the previous chainID in the auth_asym_id field can now have multiple characters. The OEResidue::GetChainID function now returns the first character of the ExtChainID variable, and OEResidue::SetChainID now overwrites and sets the ExtChainID.
    • SubChainID captures the label_asym_id field, which commonly seems to be a further subdividing of the auth_asym_id field.

Minor bug fixes

  • A bug that caused OEWriteMolReturnCode::Success to be returned even though an invalid output stream was used has been fixed.
  • A bug that caused broken perception after implicit hydrogen assignment in the OEAssignImplicitHydrogens and OEAssignMDLHydrogens functions has been fixed.
  • Handling of partially resonant nitrogen stereo perception in OE3DToAtomStereo and OE3DToInternalStereo has been improved.
  • An issue that caused OEIsCTerminalAtom to misperceive a minor number of C-terminal atoms has been fixed.
  • Unpaired interactions are no longer triggered on ligands due to nearby water molecules. Similarly, water molecules can no longer present as having unpaired interactions.

Python-specific changes

Java-specific changes

Documentation changes

OEBio TK 2.3.0

New features

Minor bug fixes

  • Perception of hydrogen bonds involving sulfur and anions in OEPerceiveInteractionHints has been improved.
  • The precedence of OEInteractionHint perception has been improved. Chelation interactions now take precedence over charge-charge interactions.
  • A check has been added to the OEPlaceHydrogens function that causes it to exit early if two heavy atoms are within 0.5A of each other, since this is considered to be bad input and causes unspecified behavior.

OESystem TK 2.3.0

New features

  • The performance of OEGetDataType, especially on Windows, has been improved. OEGetDataType is now at least 500X faster when used with a single thread and about 2X faster with many simultaneous threads on Windows.
  • A new method, OEBitVector::CountRangeBits, has been added that identifies the number of bits that are set to 1 in the given bit range.
  • A new class, OEConsoleProgressTracer, has been added that tracks the current progress of a task.
  • A new function, OEStringEquals, has been added that determines whether two strings are equivalent using a case-insensitive comparison.
  • A new function, OEGeom3DReflectCoord, has been added that reflects coordinates around a plane for a hydrogen atom.
  • A new function, OEBitIsPowerOf2, has been added that determines if a bitmask is a power of 2.

OEPlatform TK 2.3.0

New features

  • A new OEToolkitsGetRelease function has been added that displays the release name of the overall toolkit version being used.

OEGrid TK 1.6.4

  • Minor internal improvements have been made.