OEChem TK 4.3.0

New Features

  • A new function, OESweepMDLStereoGroups, has been added to strip nonstereo atoms from existing enhanced stereogroups, which can be used to reconcile the stereogroup information with the existing atom stereo parities.

  • A new function, OESameAlternateLocation, has been added to determine whether two atoms have the same alternate location set. It optionally allows for one of the states to be blank or unspecified, similar to the predicate OEHasAlternateLocation.

  • A new function, OEClearFormalCharges, has been added that resets all formal charges to zero.

  • A new OECIFData object has been added for easier access, coordination, validation, and updates to CIF header data. The full list of new features related to this object can be found on the OECIFData API page. Data available in this object reflects what is contained in the CIF data_ section.

  • A new OECIFCategory object holds CIF category data and acts as an interface to interact with this header data. The full list of new features related to this object can be found on the OECIFCategory API page. Data available in this object reflects what is contained in CIF pair or loop sections.

  • A new OECIFOptions object is used during CIF update functions and informs what categories and data items in the CIF header will be updated.

  • The OESetCIFData function can also take an OECIFData object as an input to save data stored in the object on the input molecule.

  • The new function OEUpdateCIFData will update the molecule’s CIF header data based on the molecule’s current structure.

  • The new function OESetMMCIFChemCompData was created to override mmCIF chemical component data on the molecule’s CIF header data.

  • The new function OEIsCIFHeaderCompliant takes the RCSB’s PDB Exchange Dictionary as input and checks if the CIF categories stored on the molecule are supported by the RCSB.

  • A new OEOFlavor for mmCIF, PerceiveMetadata, can be used to perceive all CIF header metadata at write time, based on the molecule’s structure.

  • Improvements have been made to CIF file reads that utilize chemical component header sections.

  • The OEIsDisulfideBridgeBond functor identifies inter-residue disulfide bridge bonds and follows the same bond identification criteria that was in the OEBio OEIsDisulfideBond functor.

  • The new OEIsAmideBond functor identifies inter-residue amide bonds.

  • The new OEIsIntraResidueBond functor identifies inter-residue bonds.

Major Bug Fixes

  • Improvements have been made to mmCIF file writes for stability to minimize overwriting data stored in the header.

  • Improved mmCIF file write stability has been added.

Minor Bug Fixes

  • A coding error in the assignment operator for OEMiniMol has been fixed.

  • An issue with invalid object pointers returned from OEGetAutomorphs has been fixed.

  • Various stability improvements to CIF header writes have been made.

  • An issue reading certain LINK records from PDB files has been fixed

OEBio TK 4.3.0

New Features

Major Bug Fixes

Minor Bug Fixes

  • The following were removed from the polymers category in the residue database: ZYA, R99, RL2, VSC, ZU5, S89, 0I5, 0D6, 0E6, ZRA, I0Y, and K36.

  • The OEIsDisulfideBond functor now uses the OEChem OEIsDisulfideBridgeBond functor for its implementation.

  • The covalent perception distance in design unit splitting to components has been relaxed.

OEGrid 4.3.0

New Features