SPRUCE 1.4.0

Fall 2021

New Features

  • The application loopdb_builder now reads MMCIF files. If the same structure is available in both PDB and MMCIF format in the provided directory, the PDB file is used.

Minor Bug Fixes

  • A minor bugfix affecting stability of the loopdb_builder has been fixed.

Spruce TK 1.4.0

Fall 2021

New features

  • A new method, OECapBuilderOptions.SetForceCapping, has been added to enable capping even if it will result in a clash.

  • Two new methods, OELoopBuilderOptions.SetBuildTails and OELoopBuilderOptions.GetBuildTails, have been added to set and get an option that controls whether to build tails when there is missing residues at the N- and C- termini.

  • OESuperPoseOptions::SiteHopper is now a supported superposition method in OESuperpose, and can be set using SetMEthod.

  • All Options classes have been modified to derive from OEOptions. This affects classes:

    • OEDesignUnitEnumerateSitesOptions

    • OEProtonateDesignUnitOptions

    • OEDesignUnitBuildOptions

    • OEDesignUnitPrepOptions

    • OEDesignUnitSplitOptions

    • OEBioUnitExtractionOptions

    • OEMakeDesignUnitOptions

    • OEPlaceHydrogensOptions

Major bug fixes

  • An issue causing capping a non-standard residue to fail has been fixed.

  • An issue causing covalent ligands to have their covalent bond broken when there were alternate locations in the structure, has been fixed.

  • An issue causing side-chains to either not be built or being built in non-optimal configurations has been fixed.

  • An issue with pockets identifying liganded sites in OEMakeDesignUnitFromPocket not generating a proper design unit with a ligand bound in the identified site has been fixed.

Minor bug fixes

  • An issue causing the warning message ‘Truncated cap due to clash’ to appear when OECapBuilderOptions.SetAllowTruncate is False has been fixed.

  • An issue caused by Heuristic score offset beeing added before comparing to original structure therefore unable to pick the more energy favorable conformation has been fixed.

  • An issue causing the gap finding code to mis-identify gaps in the protein structure due to residues with missing backbone atoms has been fixed. The function now removes these residues prior to gap detection inside OEBuildLoops.

  • An issue caused by malformed PDB Header data, specifically with regards to REMARK 300 sections, has been fixed.