Spruce TK 1.4.0

Fall 2021

New features

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

• Two new methods, SetBuildTails and 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.

• SiteHopper is now a supported superposition method in OESuperpose, and can be set using the SetMethod method of OESuperpose.

• 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 nonstandard 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 SetAllowTruncate is False has been fixed.

• An issue caused by Heuristic score offset being 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.