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:

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.

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.