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.

Fall 2021

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:

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.

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.