Spruce TK 1.8.0

New Features

The function OEBuildSingleLoop now checks for loop clashes after minimization. The option can be set using SetRejectClashingLoopsPostMinimization.
The function OEBuildSingleLoop can now delete residues already present at sites where a new loop needs to be built. The option can be set using SetDeleteExistingResidues.
The function OEBuildSidechains can now partially build target residues in the event that some targets fail.
Improved loop modeling has been added involving disulfide bridge creation by adding a bond length check.
When running with OESpruceFilter::FixResStates set to true, if the input molecule contains CIF header data, the filter will utilize the chemical component header section to inform a residue’s bond order and subsequent formal charge.
A new method, OESuperposeOptions::SetUseSeqScoreChainMatching, has been added to OESuperposeOptions that, when enabled, optimizes the sequence score over the overall RMSD when matching on multiple protein chains.

An issue has been fixed where gaps in the protein structure were misidentified due to unconventional insert code usage.

Loop modeling results have been improved by setting OELoopBuilderOptions StrictProlineMatch to False by default. The updated default is due to an improved side chain building routine in a prior toolkit release.
An issue has been fixed to ensure loops extracted from the loop database had the desired structural properties.
When truncating a residue or converting a residue to a capping group, if that residue had a crosslink bond, the residue opposite would retain an atom in a bad valence state. That issue has been fixed.
An issue has been fixed in the routine to reassign ambiguous water and metals from packing residues to the protein chain of interest. The issue caused HEME-analogs and connected amino acids to be soaked into a given chain ID.
An issue has been fixed causing loop-relevant information with insert codes in an mmCIF header to be incorrectly read.
The OECapCTermini, OECapNTermini, and OECapTermini functions address an issue that could result in an incorrectly labeled cap residue SequenceID.
Several improvements were made to address performance issues in the OESpruceFilter.

Several examples have been added, and the advanced protein preparation tutorial has been expanded.