SPRUCE 1.6.1¶

Minor internal improvements have been made.

New features¶

Command line arguments have been added to control the gap and extend penalties for the sequence alignment used for loop building.

OEBuildSidechains now minimizes target side chains by default. Minimization can be controlled by setting minimizeSidechains and minimizeSidechainsShell options in the OESidechainBuilderOptions class.
A feature has been added to support a next generation mmCIF feature, such that when an mmCIF file provides a connectivity record for the heterogens, Spruce will no longer look up the heterogen in the Chemical Component Dictionary but trust the input provided.
A feature has been added that allows in-plane flipping of a single hydrogen on a double bonded nitrogen, when a clash is detected as part of hydrogen bond network optimization.

An issue has been fixed related to using the OEHeterogenMetadata class, where the provided SMILES string was not respected for tautomer generation; when tautomers were not provided; and when the title (residue name) collided with existing residue names in the stored Chemical Component Dictionary.
An issue has been fixed related to covalently bound ligands, where the pre-reaction input SMILES and related tautomers were not adjusted properly when accounting for the formed covalent bond.
An issue has been fixed where the Spruce filter deleted single (disconnected) amino acid residues when they were marked HETATMs and were not real “floating” residues in part of the regular protein sequence.

OEMutateResidues, OEMutateResidue, and OEBuildSidechains now reduce failures arising from clashes by using shell minimization by default.
An issue has been fixed that caused HEME-like molecules to be excluded from the stored chemical component database.

Information has been added about setting and getting minimizeSidechains and minimizeSidechainsShell options in the OESidechainBuilderOptions class.