Spruce TK 1.1.0

New features

  • Two new APIs, OEBuildSingleLoop and OEBuildLoops, have been added that provide loop modeling capability. This capability relies on either the SEQRES in the PDB header (or equivalent for MMCIF files) or the user passing metadata about the sequences. The functions take an options class, OELoopBuilderOptions, as an argument to specify the file name of the required loop template database. This database is available for download in a platform-independent format.

  • A new parameter, siteResidue, has been added to the OEMakeDesignUnits function. This allows users to specify a single residue in the binding site for APO structures when using the OEEnumerateSites function. The function checks whether the detected site has a large enough volume and whether there is anything in the binding site that the splitter failed to identify as a potential ligand.

  • The options class OEDesignUnitBuildOptions has been updated to hold options classes for the different builder options available. This also changes the options class structure for OEMakeDesignUnitOptions.

  • A new low level class, OECapBuilderOptions, that determines behavior when building caps on proteins, has been added to replace passing different parameters to the functions OECapTermini, OECapNTermini, and OECapCTermini.

  • OESidechainBuilderOptions, a low level class that determines the behavior when building sidechains on proteins, replaces passing different parameters to the function OEBuildSidechains.

  • The preliminary API options class OEDesignUnitMutationOptions has been removed. OEMutateResidues has been added to take a map of mutations, along with OESidechainBuilderOptions to control the behavior when building the mutated residue sidechain.

  • A new function, OEFixBackbone, has been added that builds =O and/or OXT, if necessary, and ensures that all formal charges and valence states are correct on all backbone atoms. The function removes a residue completely if the primary backbone atoms, N, CA, and C, are missing. The residues can be built correctly later with OEBuildLoops.

  • A strict protonation mode has been added to OEDesignUnitPrepOptions, enforcing that when an error occurs during addition and optimization of hydrogens to the system, the preparation processes now stop and fail.

  • A new options class, OEPlaceHydrogensOptions, has been added to OEProtonateDesignUnitOptions. This option allows users more control over the protonation processes; for example, by passing a bypass or no-flip predicate that will prevent the protonation process from altering the residues in the predicate.

  • The design units produced by OEMakeDesignUnits are now ordered by the quality of the Iridium classification data.

Major bug fixes

  • A bug in OEExtractBioUnits that occurred when using a reference has been fixed. Previously, it resulted in incorrect biological units being produced under certain conditions. The algorithm has also been improved to more often produce the correct biological unit based on symmetry expansion.

Minor bug fixes

  • Metal co-factors previously had not been properly identified in the binding site during design unit generation due to the distance threshold from a ligand that was too strict. This has been fixed.

  • Ligands with an incorrect alternate location assignment but that were in the same location were previously not correctly identified and were assigned alternate locations. This was due to the threshold being too strict and has been fixed.

  • In cases where a residue is itself converted to a cap and where building a cap would result in the cap strongly clashing, the cap number no longer adds an insert code or alters the residue number. In addition, valence states resulting from the residue conversion are being more thoroughly validated and fixed, if necessary.

  • Some instances of functions changing the location of the OEThrow output and their levels have been fixed.

  • An issue in OEExtractBioUnits had previously occurred when structures with the historical convention of putting waters and metals into specific chain IDs (i.e., W and S, respectively) caused the molecules, after symmetry expansion, to have identical residue information. This has been fixed.

  • An issue with the side-chain builder miscounting side-chain atoms when involving a residue in cross-linking has been fixed.

  • An issue that occurred when a single ligand atom (per design) was not properly detected as a ligand has been fixed.

Documentation changes

  • Documentation and examples have been modified to omit the step where alternate locations are collapsed. The function OEMakeDesignUnits handles alternate location collapse or enumeration and should provide all available data.

  • Examples in C++ and Python have been enhanced to include passing electron density maps, and a new example has been added for making APO design units using a site residue or reference structure. The examples also illustrate how to enable Spruce TK to build missing loops.