getstructure now retrieves structures using a secure HTTPS connection using openSSL.
A no-prep option has been added to SPRUCE to enable conversion of prepared structures into the OEDesignUnit format. This option supersedes all other options.
-outparameter has been added to SPRUCE, for specifying the output filename. SPRUCE can write multiple design units per PDB file, and the default option is to write all of them to the single specified file. An additional option
-wartshas been added that will postfix a #n (n being an incrementing number) to the output filename.
OEReceptoris now added by default when using SPRUCE. The feature can be turned off using the -add_receptors false flag. A -targetMask can be specified to augment the receptor content. Furthermore, these OEDesignUnits with receptors can be further edited in the make_receptor GUI application.
Options for setting the RMSD, sequence alignment score, and Tanimoto thresholds for validating the superposition result have been added to superposition.
Spruce TK 1.3.0¶
A molecule-based API for
OEMakeDesignUnitFromPockethas been added.
New high-level superposition APIs were added that unify the sequence-based (
OEStructuralSuperposition) and shape-based (
OESecondaryStructureSuperposition) APIs. This includes new classes:
OESuperposethat calculates different types of structural superposition.
OESuperposeOptionsthat allows users to control various behaviors of the superposition calculation (e.g. the superposition method).
OESuperposeResultswhich contains the transformation and scores of the superposition.
More detailed changes are as follows:
OESuperposeclass can take either
OEDesignUnitas the reference for the fit molecule(s). The reference molecule can be set by using the
OESuperpose.SetupRefmethod, and the superposition can be calculated via
OESuperpose.Superposewith the fit molecule supplied as one of its arguments.
OESuperposeMethodnamespace was added that contains the constants for different superposition methods. Functions
OEGetSuperposeMethodFromNamewere added to obtain the superposition method’s name (as a string literal) from its designated constant and vice versa.
OESuperposeOptions.SetValidTanimotohave been added. These methods can be used to set score thresholds for validating superposition results in the new
OESuperposeOptionsclass. The validity of the superposition result can be obtained by
OESuperposeResults.IsValidfrom the new
OESuperposeAPI returns an
OESuperposeResultsobject that can be used to transform the fit molecule to its superposed position with its
OESuperposeResults.Transformmethod. Alternatively, users can use
OESuperposeResults.GetTranslationto obtain the rotation matrix and translation vector, respectively, for their analyses. The RMSD and sequence alignment score after the superposition can be obtained using
OESuperposeResults.GetSeqScoremethods for sequence-based superpositions, and the Tanimoto score can be obtained using
Please refer to the documentation for more information on these new superposition APIs.
Minor bug fixes¶
A bug that caused the loop modeling algorithm to crash in rare instances has been fixed.
Examples have been modified to use appropriate command-line arguments.
An issue that caused style on
OEProtonateDesignUnithas been fixed.
An issue in
OEMakeDesignUnitFromPocketthat caused style to remain on both the previous binding site and the one defined from the pocket has been fixed.
An issue with the return value of superposition when two structures cannot be superposed has been fixed. It now properly returns a -1.00 RMSD.
A bug in superposition that resulted in a crash when using site residues that were not present on a design unit has been fixed.
A bug that kept the insert code from its anchor residue when there was an N-terminal cap has been fixed.