SPRUCE 1.3.0

July 2021

New Features

• 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.

• An optional -out parameter 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 -warts has been added that will postfix a #n (n being an incrementing number) to the output filename.

• An OEReceptor is 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.

• The names of the available superposition methods for SPRUCE, enumsites, and superposition have been unified.

Spruce TK 1.3.0

July 2021

New features

• A molecule-based API for OEMakeDesignUnitFromPocket has been added.

• New high-level superposition APIs were added that unify the sequence-based (OEStructuralSuperposition) and shape-based (OESecondaryStructureSuperposition) APIs. This includes a new OESuperpose class that can calculate different types of structural superposition, a new OESuperposeOptions class that allows the users to control various behaviors of the superposition calculation, such as the superposition method, and a new OESuperposeResults class that holds the transformation and scores of the superposition. More detailed changes are as follows:

  • The new OESuperpose class can take either OEMol or OEDesignUnit as the reference for the fit molecule. The reference molecule can be set by using the SetupRef method, and the superposition can be calculated via OESuperpose with the fit molecule supplied as one of its arguments.

  • A new OESuperposeMethod namespace was added that contains the constants for different superposition methods. Functions OEGetSuperposeMethodName and OEGetSuperposeMethodFromName were added to obtain the superposition method’s name (as a string literal) from its designated constant and vice versa.

  • Methods OESuperposeOptions, OESuperposeOptions, and OESuperposeOptions have been added. These methods can be used to set score thresholds for validating superposition results in the new OESuperposeOptions class. The validity of the superposition result can be obtained by OESuperposeResults from the new OESuperposeResults class.

  • The new OESuperpose API returns an OESuperposeResults object that can be used to transform the fit molecule to its superposed position with its Transform method. Alternatively, the users can use GetRotMatrix and GetTranslation to 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’s GetRMSD and GetSeqScore methods for sequence-based superpositions, and the Tanimoto score can be obtained using GetTanimoto.

  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 OEDesignUnit objects to disappear when calling OEProtonateDesignUnit 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.

• An issue in OEMakeDesignUnitFromPocket that caused style to remain on both the previous binding site and the one defined from the pocket has been fixed.

• 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.

Documentation changes

• Documentation has been added for the Iridium classification. Iridium.

• Documentation has been added for the new superposition APIs. Superposition related APIs are now fully supported. Superposition.