Spruce TK 1.3.0¶
June 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 newOESuperpose
class that can calculate different types of structural superposition, a newOESuperposeOptions
class that allows the users to control various behaviors of the superposition calculation, such as the superposition method, and a newOESuperposeResults
class that holds the transformation and scores of the superposition. More detailed changes are as follows:The new
OESuperpose
class can take eitherOEMol
orOEDesignUnit
as the reference for the fit molecule. The reference molecule can be set by using theOESuperpose.SetupRef
method, and the superposition can be calculated viaOESuperpose.Superpose
with the fit molecule supplied as one of its arguments.A new
OESuperposeMethod
namespace was added that contains the constants for different superposition methods. FunctionsOEGetSuperposeMethodName
andOEGetSuperposeMethodFromName
were added to obtain the superposition method’s name (as a string literal) from its designated constant and vice versa.Methods
OESuperposeOptions.SetValidRMSD
,OESuperposeOptions.SetValidSeqScore
, andOESuperposeOptions.SetValidTanimoto
have been added. These methods can be used to set score thresholds for validating superposition results in the newOESuperposeOptions
class. The validity of the superposition result can be obtained byOESuperposeResults.IsValid
from the newOESuperposeResults
class.The new
OESuperpose
API returns anOESuperposeResults
object that can be used to transform the fit molecule to its superposed position with itsOESuperposeResults.Transform
method. Alternatively, the users can useOESuperposeResults.GetRotMatrix
andOESuperposeResults.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 usingOESuperposeResults
’sOESuperposeResults.GetRMSD
andOESuperposeResults.GetSeqScore
methods for sequence-based superpositions, and the Tanimoto score can be obtained usingOESuperposeResults.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
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.