OESuperpose

Attention

This API is currently available in C++ and Python.
class OESuperpose
This class performs a structural superposition of a fit protein onto a reference protein. The superposition method (see OESuperposeMethod) and other options are controlled through the OESuperposeOptions class. Results including RMSD and TM-score are returned via OESuperposeResults.

See also

OESuperposeOptions class

OESuperposeResults class

Code Example

Calculating superposition example
Constructors
OESuperpose(opts: OESuperposeOptions = OESuperposeOptions(OESuperposeMethod_Default)) -> OESuperpose
Constructor for superposing molecules given the specified method and other options. If no OESuperposeOptions are passed in as opts, then the default behavior of using a superposition to all globally matched atoms will be used.
OESuperpose(rhs: OESuperpose) -> OESuperpose
Copy constructor.
HasRef
HasRef() -> bool
Returns whether or not the reference is set.
HasConstraintMol
HasConstraintMol() -> bool
Returns whether or not the constraint molecule is set.
Clear
Clear() -> None
Clears the reference and the constraint molecule.
SetOptions
SetOptions(opts: OESuperposeOptions) -> bool
Sets the options for the superposition.
SetupRef
SetupRef(refDU: OEDesignUnit,
         refPred: OEUnaryAtomPred = OEIsTrueAtom()) -> bool
SetupRef(refMol: Union[OEGraphMol,OEMol,OEQMol],
         refPred: OEUnaryAtomPred = OEIsTrueAtom()) -> bool
SetupRef(refMol: Union[OEGraphMol,OEMol,OEQMol],
         refConstraintMol: Union[OEGraphMol,OEMol,OEQMol],
         refPred: OEUnaryAtomPred = OEIsTrueAtom()) -> bool
SetupRef(refMol: Union[OEGraphMol,OEMol,OEQMol],
         siteResidues: OEStringVector,
         refPred: OEUnaryAtomPred = OEIsTrueAtom()) -> bool
SetupRef(refMol: Union[OEGraphMol,OEMol,OEQMol],
         refConstraintMol: Union[OEGraphMol,OEMol,OEQMol],
         siteResidues: OEStringVector,
         refPred: OEUnaryAtomPred = OEIsTrueAtom()) -> bool
Sets up the reference molecule, constraint molecule, or site residues if given. A predicate (refPred) can be passed to subset the reference. If the reference is given as an OEDesignUnit object, then the constraint molecule (ligand) and the site residues will be set if such information is available in the design unit. The function returns true if the setup is successful.

The refMol argument must have 3D coordinates assigned.

SetMethod

bool SetMethod(unsigned value)
Sets the type of superposition to be performed. Types are taken from the constants given in OESuperposeMethod.

Note

This switches the method used during superposition, but not the default, user defined, valid RMSD, seqScore, or Tanimoto values. This means switching between a shape and sequence based method requires the user to explicitly set proper values for these or, alternatively, reconstruct the class with a new method.

Superpose

Superpose(results: OESuperposeResults,
          fitMol: Union[OEGraphMol,OEMol,OEQMol],
          fitPred: OEUnaryAtomPred = OEIsTrueAtom()) -> bool
Superpose(results: OESuperposeResults,
          fitMol: Union[OEGraphMol,OEMol,OEQMol],
          fitConstraintMol: Union[OEGraphMol,OEMol,OEQMol],
          fitPred: OEUnaryAtomPred = OEIsTrueAtom()) -> bool
Superpose(results: OESuperposeResults, fitDU: OEDesignUnit,
          fitPred: OEUnaryAtomPred = OEIsTrueAtom()) -> bool

Superimposes the fit molecule onto the reference. A predicate (fitPred) can be passed to subset the reference. The results for the superposition will be stored in results. The function returns results.IsValid().