PRELIMINARY-IMAGE This is a preliminary API until Fall 2020 and may be improved based on user feedback. It is currently available in C++ and Python.

class OESecondaryStructureSuperposition

This class represents OESecondaryStructureSuperposition that performs a structural superposition on fit protein to a reference using a shape-based alignment of the secondary structure elements.

Code Example

  • spruce_examples_secondarystructuresuperposition example


OESecondaryStructureSuperposition(const OEChem::OEMolBase &refMol,
                                  const OEChem::OEMolBase &fitMol,
                                  const OESuperpositionOptions& argOpts = OESuperpositionOptions())

Constructor that superimposes the fitMol to the refMol by using a shape-based alignment to the secondary structure elements. If no OESuperpositionOptions are passed in as argOpts, then the default behavior of using a superposition to all globally matched atoms will be used.

OESecondaryStructureSuperposition(const OESecondaryStructureSuperposition &rhs)

Copy constructor.


OESecondaryStructureSuperposition &
  operator=(const OESecondaryStructureSuperposition &rhs)

Assignment operator.

operator bool

operator bool() const

Returns whether the OESecondaryStructureSuperposition object is valid.


std::vector<std::string> GetFitChains() const

Returns 1-letter code of all names of fit protein chains.


std::vector<std::string> GetRefChains() const

Returns 1-letter code of all names of reference protein chains.


bool GetRotMatrix(double *rmat) const

Returns by reference the rotation matrix of the superposition.


double GetTanimoto() const

Returns the Tanimoto score for the structural superposition.


bool GetTranslation(double *trans) const

Returns by reference the translation vector of the superposition.


void Transform(OEChem::OEMolBase& mol)

Transforms the input molecule using the stored rotation matrix and translation vector from the superposition.