OESuperpose

Attention

This API is currently available in C++ and Python.

class OESuperpose

This class represents OESuperpose that performs a structural superposition on fit protein to a reference protein, using a superposition method given as an optional parameter.

See also

Code Example

Constructors

OESuperpose(const OESuperposeOptions& opts = OESuperposeOptions(OESuperposeMethod::Default));

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(const OESuperpose& rhs);

Copy constructor.

operator=

OESuperpose& operator=(const OESuperpose& rhs);

Assignment operator.

HasRef

bool HasRef() const

Returns whether or not the reference is set.

HasConstraintMol

bool HasConstraintMol() const

Returns whether or not the constraint molecule is set.

Clear

void Clear();

Clears the reference and the constraint molecule.

SetOptions

bool SetOptions(const OESuperposeOptions& opts);

Sets the options for the superposition.

SetupRef

bool SetupRef(const OEBio::OEDesignUnit& refDU,
            const OESystem::OEUnaryPredicate<OEChem::OEAtomBase>& refPred=OEChem::OEIsTrueAtom())
bool SetupRef(const OEChem::OEMolBase& refMol,
            const OESystem::OEUnaryPredicate<OEChem::OEAtomBase>& refPred=OEChem::OEIsTrueAtom())
bool SetupRef(const OEChem::OEMolBase& refMol,
            const OEChem::OEMolBase& refConstraintMol,
            const OESystem::OEUnaryPredicate<OEChem::OEAtomBase>& refPred=OEChem::OEIsTrueAtom())
bool SetupRef(const OEChem::OEMolBase& refMol,
            const std::vector<std::string>& siteResidues,
            const OESystem::OEUnaryPredicate<OEChem::OEAtomBase>& refPred=OEChem::OEIsTrueAtom())
bool SetupRef(const OEChem::OEMolBase& refMol,
            const OEChem::OEMolBase& refConstraintMol,
            const std::vector<std::string>& siteResidues,
            const OESystem::OEUnaryPredicate<OEChem::OEAtomBase>& refPred=OEChem::OEIsTrueAtom())

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.

Superpose

bool Superpose(OESuperposeResults& results,
               const OEChem::OEMolBase& fitMol,
               const OESystem::OEUnaryPredicate<OEChem::OEAtomBase>& fitPred=OEChem::OEIsTrueAtom()) const
bool Superpose(OESuperposeResults& results,
               const OEChem::OEMolBase& fitMol,
               const OEChem::OEMolBase& fitConstraintMol,
               const OESystem::OEUnaryPredicate<OEChem::OEAtomBase>& fitPred=OEChem::OEIsTrueAtom()) const
bool Superpose(OESuperposeResults& results,
               const OEBio::OEDesignUnit& fitDU,
               const OESystem::OEUnaryPredicate<OEChem::OEAtomBase>& fitPred=OEChem::OEIsTrueAtom()) const

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().