numeric::alignment::QCPKernel< Real > Class Template Reference

#include <QCPKernel.hh>

Public Types
typedef Eigen::Matrix< Real, 3, 1 >	Point
typedef Eigen::Matrix< Real, 3, Eigen::Dynamic >	Coords
typedef Eigen::Map< Coords >	CoordMap

Static Public Member Functions
template<typename DerivedA , typename DerivedB >
static void	inner_product (Real *A, Real &E0, const Eigen::DenseBase< DerivedA > &first_coords, const Point &first_coords_center_of_mass, const Eigen::DenseBase< DerivedB > &second_coords, const Point &second_coords_center_of_mass)
static Real	calc_rmsd_Theobald_method (Real *A, Real E0, size_t number_of_atoms, Real *rot_matrix)
template<typename DerivedA , typename DerivedB >
static Real	calc_coordinate_rmsd (const Eigen::DenseBase< DerivedA > &first_coords, const Eigen::DenseBase< DerivedB > &second_coords)
template<typename DerivedA , typename DerivedB >
static Real	calc_coordinate_rmsd (const Eigen::DenseBase< DerivedA > &first_coords, const Point &first_coords_center_of_mass, const Eigen::DenseBase< DerivedB > &second_coords, const Point &second_coords_center_of_mass)
template<typename DerivedA , typename DerivedB >
static Real	calc_coordinate_superposition (const Eigen::DenseBase< DerivedA > &src_coords, const Point &src_center_of_mass, const Eigen::DenseBase< DerivedB > &onto_coords, const Point &onto_center_of_mass, Eigen::Transform< Real, 3, Eigen::Affine > &superposition_transform)
template<typename DerivedA , typename DerivedB >
static Real	calc_coordinate_superposition (const Eigen::DenseBase< DerivedA > &src_coords, const Eigen::DenseBase< DerivedB > &onto_coords, Eigen::Transform< Real, 3, Eigen::Affine > &superposition_transform)

Member Typedef Documentation

template<class Real>

typedef Eigen::Map< Coords > numeric::alignment::QCPKernel< Real >::CoordMap

template<class Real>

typedef Eigen::Matrix< Real, 3, Eigen::Dynamic > numeric::alignment::QCPKernel< Real >::Coords

template<class Real>

typedef Eigen::Matrix< Real, 3, 1 > numeric::alignment::QCPKernel< Real >::Point

Member Function Documentation

template<class Real>

template<typename DerivedA , typename DerivedB >

static Real numeric::alignment::QCPKernel< Real >::calc_coordinate_rmsd ( const Eigen::DenseBase< DerivedA > &  first_coords, const Eigen::DenseBase< DerivedB > &  second_coords  )

inlinestatic

Referenced by numeric::alignment::coordinate_array_broadcast_rmsd(), numeric::alignment::coordinate_array_rmsd(), numeric::coordinate_fitting::CoordinateArray_RMSD_FlatLookup< Real >::entry_distance(), and numeric::alignment::indexed_coordinate_array_broadcast_rmsd().

template<class Real>

template<typename DerivedA , typename DerivedB >

static Real numeric::alignment::QCPKernel< Real >::calc_coordinate_rmsd ( const Eigen::DenseBase< DerivedA > &  first_coords, const Point &  first_coords_center_of_mass, const Eigen::DenseBase< DerivedB > &  second_coords, const Point &  second_coords_center_of_mass  )

inlinestatic

References numeric::alignment::QCPKernel< Real >::calc_rmsd_Theobald_method(), and numeric::alignment::QCPKernel< Real >::inner_product().

template<class Real>

template<typename DerivedA , typename DerivedB >

static Real numeric::alignment::QCPKernel< Real >::calc_coordinate_superposition ( const Eigen::DenseBase< DerivedA > &  src_coords, const Point &  src_center_of_mass, const Eigen::DenseBase< DerivedB > &  onto_coords, const Point &  onto_center_of_mass, Eigen::Transform< Real, 3, Eigen::Affine > &  superposition_transform  )

inlinestatic

References numeric::alignment::QCPKernel< Real >::calc_rmsd_Theobald_method(), numeric::alignment::QCPKernel< Real >::inner_product(), basic::options::OptionKeys::AnchoredDesign::rmsd, and numeric::rotation_matrix().

Referenced by numeric::alignment::QCPKernel< Real >::calc_coordinate_superposition(), and numeric::alignment::coordinate_array_superimpose().

template<class Real>

template<typename DerivedA , typename DerivedB >

static Real numeric::alignment::QCPKernel< Real >::calc_coordinate_superposition ( const Eigen::DenseBase< DerivedA > &  src_coords, const Eigen::DenseBase< DerivedB > &  onto_coords, Eigen::Transform< Real, 3, Eigen::Affine > &  superposition_transform  )

inlinestatic

References numeric::alignment::QCPKernel< Real >::calc_coordinate_superposition().

template<class Real>

static Real numeric::alignment::QCPKernel< Real >::calc_rmsd_Theobald_method ( Real *  A, Real  E0, size_t  number_of_atoms, Real *  rot_matrix  )

inlinestatic

References a, test.Workshop3test::a2, basic::options::OptionKeys::score::fiber_diffraction::b, C, test.T009_Exceptions::e, test.T150_PyMOL_Integration::i, fmt::internal::isnan(), and basic::options::OptionKeys::motifs::z2.

Referenced by numeric::alignment::QCPKernel< Real >::calc_coordinate_rmsd(), and numeric::alignment::QCPKernel< Real >::calc_coordinate_superposition().

template<class Real>

template<typename DerivedA , typename DerivedB >

static void numeric::alignment::QCPKernel< Real >::inner_product ( Real *  A, Real &  E0, const Eigen::DenseBase< DerivedA > &  first_coords, const Point &  first_coords_center_of_mass, const Eigen::DenseBase< DerivedB > &  second_coords, const Point &  second_coords_center_of_mass  )

inlinestatic

References test.T150_PyMOL_Integration::i, basic::options::OptionKeys::motifs::z1, and basic::options::OptionKeys::motifs::z2.

Referenced by numeric::alignment::QCPKernel< Real >::calc_coordinate_rmsd(), and numeric::alignment::QCPKernel< Real >::calc_coordinate_superposition().

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The documentation for this class was generated from the following file:

• src/numeric/alignment/QCPKernel.hh