numeric::alignment Namespace Reference

Classes
class	QCPKernel
class	rmsd_calc

Functions
template void	coordinate_array_rmsd< numeric::Real > (ndarray::Array< numeric::Real, 3, 1 > const &first_coordinates, ndarray::Array< numeric::Real, 3, 1 > const &second_coordinates, ndarray::Array< numeric::Real, 1 > out)
template void	coordinate_array_superimpose< numeric::Real > (ndarray::Array< numeric::Real, 3, 1 > const &src_coordinates, ndarray::Array< numeric::Real, 3, 1 > const &onto_coordinates, ndarray::Array< numeric::Real, 3, 1 > const &superimpose_coordinates, ndarray::Array< numeric::Real, 1 > out)
template void	coordinate_array_broadcast_rmsd< numeric::Real > (ndarray::Array< numeric::Real, 3, 1 > const &first_coordinates, ndarray::Array< numeric::Real, 3, 1 > const &second_coordinates, ndarray::Array< numeric::Real, 2 > out)
template void	indexed_coordinate_array_broadcast_rmsd< numeric::Size, numeric::Real > (numeric::Size coordinates_per_entry, ndarray::Array< numeric::Real, 2, 1 > const &first_coordinates, ndarray::Array< numeric::Size, 1 > const &first_coordinate_indicies, ndarray::Array< numeric::Real, 2, 1 > const &second_coordinates, ndarray::Array< numeric::Size, 1 > const &second_coordinate_indicies, ndarray::Array< numeric::Real, 2 > out)
template void	indexed_coordinate_array_broadcast_rmsd< numeric::SSize, numeric::Real > (numeric::SSize coordinates_per_entry, ndarray::Array< numeric::Real, 2, 1 > const &first_coordinates, ndarray::Array< numeric::SSize, 1 > const &first_coordinate_indicies, ndarray::Array< numeric::Real, 2, 1 > const &second_coordinates, ndarray::Array< numeric::SSize, 1 > const &second_coordinate_indicies, ndarray::Array< numeric::Real, 2 > out)
template void	coordinate_array_rmsd< float > (ndarray::Array< float, 3, 1 > const &first_coordinates, ndarray::Array< float, 3, 1 > const &second_coordinates, ndarray::Array< float, 1 > out)
template void	coordinate_array_superimpose< float > (ndarray::Array< float, 3, 1 > const &src_coordinates, ndarray::Array< float, 3, 1 > const &onto_coordinates, ndarray::Array< float, 3, 1 > const &superimpose_coordinates, ndarray::Array< float, 1 > out)
template void	coordinate_array_broadcast_rmsd< float > (ndarray::Array< float, 3, 1 > const &first_coordinates, ndarray::Array< float, 3, 1 > const &second_coordinates, ndarray::Array< float, 2 > out)
template void	indexed_coordinate_array_broadcast_rmsd< numeric::Size, float > (numeric::Size coordinates_per_entry, ndarray::Array< float, 2, 1 > const &first_coordinates, ndarray::Array< numeric::Size, 1 > const &first_coordinate_indicies, ndarray::Array< float, 2, 1 > const &second_coordinates, ndarray::Array< numeric::Size, 1 > const &second_coordinate_indicies, ndarray::Array< float, 2 > out)
template void	indexed_coordinate_array_broadcast_rmsd< numeric::SSize, float > (numeric::SSize coordinates_per_entry, ndarray::Array< float, 2, 1 > const &first_coordinates, ndarray::Array< numeric::SSize, 1 > const &first_coordinate_indicies, ndarray::Array< float, 2, 1 > const &second_coordinates, ndarray::Array< numeric::SSize, 1 > const &second_coordinate_indicies, ndarray::Array< float, 2 > out)
template<class Real >
void	coordinate_array_rmsd (ndarray::Array< Real, 3, 1 > const &first_coordinates, ndarray::Array< Real, 3, 1 > const &second_coordinates, ndarray::Array< Real, 1 > out)
template<class Real >
void	coordinate_array_superimpose (ndarray::Array< Real, 3, 1 > const &src_coordinates, ndarray::Array< Real, 3, 1 > const &onto_coordinates, ndarray::Array< Real, 3, 1 > const &superimpose_coordinates, ndarray::Array< Real, 1 > out)
template<class Real >
void	coordinate_array_broadcast_rmsd (ndarray::Array< Real, 3, 1 > const &first_coordinates, ndarray::Array< Real, 3, 1 > const &second_coordinates, ndarray::Array< Real, 2 > out)
template<typename Index , typename Real >
void	indexed_coordinate_array_broadcast_rmsd (Index coordinates_per_entry, ndarray::Array< Real, 2, 1 > const &first_coordinates, ndarray::Array< Index, 1 > const &first_coordinate_indicies, ndarray::Array< Real, 2, 1 > const &second_coordinates, ndarray::Array< Index, 1 > const &second_coordinate_indicies, ndarray::Array< Real, 2 > out)
template void	coordinate_array_rmsd (ndarray::Array< numeric::Real, 3, 1 > const &first_coordinates, ndarray::Array< numeric::Real, 3, 1 > const &second_coordinates, ndarray::Array< numeric::Real, 1 > out)
template void	coordinate_array_superimpose (ndarray::Array< numeric::Real, 3, 1 > const &src_coordinates, ndarray::Array< numeric::Real, 3, 1 > const &onto_coordinates, ndarray::Array< numeric::Real, 3, 1 > const &superimpose_coordinates, ndarray::Array< numeric::Real, 1 > out)
template void	coordinate_array_broadcast_rmsd (ndarray::Array< numeric::Real, 3, 1 > const &first_coordinates, ndarray::Array< numeric::Real, 3, 1 > const &second_coordinates, ndarray::Array< numeric::Real, 2 > out)
template void	indexed_coordinate_array_broadcast_rmsd (numeric::Size coordinates_per_entry, ndarray::Array< numeric::Real, 2, 1 > const &first_coordinates, ndarray::Array< numeric::Size, 1 > const &first_coordinate_indicies, ndarray::Array< numeric::Real, 2, 1 > const &second_coordinates, ndarray::Array< numeric::Size, 1 > const &second_coordinate_indicies, ndarray::Array< numeric::Real, 2 > out)
template void	indexed_coordinate_array_broadcast_rmsd (numeric::SSize coordinates_per_entry, ndarray::Array< numeric::Real, 2, 1 > const &first_coordinates, ndarray::Array< numeric::SSize, 1 > const &first_coordinate_indicies, ndarray::Array< numeric::Real, 2, 1 > const &second_coordinates, ndarray::Array< numeric::SSize, 1 > const &second_coordinate_indicies, ndarray::Array< numeric::Real, 2 > out)
template void	coordinate_array_rmsd (ndarray::Array< float, 3, 1 > const &first_coordinates, ndarray::Array< float, 3, 1 > const &second_coordinates, ndarray::Array< float, 1 > out)
template void	coordinate_array_superimpose (ndarray::Array< float, 3, 1 > const &src_coordinates, ndarray::Array< float, 3, 1 > const &onto_coordinates, ndarray::Array< float, 3, 1 > const &superimpose_coordinates, ndarray::Array< float, 1 > out)
template void	coordinate_array_broadcast_rmsd (ndarray::Array< float, 3, 1 > const &first_coordinates, ndarray::Array< float, 3, 1 > const &second_coordinates, ndarray::Array< float, 2 > out)
template void	indexed_coordinate_array_broadcast_rmsd (numeric::Size coordinates_per_entry, ndarray::Array< float, 2, 1 > const &first_coordinates, ndarray::Array< numeric::Size, 1 > const &first_coordinate_indicies, ndarray::Array< float, 2, 1 > const &second_coordinates, ndarray::Array< numeric::Size, 1 > const &second_coordinate_indicies, ndarray::Array< float, 2 > out)
template void	indexed_coordinate_array_broadcast_rmsd (numeric::SSize coordinates_per_entry, ndarray::Array< float, 2, 1 > const &first_coordinates, ndarray::Array< numeric::SSize, 1 > const &first_coordinate_indicies, ndarray::Array< float, 2, 1 > const &second_coordinates, ndarray::Array< numeric::SSize, 1 > const &second_coordinate_indicies, ndarray::Array< float, 2 > out)
template<typename Module >
void	bind_rmsd_calc (Module &m)

Function Documentation

bind_rmsd_calc()

template<typename Module >

void numeric::alignment::bind_rmsd_calc

(

Module &

m

)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::m.

coordinate_array_broadcast_rmsd() [1/3]

template void numeric::alignment::coordinate_array_broadcast_rmsd	(	ndarray::Array< float, 3, 1 > const &	first_coordinates,
		ndarray::Array< float, 3, 1 > const &	second_coordinates,
		ndarray::Array< float, 2 >	out
	)

coordinate_array_broadcast_rmsd() [2/3]

template void numeric::alignment::coordinate_array_broadcast_rmsd	(	ndarray::Array< numeric::Real, 3, 1 > const &	first_coordinates,
		ndarray::Array< numeric::Real, 3, 1 > const &	second_coordinates,
		ndarray::Array< numeric::Real, 2 >	out
	)

coordinate_array_broadcast_rmsd() [3/3]

template<class Real >

void numeric::alignment::coordinate_array_broadcast_rmsd	(	ndarray::Array< Real, 3, 1 > const &	first_coordinates,
		ndarray::Array< Real, 3, 1 > const &	second_coordinates,
		ndarray::Array< Real, 2 >	out
	)

References numeric::alignment::QCPKernel< Real >::calc_coordinate_rmsd(), create_a3b_hbs::i, create_a3b_hbs::j, and erraser_single_res_analysis::out.

coordinate_array_broadcast_rmsd< float >()

template void numeric::alignment::coordinate_array_broadcast_rmsd< float >	(	ndarray::Array< float, 3, 1 > const &	first_coordinates,
		ndarray::Array< float, 3, 1 > const &	second_coordinates,
		ndarray::Array< float, 2 >	out
	)

coordinate_array_broadcast_rmsd< numeric::Real >()

template void numeric::alignment::coordinate_array_broadcast_rmsd< numeric::Real >	(	ndarray::Array< numeric::Real, 3, 1 > const &	first_coordinates,
		ndarray::Array< numeric::Real, 3, 1 > const &	second_coordinates,
		ndarray::Array< numeric::Real, 2 >	out
	)

coordinate_array_rmsd() [1/3]

template void numeric::alignment::coordinate_array_rmsd	(	ndarray::Array< float, 3, 1 > const &	first_coordinates,
		ndarray::Array< float, 3, 1 > const &	second_coordinates,
		ndarray::Array< float, 1 >	out
	)

coordinate_array_rmsd() [2/3]

template void numeric::alignment::coordinate_array_rmsd	(	ndarray::Array< numeric::Real, 3, 1 > const &	first_coordinates,
		ndarray::Array< numeric::Real, 3, 1 > const &	second_coordinates,
		ndarray::Array< numeric::Real, 1 >	out
	)

coordinate_array_rmsd() [3/3]

template<class Real >

void numeric::alignment::coordinate_array_rmsd	(	ndarray::Array< Real, 3, 1 > const &	first_coordinates,
		ndarray::Array< Real, 3, 1 > const &	second_coordinates,
		ndarray::Array< Real, 1 >	out
	)

References numeric::alignment::QCPKernel< Real >::calc_coordinate_rmsd(), create_a3b_hbs::i, create_a3b_hbs::j, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, and erraser_single_res_analysis::out.

coordinate_array_rmsd< float >()

template void numeric::alignment::coordinate_array_rmsd< float >	(	ndarray::Array< float, 3, 1 > const &	first_coordinates,
		ndarray::Array< float, 3, 1 > const &	second_coordinates,
		ndarray::Array< float, 1 >	out
	)

coordinate_array_rmsd< numeric::Real >()

template void numeric::alignment::coordinate_array_rmsd< numeric::Real >	(	ndarray::Array< numeric::Real, 3, 1 > const &	first_coordinates,
		ndarray::Array< numeric::Real, 3, 1 > const &	second_coordinates,
		ndarray::Array< numeric::Real, 1 >	out
	)

coordinate_array_superimpose() [1/3]

template void numeric::alignment::coordinate_array_superimpose	(	ndarray::Array< float, 3, 1 > const &	src_coordinates,
		ndarray::Array< float, 3, 1 > const &	onto_coordinates,
		ndarray::Array< float, 3, 1 > const &	superimpose_coordinates,
		ndarray::Array< float, 1 >	out
	)

coordinate_array_superimpose() [2/3]

template void numeric::alignment::coordinate_array_superimpose	(	ndarray::Array< numeric::Real, 3, 1 > const &	src_coordinates,
		ndarray::Array< numeric::Real, 3, 1 > const &	onto_coordinates,
		ndarray::Array< numeric::Real, 3, 1 > const &	superimpose_coordinates,
		ndarray::Array< numeric::Real, 1 >	out
	)

coordinate_array_superimpose() [3/3]

template<class Real >

void numeric::alignment::coordinate_array_superimpose	(	ndarray::Array< Real, 3, 1 > const &	src_coordinates,
		ndarray::Array< Real, 3, 1 > const &	onto_coordinates,
		ndarray::Array< Real, 3, 1 > const &	superimpose_coordinates,
		ndarray::Array< Real, 1 >	out
	)

References numeric::alignment::QCPKernel< Real >::calc_coordinate_superposition(), create_a3b_hbs::i, and erraser_single_res_analysis::out.

coordinate_array_superimpose< float >()

template void numeric::alignment::coordinate_array_superimpose< float >	(	ndarray::Array< float, 3, 1 > const &	src_coordinates,
		ndarray::Array< float, 3, 1 > const &	onto_coordinates,
		ndarray::Array< float, 3, 1 > const &	superimpose_coordinates,
		ndarray::Array< float, 1 >	out
	)

coordinate_array_superimpose< numeric::Real >()

template void numeric::alignment::coordinate_array_superimpose< numeric::Real >	(	ndarray::Array< numeric::Real, 3, 1 > const &	src_coordinates,
		ndarray::Array< numeric::Real, 3, 1 > const &	onto_coordinates,
		ndarray::Array< numeric::Real, 3, 1 > const &	superimpose_coordinates,
		ndarray::Array< numeric::Real, 1 >	out
	)

indexed_coordinate_array_broadcast_rmsd() [1/5]

template<typename Index , typename Real >

void numeric::alignment::indexed_coordinate_array_broadcast_rmsd	(	Index	coordinates_per_entry,
		ndarray::Array< Real, 2, 1 > const &	first_coordinates,
		ndarray::Array< Index, 1 > const &	first_coordinate_indicies,
		ndarray::Array< Real, 2, 1 > const &	second_coordinates,
		ndarray::Array< Index, 1 > const &	second_coordinate_indicies,
		ndarray::Array< Real, 2 >	out
	)

References numeric::alignment::QCPKernel< Real >::calc_coordinate_rmsd(), create_a3b_hbs::i, create_a3b_hbs::j, and erraser_single_res_analysis::out.

indexed_coordinate_array_broadcast_rmsd() [2/5]

template void numeric::alignment::indexed_coordinate_array_broadcast_rmsd	(	numeric::Size	coordinates_per_entry,
		ndarray::Array< float, 2, 1 > const &	first_coordinates,
		ndarray::Array< numeric::Size, 1 > const &	first_coordinate_indicies,
		ndarray::Array< float, 2, 1 > const &	second_coordinates,
		ndarray::Array< numeric::Size, 1 > const &	second_coordinate_indicies,
		ndarray::Array< float, 2 >	out
	)

indexed_coordinate_array_broadcast_rmsd() [3/5]

template void numeric::alignment::indexed_coordinate_array_broadcast_rmsd	(	numeric::Size	coordinates_per_entry,
		ndarray::Array< numeric::Real, 2, 1 > const &	first_coordinates,
		ndarray::Array< numeric::Size, 1 > const &	first_coordinate_indicies,
		ndarray::Array< numeric::Real, 2, 1 > const &	second_coordinates,
		ndarray::Array< numeric::Size, 1 > const &	second_coordinate_indicies,
		ndarray::Array< numeric::Real, 2 >	out
	)

indexed_coordinate_array_broadcast_rmsd() [4/5]

template void numeric::alignment::indexed_coordinate_array_broadcast_rmsd	(	numeric::SSize	coordinates_per_entry,
		ndarray::Array< float, 2, 1 > const &	first_coordinates,
		ndarray::Array< numeric::SSize, 1 > const &	first_coordinate_indicies,
		ndarray::Array< float, 2, 1 > const &	second_coordinates,
		ndarray::Array< numeric::SSize, 1 > const &	second_coordinate_indicies,
		ndarray::Array< float, 2 >	out
	)

indexed_coordinate_array_broadcast_rmsd() [5/5]

template void numeric::alignment::indexed_coordinate_array_broadcast_rmsd	(	numeric::SSize	coordinates_per_entry,
		ndarray::Array< numeric::Real, 2, 1 > const &	first_coordinates,
		ndarray::Array< numeric::SSize, 1 > const &	first_coordinate_indicies,
		ndarray::Array< numeric::Real, 2, 1 > const &	second_coordinates,
		ndarray::Array< numeric::SSize, 1 > const &	second_coordinate_indicies,
		ndarray::Array< numeric::Real, 2 >	out
	)

indexed_coordinate_array_broadcast_rmsd< numeric::Size, float >()

template void numeric::alignment::indexed_coordinate_array_broadcast_rmsd< numeric::Size, float >	(	numeric::Size	coordinates_per_entry,
		ndarray::Array< float, 2, 1 > const &	first_coordinates,
		ndarray::Array< numeric::Size, 1 > const &	first_coordinate_indicies,
		ndarray::Array< float, 2, 1 > const &	second_coordinates,
		ndarray::Array< numeric::Size, 1 > const &	second_coordinate_indicies,
		ndarray::Array< float, 2 >	out
	)

indexed_coordinate_array_broadcast_rmsd< numeric::Size, numeric::Real >()

template void numeric::alignment::indexed_coordinate_array_broadcast_rmsd< numeric::Size, numeric::Real >	(	numeric::Size	coordinates_per_entry,
		ndarray::Array< numeric::Real, 2, 1 > const &	first_coordinates,
		ndarray::Array< numeric::Size, 1 > const &	first_coordinate_indicies,
		ndarray::Array< numeric::Real, 2, 1 > const &	second_coordinates,
		ndarray::Array< numeric::Size, 1 > const &	second_coordinate_indicies,
		ndarray::Array< numeric::Real, 2 >	out
	)

indexed_coordinate_array_broadcast_rmsd< numeric::SSize, float >()

template void numeric::alignment::indexed_coordinate_array_broadcast_rmsd< numeric::SSize, float >	(	numeric::SSize	coordinates_per_entry,
		ndarray::Array< float, 2, 1 > const &	first_coordinates,
		ndarray::Array< numeric::SSize, 1 > const &	first_coordinate_indicies,
		ndarray::Array< float, 2, 1 > const &	second_coordinates,
		ndarray::Array< numeric::SSize, 1 > const &	second_coordinate_indicies,
		ndarray::Array< float, 2 >	out
	)

indexed_coordinate_array_broadcast_rmsd< numeric::SSize, numeric::Real >()

template void numeric::alignment::indexed_coordinate_array_broadcast_rmsd< numeric::SSize, numeric::Real >	(	numeric::SSize	coordinates_per_entry,
		ndarray::Array< numeric::Real, 2, 1 > const &	first_coordinates,
		ndarray::Array< numeric::SSize, 1 > const &	first_coordinate_indicies,
		ndarray::Array< numeric::Real, 2, 1 > const &	second_coordinates,
		ndarray::Array< numeric::SSize, 1 > const &	second_coordinate_indicies,
		ndarray::Array< numeric::Real, 2 >	out
	)