Namespaces
	periodic_range

	spline

Classes
class	Histogram
	A histogram with fixed-width bins. More...

struct	HistogramOP

struct	HistogramCOP

struct	HistogramAP

struct	HistogramCAP

class	InterpolatedPotential

struct	TempStruct

struct	TempStruct< T, 1 >

Enumerations
enum	CatmullRomSplineBoundaryType { PERIODIC , FLAT , LINEAR }

enum class	SplineFromStreamMode { none = 0 , x_axis , y_axis , lb_or_ub_function }
	A little helper enum to determine what I'm reading right now in the spline_from_stream() function. More...

Functions
template<Size N>
void	polycubic_interpolation (numeric::interpolation::InterpolatedPotential< N > const &interpolated_potential, utility::fixedsizearray1< Real, N > const &values, Real &score, utility::fixedsizearray1< Real, N > &dscoreddof)

template<typename X , typename F >
F	interpolated (X const &x, X const &x1, X const &x2, F const &f1, F const &f2)
	Linearly interpolated value: f( x ) More...

template<typename X , typename F >
F	interpolated (X const &a, F const &f1, F const &f2)
	Linearly interpolated value: f( x ) More...

template<typename X , typename F >
F	interpolated_delta (X const &a, F const &f1, F const &f2)
	Linearly interpolated delta value: f( x ) - f1. More...

template<typename X , typename Y , typename F >
F	bilinearly_interpolated (X const &x, X const &x1, X const &x2, Y const &y, Y const &y1, Y const &y2, F const &f11, F const &f12, F const &f21, F const &f22)
	Bilinearly interpolated value: f( x, y ) More...

template<typename X , typename Y , typename F >
F	bilinearly_interpolated (X const &ax, Y const &ay, F const &f11, F const &f12, F const &f21, F const &f22)
	Bilinearly interpolated value. More...

template<typename X , typename Y , typename F >
F	bilinearly_interpolated (X const &ax, Y const &ay, X const &bx, Y const &by, F const &f11, F const &f12, F const &f21, F const &f22)
	Bilinearly interpolated value. More...

template<typename T , numeric::Size N>
Real	multilinear_interpolation (MathNTensor< T, N > const &tensor, utility::fixedsizearray1< Real, N > const &minval, utility::fixedsizearray1< Real, N > const &binwidth, utility::fixedsizearray1< Real, N > const &xs, utility::fixedsizearray1< Real, N > &deriv, bool const &compute_deriv=true)
	Perform multilinear interpolation over an N-dimensional tensor, with derivatives. More...

template<typename T , numeric::Size N>
numeric::Real	multilinear_interpolation (numeric::MathNTensor< T, N > const &tensor, utility::fixedsizearray1< numeric::Real, N > const &minval, utility::fixedsizearray1< numeric::Real, N > const &binwidth, utility::fixedsizearray1< numeric::Real, N > const &xs)
	Perform multilinear interpolation over an N-dimensional tensor (without derivative computation) More...

template<Size N>
void	polycubic_interpolation (utility::fixedsizearray1< utility::fixedsizearray1< Real,(1<< N) >,(1<< N) > n_derivs, utility::fixedsizearray1< Real, N > dbbp, utility::fixedsizearray1< Real, N > binwbb, Real &val, utility::fixedsizearray1< Real, N > &dvaldbb)
	Perform cubic interpolation over each of N axes, using the 2^N derivatives at 2^N gridpoints. More...

std::string	to_string (CatmullRomSplineBoundaryType const &type)

template<typename T >
T	catmull_rom_interpolate_basic (utility::fixedsizearray1< T, 4 > const &p, Real const &x, Real &dval_dx, utility::fixedsizearray1< T, 4 > &dval_dp, bool const compute_deriv=true)

template<typename T >
T	catmull_rom_interpolate_basic (utility::fixedsizearray1< T, 4 > const &p, T const &x, T &dval_dx, bool const compute_deriv=true)

template<typename T >
T	catmull_rom_interpolate_basic (utility::fixedsizearray1< T, 4 > const &p, T const &x)

template<typename T , numeric::Size N>
T	catmull_rom_interpolate (utility::fixedsizearray1< T, 1<<(2 *N) > const &F_patch, utility::fixedsizearray1< T, N > const &d, utility::fixedsizearray1< T, N > &deriv, bool const compute_deriv)

template<typename T , numeric::Size N>
T	get_val (MathNTensor< T, N > const &F, utility::fixedsizearray1< int, N > &idx, utility::fixedsizearray1< CatmullRomSplineBoundaryType, N > const &boundary, Size const which_dim)

template<typename T , numeric::Size N>
void	get_patch (utility::fixedsizearray1< T, 1<<(2 *N) > &F_patch, utility::fixedsizearray1< Real, N > &d, MathNTensor< T, N > const &F, utility::fixedsizearray1< Real, N > const &minval, utility::fixedsizearray1< Real, N > const &binwidth, utility::fixedsizearray1< Real, N > const &xs, utility::fixedsizearray1< CatmullRomSplineBoundaryType, N > const &boundary)

template<typename T , numeric::Size N>
T	polycubic_interpolate_catmull_rom (MathNTensor< T, N > const &F, utility::fixedsizearray1< Real, N > const &minval, utility::fixedsizearray1< Real, N > const &binwidth, utility::fixedsizearray1< Real, N > const &xs, utility::fixedsizearray1< CatmullRomSplineBoundaryType, N > const &boundary, utility::fixedsizearray1< Real, N > &deriv, bool const &compute_deriv=true)
	Catmull-Rom spline interpolation of an N-dimensional tensor defined on a equispaced grid. More...

template<typename T , numeric::Size N>
T	polycubic_interpolate_catmull_rom (MathNTensor< T, N > const &F, utility::fixedsizearray1< Real, N > const &minval, utility::fixedsizearray1< Real, N > const &binwidth, utility::fixedsizearray1< Real, N > const &xs, utility::fixedsizearray1< CatmullRomSplineBoundaryType, N > const &boundary)
	Catmull-Rom spline interpolation of an N-dimensional tensor defined on a equispaced grid, without derivative computation. More...

spline::SplineGenerator	make_spline (utility::vector1< platform::Real > const &bins_vect, utility::vector1< platform::Real > const &potential_vect, platform::Real const bin_size, utility::vector1< std::tuple< std::string, platform::Real, platform::Real, platform::Real >> const &boundary_functions=utility::vector1< std::tuple< std::string, platform::Real, platform::Real, platform::Real >>())
	given a file, return a 2D spline More...

spline::SplineGenerator	spline_from_file (std::string const &filename, platform::Real const bin_size)

spline::SplineGenerator	spline_from_stream (std::istream &iss, platform::Real const bin_size)
	Initialize a SplineGenerator from a std::istream. Note: only reads from the currenet line of the istream. More...

Enumeration Type Documentation

◆ CatmullRomSplineBoundaryType

enum numeric::interpolation::CatmullRomSplineBoundaryType

Enumerator
PERIODIC
FLAT
LINEAR

◆ SplineFromStreamMode

enum numeric::interpolation::SplineFromStreamMode

strong

A little helper enum to determine what I'm reading right now in the spline_from_stream() function.

Author: Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

Enumerator
none
x_axis
y_axis
lb_or_ub_function

Function Documentation

◆ bilinearly_interpolated() [1/3]

template<typename X , typename Y , typename F >

F numeric::interpolation::bilinearly_interpolated	(	X const &	ax,
		Y const &	ay,
		F const &	f11,
		F const &	f12,
		F const &	f21,
		F const &	f22
	)

inline

Bilinearly interpolated value.

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::ax, and spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::Y.

◆ bilinearly_interpolated() [2/3]

template<typename X , typename Y , typename F >

F numeric::interpolation::bilinearly_interpolated	(	X const &	ax,
		Y const &	ay,
		X const &	bx,
		Y const &	by,
		F const &	f11,
		F const &	f12,
		F const &	f21,
		F const &	f22
	)

inline

Bilinearly interpolated value.

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::ax, numeric::eq_tol(), and spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::Y.

◆ bilinearly_interpolated() [3/3]

template<typename X , typename Y , typename F >

F numeric::interpolation::bilinearly_interpolated	(	X const &	x,
		X const &	x1,
		X const &	x2,
		Y const &	y,
		Y const &	y1,
		Y const &	y2,
		F const &	f11,
		F const &	f12,
		F const &	f21,
		F const &	f22
	)

inline

Bilinearly interpolated value: f( x, y )

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::ax, x, predPRE::y, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::Y, y1, and y2.

◆ catmull_rom_interpolate()

template<typename T , numeric::Size N>

T numeric::interpolation::catmull_rom_interpolate ( )

inline

Referenced by polycubic_interpolate_catmull_rom().

◆ catmull_rom_interpolate_basic() [1/3]

template<typename T >

T numeric::interpolation::catmull_rom_interpolate_basic	(	utility::fixedsizearray1< T, 4 > const &	p,
		Real const &	x,
		Real &	dval_dx,
		utility::fixedsizearray1< T, 4 > &	dval_dp,
		bool const	compute_deriv = `true`
	)

inline

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, and x.

Referenced by catmull_rom_interpolate_basic(), numeric::interpolation::TempStruct< T, N >::operator()(), and numeric::interpolation::TempStruct< T, 1 >::operator()().

◆ catmull_rom_interpolate_basic() [2/3]

template<typename T >

T numeric::interpolation::catmull_rom_interpolate_basic	(	utility::fixedsizearray1< T, 4 > const &	p,
		T const &	x
	)

inline

References catmull_rom_interpolate_basic(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, and x.

◆ catmull_rom_interpolate_basic() [3/3]

template<typename T >

T numeric::interpolation::catmull_rom_interpolate_basic	(	utility::fixedsizearray1< T, 4 > const &	p,
		T const &	x,
		T &	dval_dx,
		bool const	compute_deriv = `true`
	)

inline

References catmull_rom_interpolate_basic(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, and x.

◆ get_patch()

template<typename T , numeric::Size N>

void numeric::interpolation::get_patch ( )

inline

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, ObjexxFCL::format::F(), get_val(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::idx, enumerate_junctions::int, create_a3b_hbs::k, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, N, ObjexxFCL::pow(), runtime_assert, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::xs.

Referenced by polycubic_interpolate_catmull_rom().

◆ get_val()

template<typename T , numeric::Size N>

T numeric::interpolation::get_val	(	MathNTensor< T, N > const &	F,
		utility::fixedsizearray1< int, N > &	idx,
		utility::fixedsizearray1< CatmullRomSplineBoundaryType, N > const &	boundary,
		Size const	which_dim
	)

inline

References enumerate_junctions::default, ObjexxFCL::format::F(), FLAT, kmeans_adaptive_kernel_density_bb_dependent_rotlib::idx, LINEAR, utility::modulo(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, N, PERIODIC, runtime_assert, and utility_exit_with_message.

Referenced by get_patch().

◆ interpolated() [1/2]

template<typename X , typename F >

F numeric::interpolation::interpolated	(	X const &	a,
		F const &	f1,
		F const &	f2
	)

inline

Linearly interpolated value: f( x )

Note: Extrapolates if a not in [ 0, 1 ]

References a, and vancomycin::f2.

◆ interpolated() [2/2]

template<typename X , typename F >

F numeric::interpolation::interpolated	(	X const &	x,
		X const &	x1,
		X const &	x2,
		F const &	f1,
		F const &	f2
	)

inline

Linearly interpolated value: f( x )

Note: Extrapolates if x not in [ x1, x2 ]

References vancomycin::f2, and x.

Referenced by numeric::interpolation::Histogram< X, Y >::interpolate_linear(), numeric::interpolation::periodic_range::full::interpolated(), and numeric::interpolation::periodic_range::half::interpolated().

◆ interpolated_delta()

template<typename X , typename F >

F numeric::interpolation::interpolated_delta	(	X const &	a,
		F const &	f1,
		F const &	f2
	)

inline

Linearly interpolated delta value: f( x ) - f1.

Note: Extrapolates if a not in [ 0, 1 ]

References a, and vancomycin::f2.

◆ make_spline()

spline::SplineGenerator numeric::interpolation::make_spline	(	utility::vector1< platform::Real > const &	bins_vect,
		utility::vector1< platform::Real > const &	potential_vect,
		platform::Real const	bin_size,
		utility::vector1< std::tuple< std::string, platform::Real, platform::Real, platform::Real >> const &	boundary_functions
	)

given a file, return a 2D spline

Easier make a spline wrapper from code

References numeric::interpolation::spline::SplineGenerator::add_boundary_function(), numeric::interpolation::spline::SplineGenerator::add_known_value(), a3b_test::bin_size, challenge::ss, and utility_exit_with_message.

Referenced by spline_from_file(), and spline_from_stream().

◆ multilinear_interpolation() [1/2]

template<typename T , numeric::Size N>

Real numeric::interpolation::multilinear_interpolation	(	MathNTensor< T, N > const &	tensor,
		utility::fixedsizearray1< Real, N > const &	minval,
		utility::fixedsizearray1< Real, N > const &	binwidth,
		utility::fixedsizearray1< Real, N > const &	xs,
		utility::fixedsizearray1< Real, N > &	deriv,
		bool const &	compute_deriv = `true`
	)

Perform multilinear interpolation over an N-dimensional tensor, with derivatives.

Straightforward generalization of bilinear interpolation. Currently extrapolates linearly when asked for point outside tensor range TODO: allow periodic; allow different extrapolation behavior (e.g., constant).

Parameters

[in]	tensor	is the data array, using MathNTensor
[in]	minval	is the tensor's minimum value in each direction.
[in]	binwidth	is the bin width in each direction
[in]	xs	is the position
[out]	deriv	is the interpolated derivative
[in]	compute_deriv	– set to false to reduce computation

Author: rhiju

References a, numeric::interpolation::periodic_range::half::bin(), create_a3b_hbs::i, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, max(), min(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, N, numeric::MathNTensor< T, N >::n_bins(), offset, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::xs.

Referenced by check_multilinear_interpolation(), and multilinear_interpolation().

◆ multilinear_interpolation() [2/2]

template<typename T , numeric::Size N>

numeric::Real numeric::interpolation::multilinear_interpolation	(	numeric::MathNTensor< T, N > const &	tensor,
		utility::fixedsizearray1< numeric::Real, N > const &	minval,
		utility::fixedsizearray1< numeric::Real, N > const &	binwidth,
		utility::fixedsizearray1< numeric::Real, N > const &	xs
	)

inline

Perform multilinear interpolation over an N-dimensional tensor (without derivative computation)

Straightforward generalization of bilinear interpolation. Currently extrapolates linearly when asked for point outside tensor range TODO: allow periodic; allow different extrapolation behavior (e.g., constant).

Parameters

[in]	tensor	is the data array, using MathNTensor
[in]	minval	is the tensor's minimum value in each direction.
[in]	xs	is the position at which to evaluate spline
[in]	binwidth	is the bin width in each direction

Author: rhiju

References multilinear_interpolation(), and kmeans_adaptive_kernel_density_bb_dependent_rotlib::xs.

◆ polycubic_interpolate_catmull_rom() [1/2]

template<typename T , numeric::Size N>

T numeric::interpolation::polycubic_interpolate_catmull_rom	(	MathNTensor< T, N > const &	F,
		utility::fixedsizearray1< Real, N > const &	minval,
		utility::fixedsizearray1< Real, N > const &	binwidth,
		utility::fixedsizearray1< Real, N > const &	xs,
		utility::fixedsizearray1< CatmullRomSplineBoundaryType, N > const &	boundary
	)

inline

Catmull-Rom spline interpolation of an N-dimensional tensor defined on a equispaced grid, without derivative computation.

References ObjexxFCL::format::F(), polycubic_interpolate_catmull_rom(), and kmeans_adaptive_kernel_density_bb_dependent_rotlib::xs.

◆ polycubic_interpolate_catmull_rom() [2/2]

template<typename T , numeric::Size N>

T numeric::interpolation::polycubic_interpolate_catmull_rom	(	MathNTensor< T, N > const &	F,
		utility::fixedsizearray1< Real, N > const &	minval,
		utility::fixedsizearray1< Real, N > const &	binwidth,
		utility::fixedsizearray1< Real, N > const &	xs,
		utility::fixedsizearray1< CatmullRomSplineBoundaryType, N > const &	boundary,
		utility::fixedsizearray1< Real, N > &	deriv,
		bool const &	compute_deriv = `true`
	)

inline

Catmull-Rom spline interpolation of an N-dimensional tensor defined on a equispaced grid.

References catmull_rom_interpolate(), ObjexxFCL::format::F(), get_patch(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, N, pyrosetta.distributed.cluster.exceptions::T, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::xs.

Referenced by polycubic_interpolate_catmull_rom(), and test_numerical_deriv().

◆ polycubic_interpolation() [1/2]

template<Size N>

void numeric::interpolation::polycubic_interpolation	(	numeric::interpolation::InterpolatedPotential< N > const &	interpolated_potential,
		utility::fixedsizearray1< Real, N > const &	values,
		Real &	score,
		utility::fixedsizearray1< Real, N > &	dscoreddof
	)

References numeric::interpolation::InterpolatedPotential< N >::axis_range(), numeric::interpolation::InterpolatedPotential< N >::bin_width(), bin_torsions::bins, numeric::interpolation::InterpolatedPotential< N >::get_indices(), numeric::interpolation::InterpolatedPotential< N >::grid_size(), create_a3b_hbs::ii, internal_coordinates::indices, beta_nonlocal::jj, N, and test.T040_Types::values.

◆ polycubic_interpolation() [2/2]

template<Size N>

void numeric::interpolation::polycubic_interpolation	(	utility::fixedsizearray1< utility::fixedsizearray1< Real,(1<< N) >,(1<< N) >	n_derivs,
		utility::fixedsizearray1< Real, N >	dbbp,
		utility::fixedsizearray1< Real, N >	binwbb,
		Real &	val,
		utility::fixedsizearray1< Real, N > &	dvaldbb
	)

Perform cubic interpolation over each of N axes, using the 2^N derivatives at 2^N gridpoints.

The way encoding gridpoints and derivatives into a linear structure like this is actually pretty simple. Imagine the "right or left" part of a cube, or the "derivative taken or not" on a particular variable, as zero or one. Then "just the actual function value" maps to 000, the z derivative (for example) maps to 001, d2/dydz maps to 011, etc.

Parameters

[in]	n_derivs	is a 2^N x 2^N matrix: 2^N derivatives at 2^N gridpoints
[in]	dbbp	is how far along the bin our target point is, in each direction
[in]	binwbb	is the bin width in each direction
[out]	val	is the interpolated value
[out]	dvaldbb	are the interpolated derivatives

References create_a3b_hbs::ii, beta_nonlocal::jj, and N.

◆ spline_from_file()

spline::SplineGenerator numeric::interpolation::spline_from_file	(	std::string const &	filename,
		platform::Real const	bin_size
	)

read in a file, read out a spline. The file should be tab separated, and have two lines The first field of one line should be "x_axis", the next fields should be the x values of the points for the spline The first field of the other line should be "y_axis", the next fields should be the y values for the points on the spline For an example, see "scoring/constraints/epr_distance_potential.histogram"

References a3b_test::bin_size, count, extract_by_sidechain_sasa_score::cutoff, lactamize::filename, utility::from_string(), getline(), line, make_spline(), PB_potential::potential_file, challenge::ss, utility::string_split(), basic::options::OptionKeys::sc::trim, and utility_exit_with_message.

◆ spline_from_stream()

spline::SplineGenerator numeric::interpolation::spline_from_stream	(	std::istream &	iss,
		platform::Real const	bin_size
	)

Initialize a SplineGenerator from a std::istream. Note: only reads from the currenet line of the istream.

Assumes that the stream contains only the following: "x_axis" followed by N values – mandatory. "y_axis" followed by N values – mandatory. N must match "xaxis". "lb_function" [cutoff] [slope] [intercept] – optional. "ub_function" [cutoff] [slope] [intercept] – optional.

Author: Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).; Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

References a3b_test::bin_size, extract_by_sidechain_sasa_score::cutoff, debug_assert, errmsg(), getline(), test.T008_Serialization::iss, make_spline(), SmotifHasher::mode, none, runtime_assert_string_msg, challenge::ss, x_axis, and y_axis.

◆ to_string()

std::string numeric::interpolation::to_string ( CatmullRomSplineBoundaryType const & type )

inline

References FLAT, LINEAR, and PERIODIC.

Referenced by SSM_energies::apply(), DetectSymmetry::apply(), ExemplarMover::apply(), generate_hbond_geometry::apply(), binder::bind_member_functions_for_call_back(), check_options(), check_pose_length(), determine_allowed_dofs(), devel_main(), format(), binder::function_arguments_for_lambda(), binder::function_arguments_for_py_overload(), binder::Context::generate(), utility::DenseBoolMap< NUM_ELEMS, BASE_INDEX >::get(), get_attachment_point_string(), get_rsrpl(), binder::Context::global_insertion_operator(), system_error::init(), binder::line_number(), basic::mpi::listener_tag_to_name(), utility::options::OptionCollection::load_option_cl(), utility::options::OptionCollection::load_option_file(), main(), apps::pilot::frankdt::main(), utility::excn::Exception::msg(), detail::stringifier::operator()(), output_single_motif(), pdb_id(), prepare_helix_bundles(), prepare_smotifs(), retag(), scan_hbond_jumps(), utility::DenseBoolMap< NUM_ELEMS, BASE_INDEX >::set(), FunctorTest::test_task_upload(), numeric::Quaternion< T >::to_string(), numeric::xyzVector< T >::to_string(), binder::Context::trace_line(), vformat(), detail::vformat(), and vsprintf().

Namespaces

Classes

Enumerations

Functions

Enumeration Type Documentation

◆ CatmullRomSplineBoundaryType

◆ SplineFromStreamMode

Function Documentation

◆ bilinearly_interpolated() [1/3]

◆ bilinearly_interpolated() [2/3]

◆ bilinearly_interpolated() [3/3]

◆ catmull_rom_interpolate()

◆ catmull_rom_interpolate_basic() [1/3]

◆ catmull_rom_interpolate_basic() [2/3]

◆ catmull_rom_interpolate_basic() [3/3]

◆ get_patch()

◆ get_val()

◆ interpolated() [1/2]

◆ interpolated() [2/2]

◆ interpolated_delta()

◆ make_spline()

◆ multilinear_interpolation() [1/2]

◆ multilinear_interpolation() [2/2]

◆ polycubic_interpolate_catmull_rom() [1/2]

◆ polycubic_interpolate_catmull_rom() [2/2]

◆ polycubic_interpolation() [1/2]

◆ polycubic_interpolation() [2/2]

◆ spline_from_file()

◆ spline_from_stream()

◆ to_string()