numeric::fourier::SHT Class Reference

#include <SHT.hh>

Public Member Functions
	SHT ()
	Constructor. More...
	SHT (int B, int nR)
	Construct with a given bandwidth, # of radial shells. More...
	~SHT ()
	Destructor. More...
void	init (int B, int nR)
	Initialize with a given bandwidth, # of radial shells. More...
void	sharm_transform (ObjexxFCL::FArray3D< double > const &sigR, ObjexxFCL::FArray3D< double > &sigCoefR, ObjexxFCL::FArray3D< double > &sigCoefI)
	Take spherical harmonic transform of 'sigR', result in 'sigCoefR' and 'sigCoefI'. More...
void	sharm_invTransform (ObjexxFCL::FArray3D< double > &sigR, ObjexxFCL::FArray3D< double > &sigCoefR, ObjexxFCL::FArray3D< double > &sigCoefI)
	Take inverse spherical harmonic transform of 'sigCoefR' and 'sigCoefI', result in 'sigR'. More...
void	sph_standardize (ObjexxFCL::FArray3D< double > &sigCoefR, ObjexxFCL::FArray3D< double > &sigCoefI)
	Standardize coefficients 'sigCoefR' and 'sigCoefI'. More...
void	so3_correlate (ObjexxFCL::FArray3D< double > &so3_correlation, ObjexxFCL::FArray3D< double > &sigCoefR, ObjexxFCL::FArray3D< double > &sigCoefI, ObjexxFCL::FArray3D< double > &tmpCoefR, ObjexxFCL::FArray3D< double > &tmpCoefI)
	Correlate two signals ('sigCoef' and 'tmpCoef') as a function of rotation of 'tmpCoef', result in 'so3_correlation'. More...
void	idx_to_rot (int maxloc, numeric::xyzMatrix< double > &thisRot)
	Convert an index from 'so3_correlation' into a rotation matrix. More...
void	idx_to_euler (int maxloc, numeric::xyzVector< double > &eulerAngles)
	Convert an index from 'so3_correlation' into Euler angles alpha, beta, gamma. More...

Private Member Functions
void	so3CombineCoef (utility::vector0< double > &sigCoefR, utility::vector0< double > &sigCoefI, utility::vector0< double > &tmpCoefR, utility::vector0< double > &tmpCoefI, ObjexxFCL::FArray3D< std::complex< double > > &so3Coef)
void	inverseSo3 (ObjexxFCL::FArray3D< std::complex< double > > &so3Coef, ObjexxFCL::FArray3D< std::complex< double > > &conv)
void	forwardS2 (utility::vector0< double > &rdata, utility::vector0< double > &rcoeffs, utility::vector0< double > &icoeffs)
void	inverseS2 (utility::vector0< double > &rcoeffs, utility::vector0< double > &icoeffs, utility::vector0< double > &rdata)
void	setup_Pmls ()
void	setup_Wig ()
void	setup_Weights ()

Private Attributes
int	bw
int	nRsteps
SO3coeffs	so3_
kiss_fft_cfg	p1
kiss_fftsplit_cfg	fftPlan
kiss_fftsplit_cfg	ifftPlan
kiss_dct_cfg	dctPlan
kiss_dct_cfg	idctPlan
utility::vector0< double >	weights_
utility::vector0< double >	precompute_wig_trans_
utility::vector0< utility::vector0< double > >	precompute_pml_
utility::vector0< utility::vector0< double > >	precompute_pml_trans_

Constructor & Destructor Documentation

SHT() [1/2]

numeric::fourier::SHT::SHT

(

)

Constructor.

References bw, dctPlan, fftPlan, idctPlan, ifftPlan, nRsteps, and p1.

SHT() [2/2]

numeric::fourier::SHT::SHT	(	int	B,
		int	nR
	)

Construct with a given bandwidth, # of radial shells.

References bw, dctPlan, fftPlan, idctPlan, ifftPlan, init(), nRsteps, and p1.

~SHT()

numeric::fourier::SHT::~SHT

(

)

Destructor.

References dctPlan, fftPlan, idctPlan, ifftPlan, and p1.

Member Function Documentation

forwardS2()

void numeric::fourier::SHT::forwardS2 ( utility::vector0< double > &  rdata, utility::vector0< double > &  rcoeffs, utility::vector0< double > &  icoeffs  )

private

References bw, dctPlan, fftPlan, create_a3b_hbs::i, create_a3b_hbs::j, numeric::fourier::kiss_fft_split(), numeric::fourier::SO3coeffs::Legendre(), numeric::fourier::SO3coeffs::lm_index(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, N, numeric::constants::d::pi, precompute_pml_, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::scale, so3_, basic::options::OptionKeys::hotspot::target, and weights_.

Referenced by sharm_transform().

idx_to_euler()

void numeric::fourier::SHT::idx_to_euler	(	int	maxloc,
		numeric::xyzVector< double > &	eulerAngles
	)

Convert an index from 'so3_correlation' into Euler angles alpha, beta, gamma.

References bw, create_a3b_hbs::ii, beta_nonlocal::jj, kk, and numeric::constants::d::pi.

idx_to_rot()

void numeric::fourier::SHT::idx_to_rot	(	int	maxloc,
		numeric::xyzMatrix< double > &	thisRot
	)

Convert an index from 'so3_correlation' into a rotation matrix.

References a, compute_difference::b, bw, g(), numeric::xyzMatrix< T >::identity(), create_a3b_hbs::ii, beta_nonlocal::jj, kk, and numeric::constants::d::pi.

init()

void numeric::fourier::SHT::init	(	int	B,
		int	nR
	)

Initialize with a given bandwidth, # of radial shells.

References bw, CREATE_EXCEPTION, dctPlan, fftPlan, idctPlan, ifftPlan, numeric::fourier::SO3coeffs::init(), nRsteps, p1, precompute_pml_, precompute_pml_trans_, precompute_wig_trans_, setup_Pmls(), setup_Weights(), setup_Wig(), and so3_.

Referenced by sharm_invTransform(), sharm_transform(), SHT(), and so3_correlate().

inverseS2()

void numeric::fourier::SHT::inverseS2 ( utility::vector0< double > &  rcoeffs, utility::vector0< double > &  icoeffs, utility::vector0< double > &  rdata  )

private

References bw, create_a3b_hbs::i, idctPlan, ifftPlan, numeric::fourier::SO3coeffs::InvLegendre(), numeric::fourier::kiss_fft_split(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, N, numeric::constants::d::pi, precompute_pml_trans_, basic::options::OptionKeys::out::path::scratch, and so3_.

Referenced by sharm_invTransform().

inverseSo3()

void numeric::fourier::SHT::inverseSo3 ( ObjexxFCL::FArray3D< std::complex< double > > &  so3Coef, ObjexxFCL::FArray3D< std::complex< double > > &  conv  )

private

References bw, numeric::fourier::SO3coeffs::coefLoc(), create_a3b_hbs::i, create_a3b_hbs::j, numeric::fourier::kiss_fft(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, p1, numeric::constants::d::pi, precompute_wig_trans_, basic::options::OptionKeys::james::real, numeric::fourier::SO3coeffs::sampLoc(), basic::options::OptionKeys::out::path::scratch, so3_, numeric::fourier::transpose_so3(), numeric::fourier::SO3coeffs::wignerSynthesis(), numeric::fourier::SO3coeffs::wignerSynthesisDiffSign(), and numeric::fourier::SO3coeffs::wignerSynthesisSameSign().

Referenced by so3_correlate().

setup_Pmls()

void numeric::fourier::SHT::setup_Pmls ( )

private

References bw, C, create_a3b_hbs::i, create_a3b_hbs::j, create_a3b_hbs::k, numeric::fourier::kiss_dct(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, numeric::constants::d::pi, ObjexxFCL::pow(), precompute_pml_, precompute_pml_trans_, dummy-distribution::row, subloop_histogram::size, so3_, basic::options::OptionKeys::dump_trajectory::stride, and numeric::fourier::SO3coeffs::transposeRowSize().

Referenced by init().

setup_Weights()

void numeric::fourier::SHT::setup_Weights ( )

private

References bw, create_a3b_hbs::j, create_a3b_hbs::k, numeric::constants::d::pi, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::scale, and weights_.

Referenced by init().

setup_Wig()

void numeric::fourier::SHT::setup_Wig ( )

private

References bw, numeric::fourier::SO3coeffs::genWigner_ds(), create_a3b_hbs::i, N, numeric::constants::d::pi, precompute_wig_trans_, and so3_.

Referenced by init().

sharm_invTransform()

void numeric::fourier::SHT::sharm_invTransform	(	ObjexxFCL::FArray3D< double > &	sigR,
		ObjexxFCL::FArray3D< double > &	sigCoefR,
		ObjexxFCL::FArray3D< double > &	sigCoefI
	)

Take inverse spherical harmonic transform of 'sigCoefR' and 'sigCoefI', result in 'sigR'.

References bw, ObjexxFCL::FArray3D< T >::dimension(), create_a3b_hbs::i, init(), inverseS2(), nRsteps, docking::R, ObjexxFCL::FArray3D< T >::u2(), and ObjexxFCL::FArray3D< T >::u3().

sharm_transform()

void numeric::fourier::SHT::sharm_transform	(	ObjexxFCL::FArray3D< double > const &	sigR,
		ObjexxFCL::FArray3D< double > &	sigCoefR,
		ObjexxFCL::FArray3D< double > &	sigCoefI
	)

Take spherical harmonic transform of 'sigR', result in 'sigCoefR' and 'sigCoefI'.

References bw, ObjexxFCL::FArray3D< T >::dimension(), forwardS2(), create_a3b_hbs::i, init(), nRsteps, docking::R, ObjexxFCL::FArray3D< T >::u2(), and ObjexxFCL::FArray3D< T >::u3().

so3_correlate()

void numeric::fourier::SHT::so3_correlate	(	ObjexxFCL::FArray3D< double > &	so3_correlation,
		ObjexxFCL::FArray3D< double > &	sigCoefR,
		ObjexxFCL::FArray3D< double > &	sigCoefI,
		ObjexxFCL::FArray3D< double > &	tmpCoefR,
		ObjexxFCL::FArray3D< double > &	tmpCoefI
	)

Correlate two signals ('sigCoef' and 'tmpCoef') as a function of rotation of 'tmpCoef', result in 'so3_correlation'.

References bw, ObjexxFCL::FArray3D< T >::dimension(), create_a3b_hbs::i, init(), inverseSo3(), nRsteps, docking::R, so3CombineCoef(), numeric::square(), ObjexxFCL::FArray3D< T >::u2(), and ObjexxFCL::FArray3D< T >::u3().

so3CombineCoef()

void numeric::fourier::SHT::so3CombineCoef ( utility::vector0< double > &  sigCoefR, utility::vector0< double > &  sigCoefI, utility::vector0< double > &  tmpCoefR, utility::vector0< double > &  tmpCoefI, ObjexxFCL::FArray3D< std::complex< double > > &  so3Coef  )

private

References ObjexxFCL::abs(), bw, create_a3b_hbs::i, create_a3b_hbs::k, extract_by_sidechain_sasa_score::l, numeric::fourier::SO3coeffs::lm_index(), max(), numeric::constants::d::pi, and so3_.

Referenced by so3_correlate().

sph_standardize()

void numeric::fourier::SHT::sph_standardize	(	ObjexxFCL::FArray3D< double > &	sigCoefR,
		ObjexxFCL::FArray3D< double > &	sigCoefI
	)

Standardize coefficients 'sigCoefR' and 'sigCoefI'.

References create_a3b_hbs::i, create_a3b_hbs::j, numeric::constants::d::pi, docking::R, docking::s, basic::options::OptionKeys::stepwise::s2, numeric::square(), ObjexxFCL::FArray3D< T >::u2(), ObjexxFCL::FArray3D< T >::u3(), and orn_macrocycle::wt.

Member Data Documentation

bw

int numeric::fourier::SHT::bw

private

Referenced by forwardS2(), idx_to_euler(), idx_to_rot(), init(), inverseS2(), inverseSo3(), setup_Pmls(), setup_Weights(), setup_Wig(), sharm_invTransform(), sharm_transform(), SHT(), so3_correlate(), and so3CombineCoef().

dctPlan

kiss_dct_cfg numeric::fourier::SHT::dctPlan

private

Referenced by forwardS2(), init(), SHT(), and ~SHT().

fftPlan

kiss_fftsplit_cfg numeric::fourier::SHT::fftPlan

private

Referenced by forwardS2(), init(), SHT(), and ~SHT().

idctPlan

kiss_dct_cfg numeric::fourier::SHT::idctPlan

private

Referenced by init(), inverseS2(), SHT(), and ~SHT().

ifftPlan

kiss_fftsplit_cfg numeric::fourier::SHT::ifftPlan

private

Referenced by init(), inverseS2(), SHT(), and ~SHT().

nRsteps

int numeric::fourier::SHT::nRsteps

private

Referenced by init(), sharm_invTransform(), sharm_transform(), SHT(), and so3_correlate().

p1

kiss_fft_cfg numeric::fourier::SHT::p1

private

Referenced by init(), inverseSo3(), SHT(), and ~SHT().

precompute_pml_

utility::vector0< utility::vector0<double> > numeric::fourier::SHT::precompute_pml_

private

Referenced by forwardS2(), init(), and setup_Pmls().

precompute_pml_trans_

utility::vector0< utility::vector0<double> > numeric::fourier::SHT::precompute_pml_trans_

private

Referenced by init(), inverseS2(), and setup_Pmls().

precompute_wig_trans_

utility::vector0< double > numeric::fourier::SHT::precompute_wig_trans_

private

Referenced by init(), inverseSo3(), and setup_Wig().

so3_

SO3coeffs numeric::fourier::SHT::so3_

private

Referenced by forwardS2(), init(), inverseS2(), inverseSo3(), setup_Pmls(), setup_Wig(), and so3CombineCoef().

weights_

utility::vector0< double > numeric::fourier::SHT::weights_

private

Referenced by forwardS2(), and setup_Weights().

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

• src/numeric/fourier/SHT.hh
• src/numeric/fourier/SHT.cc