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Classes | Typedefs | Functions
core::scoring::fiber_diffraction Namespace Reference

Classes

class  CentroidScatter
 silly vector1 wrapper class so we can derive from PoseCachedData More...
 
class  FAScatter
 silly vector1 wrapper class so we can derive from PoseCachedData More...
 
class  FiberDiffraction
 
struct  Hankel
 
class  KromerMann
 
class  OneGaussianScattering
 

Typedefs

typedef utility::pointer::shared_ptr< CentroidScatter > CentroidScatterOP
 
typedef utility::pointer::shared_ptr< FAScatter > FAScatterOP
 
typedef utility::pointer::shared_ptr< FiberDiffraction > FiberDiffractionOP
 
typedef utility::pointer::shared_ptr< FiberDiffraction const > FiberDiffractionCOP
 
typedef struct core::scoring::fiber_diffraction::Hankel Hankel
 

Functions

CentroidScatter & retrieve_centroid_scatter_from_pose (pose::Pose &pose)
 helper routine More...
 
FAScatter & retrieve_fa_scatter_from_pose (pose::Pose &pose)
 helper routine More...
 
static basic::Tracer TR ("core.scoring.fiber_diffraction.FiberDiffraction")
 
FiberDiffraction & getFiberDiffractionData (core::Real c=0.0, core::Real res_cutoff_high=0.0, core::Real res_cutoff_low=0.0, bool force_reload=false)
 The EDM instance. More...
 
FiberDiffraction & getFiberDiffractionData_legacy (core::Real c=0.0, core::Real res_cutoff_high=0.0, core::Real res_cutoff_low=0.0, bool force_reload=false)
 The EDM instance. More...
 
void calculate_intensity_gpu (Size const l_max, Size const natoms, utility::vector0< utility::vector0< int > >::iterator &nvals, utility::vector0< utility::vector1< core::Real > >::iterator &layer_lines_R, utility::vector0< utility::vector1< core::Real > > &I, utility::vector0< utility::vector1< utility::vector1< core::Real > > >::iterator &form_factors, utility::vector1< Real > &phi, utility::vector1< Real > &z, utility::vector1< Real > &r, utility::vector1< Size > &atom_type_number, Real const c_, Real const res_cutoff_low_, Real const res_cutoff_high_, int const gpu_processor_)
 
void calculate_derivatives_gpu (Size const l_max, Size const natoms, utility::vector0< utility::vector0< int > >::iterator &nvals, utility::vector0< utility::vector1< Real > >::iterator &layer_lines_R, utility::vector0< utility::vector1< Real > >::iterator &layer_lines_I, utility::vector0< utility::vector1< Real > > &I, utility::vector0< utility::vector1< utility::vector1< Real > > >::iterator &form_factors, utility::vector1< Real > &phi, utility::vector1< Real > &z, utility::vector1< Real > &r, utility::vector1< Size > &atom_type_number, utility::vector1< numeric::xyzVector< core::Real > > &dchi2_d, utility::vector1< numeric::xyzVector< core::Real > > &dchi2_d_cross_R, Real const c_, Real const res_cutoff_low_, Real const res_cutoff_high_, Real const scale_factor_, Real const square_obs_, int const gpu_processor_, bool rfactor_refinement)
 
core::Real alpha_func (core::Size n, core::Real k1, core::Real k2, core::Real alpha)
 
core::Real alpha_deriv_func (core::Size n, core::Real alpha)
 
void hankel_set_alpha (Hankel *p_hankel)
 
void c_array_mult (core::Size length, core::Real *dp_1, core::Real *dp_2)
 
void hankel_free (Hankel *p_hankel)
 
void c_mult_ip (core::Real *one, const core::Real *two)
 
void hankel_r_mult (Hankel *p_hankel)
 
void hankel_r_div (Hankel *p_hankel)
 
void hankel_trans_no_lec (Hankel *p_hankel)
 
core::Real hankel_get_p0 (Hankel *p_hankel)
 
void hankel_make_snn (Hankel *p_hankel)
 
void hankel_in_machine (Hankel *p_hankel)
 
core::Real hankel_get_rc (Hankel *p_hankel)
 
void hankel_make_j (Hankel *p_hankel)
 
void hankel_make_rp (Hankel *p_hankel)
 
Hankel * hankel_make_input (core::Size length, core::Real k1, core::Real k2, core::Real b, int lec_order, core::Real *f0, ObjexxFCL::FArray3D< std::complex< float > > &hankel_in, core::Size &lindex, core::Size &nindex, int l)
 
void d_array_scale (core::Size length, core::Real factor, core::Real *dp_in)
 
void set_r_array (core::Size num_r_points, core::Real k1, core::Real k2, core::Real max_r, ObjexxFCL::FArray1D< float > &rc)
 
void set_r_inv_array (core::Size num_r_points, core::Real k1, core::Real k2, core::Real max_r, ObjexxFCL::FArray1D< float > &Rinv)
 
void dfour1_plan (core::Real *data, core::Size nn, int isign, std::complex< core::Real > *in)
 
core::Real NRbisafe (core::Size n, core::Real k1, core::Real k2, core::Real X1, core::Real X2)
 
static basic::Tracer TR ("core.scoring.fiber_diffraction.util")
 
void setup_cylindrical_coords (pose::Pose const &pose, core::Size &natoms, utility::vector1< Size > &atom_type_number, std::map< core::id::AtomID, core::Size > &AtomID_to_atomnbr, utility::vector1< Real > &phi, utility::vector1< Real > &z, utility::vector1< Real > &r, utility::vector1< Real > &bfactors)
 
void find_pitch (pose::Pose const &pose, core::Real &pitch)
 
void find_min_xyz (pose::Pose const &pose, core::Real &minX, core::Real &minY, core::Real &minZ, core::Real &maxX, core::Real &maxY, core::Real &maxZ)
 
void find_max_r (pose::Pose const &pose, core::Real &maxR)
 
void find_num_scattering_atoms (pose::Pose &pose, core::Size &nscatterers)
 
void centroid_scatter (const std::string &res_name, OneGaussianScattering &sig_centroid)
 
utility::vector1< OneGaussianScattering > setup_centroid_scatter (pose::Pose &pose)
 
bool isPowerOfTwo (int n)
 
utility::vector0< utility::vector1< utility::vector1< core::Real > > > setup_form_factors (pose::Pose &pose, core::Size const &lmax, utility::vector0< utility::vector1< core::Real > >::iterator const &layer_lines_R, core::Real const &c, core::Real const &B_factor, core::Real const &B_factor_solv, core::Real const &Ksolv)
 
void generate_shannon_points (core::Size const &lmax, core::Real const &dmax, utility::vector0< utility::vector1< core::Real > >::iterator const &layer_lines_R, utility::vector0< core::Size > ::iterator &sampling_points_l, utility::vector0< utility::vector1< core::Real > >::iterator &shannon_points_lS, utility::vector0< core::Size > ::iterator &lowest_bessel_orders_l, utility::vector0< utility::vector0< int > >::iterator const &nvals)
 
void bessel_roots (core::Size const &lmax, core::Real const &c, core::Real const &res_cutoff_high, core::Real const &res_cutoff_low, core::Real &structure_cutoff, utility::vector0< utility::vector1< core::Real > > &bessel_roots_lE_, utility::vector0< core::Size > &sampling_points_l_, utility::vector0< core::Size > &lowest_bessel_orders_l_, utility::vector0< core::Size > &highest_resolution_l_, utility::vector0< core::Size > &lowest_resolution_l_, utility::vector0< utility::vector1< core::Real > >::iterator const &layer_lines_R, utility::vector0< utility::vector0< int > >::iterator const &nvals)
 
void interpolate_sampled_to_grid (core::Size const &lmax, utility::vector0< utility::vector1< core::Real > > const &bessel_roots_lE, utility::vector0< core::Size > const &sampling_points_l, utility::vector0< core::Size > const &highest_resolution_l, utility::vector0< core::Size > const &lowest_resolution_l, utility::vector0< utility::vector1< core::Real > >::iterator const &layer_lines_R, utility::vector0< utility::vector1< core::Size > > &selected_R_l_, utility::vector0< utility::vector1< core::Real > > &selected_Rinv_l_)
 
void calculate_I_of_E (core::Size const &lmax, core::Size const &k_iteration, utility::vector0< utility::vector1< core::Real > > const &sampling_points_lE, core::Size const &natoms, core::Size const &c_, utility::vector0< utility::vector0< int > >::iterator const &nvals, utility::vector1< Size > const &atom_type_number, utility::vector1< Real > const &phi, utility::vector1< Real > const &z, utility::vector1< Real > const &r, utility::vector0< utility::vector1< utility::vector1< core::Real > > >::iterator const &form_factors, utility::vector0< utility::vector1< Real > > &I_E)
 
core::Real calculate_chi_k (core::Size const &lmax, core::Size const &k_iteration, utility::vector0< utility::vector1< core::Size > > const &selected_R_l, utility::vector0< utility::vector1< core::Real > > const &selected_Rinv_l, utility::vector0< utility::vector1< core::Real > >::iterator const &layer_lines_I, utility::vector0< utility::vector1< core::Real > > const &I_interpolated)
 
core::Real calculate_chi2_free (pose::Pose &pose, core::Size const &chi_free_iterations_, core::Size const &lmax, utility::vector0< utility::vector1< core::Real > >::iterator const &layer_lines_I, utility::vector0< utility::vector1< core::Real > >::iterator const &layer_lines_R, core::Size const &natoms, core::Size const &c_, utility::vector0< utility::vector0< int > >::iterator const &nvals, utility::vector1< Size > const &atom_type_number, utility::vector1< Real > const &phi, utility::vector1< Real > const &z, utility::vector1< Real > const &r, core::Real const b_factor_, core::Real const b_factor_solv, core::Real const b_factor_solv_K)
 
void sample_layer_lines_from_bins (core::Size const &lmax, core::Size const &k_iteration, utility::vector0< utility::vector1< core::Real > >::iterator const &layer_lines_R, utility::vector0< utility::vector1< core::Size > > &selected_R_l_, utility::vector0< utility::vector1< core::Real > > &selected_Rinv_l_)
 
void rootj (int const &N, core::Real const &CUTOFF, utility::vector1< core::Real > &zeros, core::Size &npoints)
 
void secant (int const &N, int const &nitmx, core::Real tol, core::Real *zeroJ, int *ier)
 
static basic::Tracer TR ("core.scoring.fiber_diffraction.util_ndft")
 
void FBnl_R (ObjexxFCL::FArray3D< float > &fourier_in, utility::vector0< utility::vector0< int > >::iterator &nvals, core::Size &lmax, core::Size &rindex, ObjexxFCL::FArray3D< std::complex< float > > &fourier_out)
 
void ft_nfft (ObjexxFCL::FArray3D< float > &fourier_in, utility::vector0< utility::vector0< int > >::iterator &nvals, core::Size &lmax, core::Size &total_rvals, ObjexxFCL::FArray3D< std::complex< float > > &fourier_out)
 
void ndft (ObjexxFCL::FArray1D< std::complex< float > > &fin, ObjexxFCL::FArray1D< float > &phi, ObjexxFCL::FArray1D< int > &n, ObjexxFCL::FArray1D< std::complex< float > > &fout)
 
void ndft_1d (ObjexxFCL::FArray1D< std::complex< float > > &f0, ObjexxFCL::FArray1D< float > &x0, ObjexxFCL::FArray1D< std::complex< float > > &f2)
 
int pos_mod (int x, int y)
 
float pos_mod (float x, float y)
 
core::Real pos_mod (core::Real x, core::Real y)
 
float square (float x)
 
core::Real square (core::Real x)
 
OneGaussianScattering get_A (std::string elt)
 
KromerMann get_km (std::string elt)
 
bool factorsLTE5 (int X)
 
bool factorsLTE19 (int X)
 
int findSampling5 (core::Real MINSMP, int NMUL)
 
int findSampling (core::Real MINSMP, int NMUL)
 

Typedef Documentation

◆ CentroidScatterOP

typedef utility::pointer::shared_ptr< CentroidScatter > core::scoring::fiber_diffraction::CentroidScatterOP

◆ FAScatterOP

typedef utility::pointer::shared_ptr< FAScatter > core::scoring::fiber_diffraction::FAScatterOP

◆ FiberDiffractionCOP

typedef utility::pointer::shared_ptr< FiberDiffraction const > core::scoring::fiber_diffraction::FiberDiffractionCOP

◆ FiberDiffractionOP

typedef utility::pointer::shared_ptr< FiberDiffraction > core::scoring::fiber_diffraction::FiberDiffractionOP

◆ Hankel

typedef struct core::scoring::fiber_diffraction::Hankel core::scoring::fiber_diffraction::Hankel

Function Documentation

◆ alpha_deriv_func()

core::Real core::scoring::fiber_diffraction::alpha_deriv_func ( core::Size  n,
core::Real  alpha 
)

Referenced by NRbisafe().

◆ alpha_func()

core::Real core::scoring::fiber_diffraction::alpha_func ( core::Size  n,
core::Real  k1,
core::Real  k2,
core::Real  alpha 
)

Referenced by protocols::antibody::kink_constrain_antibody_H3(), and NRbisafe().

◆ bessel_roots()

void core::scoring::fiber_diffraction::bessel_roots ( core::Size const &  lmax,
core::Real const &  c,
core::Real const &  res_cutoff_high,
core::Real const &  res_cutoff_low,
core::Real &  structure_cutoff,
utility::vector0< utility::vector1< core::Real > > &  bessel_roots_lE_,
utility::vector0< core::Size > &  sampling_points_l_,
utility::vector0< core::Size > &  lowest_bessel_orders_l_,
utility::vector0< core::Size > &  highest_resolution_l_,
utility::vector0< core::Size > &  lowest_resolution_l_,
utility::vector0< utility::vector1< core::Real > >::iterator const &  layer_lines_R,
utility::vector0< utility::vector0< int > >::iterator const &  nvals 
)

References rootj(), and protocols::noesy_assign::round().

◆ c_array_mult()

void core::scoring::fiber_diffraction::c_array_mult ( core::Size  length,
core::Real *  dp_1,
core::Real *  dp_2 
)

References c_mult_ip().

Referenced by hankel_trans_no_lec().

◆ c_mult_ip()

void core::scoring::fiber_diffraction::c_mult_ip ( core::Real *  one,
const core::Real *  two 
)

Referenced by c_array_mult().

◆ calculate_chi2_free()

core::Real core::scoring::fiber_diffraction::calculate_chi2_free ( pose::Pose &  pose,
core::Size const &  chi_free_iterations_,
core::Size const &  lmax,
utility::vector0< utility::vector1< core::Real > >::iterator const &  layer_lines_I,
utility::vector0< utility::vector1< core::Real > >::iterator const &  layer_lines_R,
core::Size const &  natoms,
core::Size const &  c_,
utility::vector0< utility::vector0< int > >::iterator const &  nvals,
utility::vector1< Size > const &  atom_type_number,
utility::vector1< Real > const &  phi,
utility::vector1< Real > const &  z,
utility::vector1< Real > const &  r,
core::Real const  b_factor_,
core::Real const  b_factor_solv,
core::Real const  b_factor_solv_K 
)

References calculate_chi_k(), calculate_I_of_E(), core::simple_metrics::metrics::mean, sample_layer_lines_from_bins(), setup_form_factors(), and TR().

Referenced by core::energy_methods::FiberDiffractionEnergy::setup_for_scoring().

◆ calculate_chi_k()

core::Real core::scoring::fiber_diffraction::calculate_chi_k ( core::Size const &  lmax,
core::Size const &  k_iteration,
utility::vector0< utility::vector1< core::Size > > const &  selected_R_l,
utility::vector0< utility::vector1< core::Real > > const &  selected_Rinv_l,
utility::vector0< utility::vector1< core::Real > >::iterator const &  layer_lines_I,
utility::vector0< utility::vector1< core::Real > > const &  I_interpolated 
)

Referenced by calculate_chi2_free().

◆ calculate_derivatives_gpu()

void core::scoring::fiber_diffraction::calculate_derivatives_gpu ( Size const  l_max,
Size const  natoms,
utility::vector0< utility::vector0< int > >::iterator &  nvals,
utility::vector0< utility::vector1< Real > >::iterator &  layer_lines_R,
utility::vector0< utility::vector1< Real > >::iterator &  layer_lines_I,
utility::vector0< utility::vector1< Real > > &  I,
utility::vector0< utility::vector1< utility::vector1< Real > > >::iterator &  form_factors,
utility::vector1< Real > &  phi,
utility::vector1< Real > &  z,
utility::vector1< Real > &  r,
utility::vector1< Size > &  atom_type_number,
utility::vector1< numeric::xyzVector< core::Real > > &  dchi2_d,
utility::vector1< numeric::xyzVector< core::Real > > &  dchi2_d_cross_R,
Real const  c_,
Real const  res_cutoff_low_,
Real const  res_cutoff_high_,
Real const  scale_factor_,
Real const  square_obs_,
int const  gpu_processor_,
bool  rfactor_refinement 
)

◆ calculate_I_of_E()

void core::scoring::fiber_diffraction::calculate_I_of_E ( core::Size const &  lmax,
core::Size const &  k_iteration,
utility::vector0< utility::vector1< core::Real > > const &  sampling_points_lE,
core::Size const &  natoms,
core::Size const &  c_,
utility::vector0< utility::vector0< int > >::iterator const &  nvals,
utility::vector1< Size > const &  atom_type_number,
utility::vector1< Real > const &  phi,
utility::vector1< Real > const &  z,
utility::vector1< Real > const &  r,
utility::vector0< utility::vector1< utility::vector1< core::Real > > >::iterator const &  form_factors,
utility::vector0< utility::vector1< Real > > &  I_E 
)

Referenced by calculate_chi2_free().

◆ calculate_intensity_gpu()

void core::scoring::fiber_diffraction::calculate_intensity_gpu ( Size const  l_max,
Size const  natoms,
utility::vector0< utility::vector0< int > >::iterator &  nvals,
utility::vector0< utility::vector1< core::Real > >::iterator &  layer_lines_R,
utility::vector0< utility::vector1< core::Real > > &  I,
utility::vector0< utility::vector1< utility::vector1< core::Real > > >::iterator &  form_factors,
utility::vector1< Real > &  phi,
utility::vector1< Real > &  z,
utility::vector1< Real > &  r,
utility::vector1< Size > &  atom_type_number,
Real const  c_,
Real const  res_cutoff_low_,
Real const  res_cutoff_high_,
int const  gpu_processor_ 
)

◆ centroid_scatter()

void core::scoring::fiber_diffraction::centroid_scatter ( const std::string &  res_name,
OneGaussianScattering &  sig_centroid 
)

References core::scoring::fiber_diffraction::OneGaussianScattering::a(), core::conformation::ResidueFactory::create_residue(), core::chemical::FA_STANDARD, get_A(), core::pose::num_atoms(), and core::scoring::fiber_diffraction::OneGaussianScattering::s().

Referenced by setup_centroid_scatter().

◆ d_array_scale()

void core::scoring::fiber_diffraction::d_array_scale ( core::Size  length,
core::Real  factor,
core::Real *  dp_in 
)

Referenced by hankel_make_j().

◆ dfour1_plan()

void core::scoring::fiber_diffraction::dfour1_plan ( core::Real *  data,
core::Size  nn,
int  isign,
std::complex< core::Real > *  in 
)

References core::conformation::membrane::in.

Referenced by hankel_make_j(), and hankel_trans_no_lec().

◆ factorsLTE19()

bool core::scoring::fiber_diffraction::factorsLTE19 ( int  X)

References protocols::comparative_modeling::features::X.

Referenced by findSampling().

◆ factorsLTE5()

bool core::scoring::fiber_diffraction::factorsLTE5 ( int  X)

References protocols::comparative_modeling::features::X.

Referenced by findSampling5().

◆ FBnl_R()

void core::scoring::fiber_diffraction::FBnl_R ( ObjexxFCL::FArray3D< float > &  fourier_in,
utility::vector0< utility::vector0< int > >::iterator &  nvals,
core::Size &  lmax,
core::Size &  rindex,
ObjexxFCL::FArray3D< std::complex< float > > &  fourier_out 
)

References ndft(), ndft_1d(), and core::scoring::packstat::old::nphi.

Referenced by ft_nfft().

◆ find_max_r()

void core::scoring::fiber_diffraction::find_max_r ( pose::Pose const &  pose,
core::Real &  maxR 
)

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::conformation::Residue::atom(), core::conformation::symmetry::SymmetryInfo::bb_is_independent(), core::pose::Pose::conformation(), core::pose::symmetry::is_symmetric(), core::conformation::Residue::nheavyatoms(), protocols::hybridization::r2, core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Atom::xyz().

Referenced by core::energy_methods::FiberDiffractionEnergy::setup_for_scoring(), and core::energy_methods::FiberDiffractionEnergyDens::setup_for_scoring().

◆ find_min_xyz()

void core::scoring::fiber_diffraction::find_min_xyz ( pose::Pose const &  pose,
core::Real &  minX,
core::Real &  minY,
core::Real &  minZ,
core::Real &  maxX,
core::Real &  maxY,
core::Real &  maxZ 
)

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::conformation::Residue::atom(), core::conformation::symmetry::SymmetryInfo::bb_is_independent(), core::pose::Pose::conformation(), core::pose::symmetry::is_symmetric(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Atom::xyz().

Referenced by core::energy_methods::FiberDiffractionEnergyDens::calculate_rho_fast2().

◆ find_num_scattering_atoms()

void core::scoring::fiber_diffraction::find_num_scattering_atoms ( pose::Pose &  pose,
core::Size &  nscatterers 
)

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::pose::symmetry::is_symmetric(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::pose::symmetry::symmetry_info().

Referenced by core::energy_methods::FiberDiffractionEnergyDens::calculate_rho_fast2().

◆ find_pitch()

void core::scoring::fiber_diffraction::find_pitch ( pose::Pose const &  pose,
core::Real &  pitch 
)

References core::conformation::symmetry::SymmetryInfo::bb_clones(), core::conformation::symmetry::SymmetryInfo::bb_is_independent(), core::pose::Pose::conformation(), core::pose::symmetry::is_symmetric(), core::pose::Pose::size(), protocols::loops::start, protocols::loops::stop, TR(), and core::pose::Pose::xyz().

Referenced by core::energy_methods::FiberDiffractionEnergy::setup_for_derivatives(), core::energy_methods::FiberDiffractionEnergy::setup_for_scoring(), and core::energy_methods::FiberDiffractionEnergyDens::setup_for_scoring().

◆ findSampling()

int core::scoring::fiber_diffraction::findSampling ( core::Real  MINSMP,
int  NMUL 
)

References factorsLTE19(), and core::chemical::element::N.

◆ findSampling5()

int core::scoring::fiber_diffraction::findSampling5 ( core::Real  MINSMP,
int  NMUL 
)

References factorsLTE5(), and core::chemical::element::N.

◆ ft_nfft()

void core::scoring::fiber_diffraction::ft_nfft ( ObjexxFCL::FArray3D< float > &  fourier_in,
utility::vector0< utility::vector0< int > >::iterator &  nvals,
core::Size &  lmax,
core::Size &  total_rvals,
ObjexxFCL::FArray3D< std::complex< float > > &  fourier_out 
)

References FBnl_R().

Referenced by core::energy_methods::gnl_R_qfht().

◆ generate_shannon_points()

void core::scoring::fiber_diffraction::generate_shannon_points ( core::Size const &  lmax,
core::Real const &  dmax,
utility::vector0< utility::vector1< core::Real > >::iterator const &  layer_lines_R,
utility::vector0< core::Size > ::iterator &  sampling_points_l,
utility::vector0< utility::vector1< core::Real > >::iterator &  shannon_points_lS,
utility::vector0< core::Size > ::iterator &  lowest_bessel_orders_l,
utility::vector0< utility::vector0< int > >::iterator const &  nvals 
)

References TR().

◆ get_A()

OneGaussianScattering core::scoring::fiber_diffraction::get_A ( std::string  elt)

References TR().

Referenced by core::energy_methods::FiberDiffractionEnergyDens::calculate_rho_fast2(), and centroid_scatter().

◆ get_km()

KromerMann core::scoring::fiber_diffraction::get_km ( std::string  elt)

References TR().

Referenced by setup_form_factors().

◆ getFiberDiffractionData()

FiberDiffraction & core::scoring::fiber_diffraction::getFiberDiffractionData ( core::Real  c,
core::Real  res_cutoff_high,
core::Real  res_cutoff_low,
bool  force_reload 
)

The EDM instance.

References getFiberDiffractionData_legacy().

Referenced by core::energy_methods::FiberDiffractionEnergy::setup_for_derivatives(), core::energy_methods::FiberDiffractionEnergy::setup_for_scoring(), and core::energy_methods::FiberDiffractionEnergyDens::setup_for_scoring().

◆ getFiberDiffractionData_legacy()

FiberDiffraction & core::scoring::fiber_diffraction::getFiberDiffractionData_legacy ( core::Real  c,
core::Real  res_cutoff_high,
core::Real  res_cutoff_low,
bool  force_reload 
)

The EDM instance.

References core::scoring::fiber_diffraction::FiberDiffraction::isFiberDataLoaded(), core::scoring::fiber_diffraction::FiberDiffraction::loadFiberDiffractionData(), core::scoring::fiber_diffraction::FiberDiffraction::setupBesselOrder(), and TR().

Referenced by getFiberDiffractionData().

◆ hankel_free()

void core::scoring::fiber_diffraction::hankel_free ( Hankel *  p_hankel)

References core::scoring::fiber_diffraction::Hankel::data_in_fft, core::scoring::fiber_diffraction::Hankel::f, core::scoring::fiber_diffraction::Hankel::f0, core::scoring::fiber_diffraction::Hankel::j, core::scoring::fiber_diffraction::Hankel::rp, and core::scoring::fiber_diffraction::Hankel::snn.

Referenced by core::energy_methods::gnl_R_qfht().

◆ hankel_get_p0()

core::Real core::scoring::fiber_diffraction::hankel_get_p0 ( Hankel *  p_hankel)

References core::scoring::fiber_diffraction::Hankel::alpha, core::scoring::fiber_diffraction::Hankel::k1, core::scoring::fiber_diffraction::Hankel::k2, and core::scoring::fiber_diffraction::Hankel::rp0.

Referenced by hankel_make_snn(), and hankel_trans_no_lec().

◆ hankel_get_rc()

core::Real core::scoring::fiber_diffraction::hankel_get_rc ( Hankel *  p_hankel)

References core::scoring::fiber_diffraction::Hankel::alpha, and core::scoring::fiber_diffraction::Hankel::rp0.

Referenced by hankel_make_snn().

◆ hankel_in_machine()

void core::scoring::fiber_diffraction::hankel_in_machine ( Hankel *  p_hankel)

References core::scoring::fiber_diffraction::Hankel::f, hankel_make_j(), hankel_make_rp(), hankel_make_snn(), core::scoring::fiber_diffraction::Hankel::l, core::scoring::fiber_diffraction::Hankel::lec_order, core::scoring::fiber_diffraction::Hankel::n, and core::scoring::fiber_diffraction::Hankel::snn.

Referenced by hankel_make_input().

◆ hankel_make_input()

Hankel * core::scoring::fiber_diffraction::hankel_make_input ( core::Size  length,
core::Real  k1,
core::Real  k2,
core::Real  b,
int  lec_order,
core::Real *  f0,
ObjexxFCL::FArray3D< std::complex< float > > &  hankel_in,
core::Size &  lindex,
core::Size &  nindex,
int  l 
)

References core::scoring::fiber_diffraction::Hankel::alpha, protocols::match::upstream::b, core::scoring::fiber_diffraction::Hankel::data_in_fft, core::scoring::fiber_diffraction::Hankel::f, core::scoring::fiber_diffraction::Hankel::f0, hankel_in_machine(), hankel_set_alpha(), core::scoring::fiber_diffraction::Hankel::k1, core::scoring::fiber_diffraction::Hankel::k2, core::scoring::fiber_diffraction::Hankel::l, core::scoring::fiber_diffraction::Hankel::lec_order, core::scoring::fiber_diffraction::Hankel::n, and core::scoring::fiber_diffraction::Hankel::rp0.

Referenced by core::energy_methods::gnl_R_qfht().

◆ hankel_make_j()

void core::scoring::fiber_diffraction::hankel_make_j ( Hankel *  p_hankel)

References core::scoring::fiber_diffraction::Hankel::alpha, d_array_scale(), core::scoring::fiber_diffraction::Hankel::data_in_fft, dfour1_plan(), core::scoring::fiber_diffraction::Hankel::j, core::scoring::fiber_diffraction::Hankel::k1, core::scoring::fiber_diffraction::Hankel::k2, core::scoring::fiber_diffraction::Hankel::l, and core::scoring::fiber_diffraction::Hankel::n.

Referenced by hankel_in_machine().

◆ hankel_make_rp()

void core::scoring::fiber_diffraction::hankel_make_rp ( Hankel *  p_hankel)

References core::scoring::fiber_diffraction::Hankel::alpha, core::scoring::fiber_diffraction::Hankel::n, and core::scoring::fiber_diffraction::Hankel::rp.

Referenced by hankel_in_machine().

◆ hankel_make_snn()

void core::scoring::fiber_diffraction::hankel_make_snn ( Hankel *  p_hankel)

References core::scoring::fiber_diffraction::Hankel::alpha, hankel_get_p0(), hankel_get_rc(), core::scoring::fiber_diffraction::Hankel::l, core::scoring::fiber_diffraction::Hankel::n, and core::scoring::fiber_diffraction::Hankel::snn.

Referenced by hankel_in_machine().

◆ hankel_r_div()

void core::scoring::fiber_diffraction::hankel_r_div ( Hankel *  p_hankel)

References core::scoring::fiber_diffraction::Hankel::f, core::scoring::fiber_diffraction::Hankel::n, core::scoring::fiber_diffraction::Hankel::rp, and core::scoring::fiber_diffraction::Hankel::rp0.

Referenced by hankel_trans_no_lec().

◆ hankel_r_mult()

void core::scoring::fiber_diffraction::hankel_r_mult ( Hankel *  p_hankel)

References core::scoring::fiber_diffraction::Hankel::f, core::scoring::fiber_diffraction::Hankel::n, core::scoring::fiber_diffraction::Hankel::rp, and core::scoring::fiber_diffraction::Hankel::rp0.

Referenced by hankel_trans_no_lec().

◆ hankel_set_alpha()

void core::scoring::fiber_diffraction::hankel_set_alpha ( Hankel *  p_hankel)

References core::scoring::fiber_diffraction::Hankel::alpha, core::scoring::fiber_diffraction::Hankel::k1, core::scoring::fiber_diffraction::Hankel::k2, core::scoring::fiber_diffraction::Hankel::n, and NRbisafe().

Referenced by hankel_make_input().

◆ hankel_trans_no_lec()

void core::scoring::fiber_diffraction::hankel_trans_no_lec ( Hankel *  p_hankel)

References c_array_mult(), core::scoring::fiber_diffraction::Hankel::data_in_fft, dfour1_plan(), core::scoring::fiber_diffraction::Hankel::f, hankel_get_p0(), hankel_r_div(), hankel_r_mult(), core::scoring::fiber_diffraction::Hankel::j, core::scoring::fiber_diffraction::Hankel::n, and core::scoring::fiber_diffraction::Hankel::rp0.

Referenced by core::energy_methods::gnl_R_qfht().

◆ interpolate_sampled_to_grid()

void core::scoring::fiber_diffraction::interpolate_sampled_to_grid ( core::Size const &  lmax,
utility::vector0< utility::vector1< core::Real > > const &  bessel_roots_lE,
utility::vector0< core::Size > const &  sampling_points_l,
utility::vector0< core::Size > const &  highest_resolution_l,
utility::vector0< core::Size > const &  lowest_resolution_l,
utility::vector0< utility::vector1< core::Real > >::iterator const &  layer_lines_R,
utility::vector0< utility::vector1< core::Size > > &  selected_R_l_,
utility::vector0< utility::vector1< core::Real > > &  selected_Rinv_l_ 
)

References protocols::match::upstream::b.

◆ isPowerOfTwo()

bool core::scoring::fiber_diffraction::isPowerOfTwo ( int  n)

◆ ndft()

void core::scoring::fiber_diffraction::ndft ( ObjexxFCL::FArray1D< std::complex< float > > &  fin,
ObjexxFCL::FArray1D< float > &  phi,
ObjexxFCL::FArray1D< int > &  n,
ObjexxFCL::FArray1D< std::complex< float > > &  fout 
)

Referenced by FBnl_R().

◆ ndft_1d()

void core::scoring::fiber_diffraction::ndft_1d ( ObjexxFCL::FArray1D< std::complex< float > > &  f0,
ObjexxFCL::FArray1D< float > &  x0,
ObjexxFCL::FArray1D< std::complex< float > > &  f2 
)

Referenced by FBnl_R().

◆ NRbisafe()

core::Real core::scoring::fiber_diffraction::NRbisafe ( core::Size  n,
core::Real  k1,
core::Real  k2,
core::Real  X1,
core::Real  X2 
)

References alpha_deriv_func(), alpha_func(), core::chemical::element::F, and core::chemical::element::Fl.

Referenced by hankel_set_alpha(), set_r_array(), and set_r_inv_array().

◆ pos_mod() [1/3]

core::Real core::scoring::fiber_diffraction::pos_mod ( core::Real  x,
core::Real  y 
)
inline

◆ pos_mod() [2/3]

float core::scoring::fiber_diffraction::pos_mod ( float  x,
float  y 
)
inline

◆ pos_mod() [3/3]

int core::scoring::fiber_diffraction::pos_mod ( int  x,
int  y 
)
inline

◆ retrieve_centroid_scatter_from_pose()

CentroidScatter & core::scoring::fiber_diffraction::retrieve_centroid_scatter_from_pose ( pose::Pose &  pose)

helper routine

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::FIBER_DIFFRACTION_CEN_SCATTERING.

Referenced by setup_centroid_scatter().

◆ retrieve_fa_scatter_from_pose()

FAScatter & core::scoring::fiber_diffraction::retrieve_fa_scatter_from_pose ( pose::Pose &  pose)

helper routine

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::FIBER_DIFFRACTION_FA_SCATTERING.

Referenced by setup_form_factors().

◆ rootj()

void core::scoring::fiber_diffraction::rootj ( int const &  N,
core::Real const &  CUTOFF,
utility::vector1< core::Real > &  zeros,
core::Size &  npoints 
)

References CUTOFF, core::chemical::element::N, and secant().

Referenced by bessel_roots().

◆ sample_layer_lines_from_bins()

void core::scoring::fiber_diffraction::sample_layer_lines_from_bins ( core::Size const &  lmax,
core::Size const &  k_iteration,
utility::vector0< utility::vector1< core::Real > >::iterator const &  layer_lines_R,
utility::vector0< utility::vector1< core::Size > > &  selected_R_l_,
utility::vector0< utility::vector1< core::Real > > &  selected_Rinv_l_ 
)

Referenced by calculate_chi2_free().

◆ secant()

void core::scoring::fiber_diffraction::secant ( int const &  N,
int const &  nitmx,
core::Real  tol,
core::Real *  zeroJ,
int *  ier 
)

References core::chemical::element::N.

Referenced by rootj().

◆ set_r_array()

void core::scoring::fiber_diffraction::set_r_array ( core::Size  num_r_points,
core::Real  k1,
core::Real  k2,
core::Real  max_r,
ObjexxFCL::FArray1D< float > &  rc 
)

References NRbisafe().

Referenced by core::energy_methods::FiberDiffractionEnergyDens::setup_for_scoring().

◆ set_r_inv_array()

void core::scoring::fiber_diffraction::set_r_inv_array ( core::Size  num_r_points,
core::Real  k1,
core::Real  k2,
core::Real  max_r,
ObjexxFCL::FArray1D< float > &  Rinv 
)

References NRbisafe().

Referenced by core::energy_methods::FiberDiffractionEnergyDens::setup_for_scoring().

◆ setup_centroid_scatter()

utility::vector1< OneGaussianScattering > core::scoring::fiber_diffraction::setup_centroid_scatter ( pose::Pose &  pose)

References protocols::cluster::calibur::aa, centroid_scatter(), core::pose::Pose::data(), core::pose::datacache::CacheableDataType::FIBER_DIFFRACTION_CEN_SCATTERING, core::scoring::fiber_diffraction::CentroidScatter::getValues(), core::chemical::name_from_aa(), core::chemical::num_canonical_aas, and retrieve_centroid_scatter_from_pose().

Referenced by core::energy_methods::FiberDiffractionEnergyDens::calculate_rho_fast2().

◆ setup_cylindrical_coords()

void core::scoring::fiber_diffraction::setup_cylindrical_coords ( pose::Pose const &  pose,
core::Size &  natoms,
utility::vector1< Size > &  atom_type_number,
std::map< core::id::AtomID, core::Size > &  AtomID_to_atomnbr,
utility::vector1< Real > &  phi,
utility::vector1< Real > &  z,
utility::vector1< Real > &  r,
utility::vector1< Real > &  bfactors 
)

References core::conformation::Residue::atom_type_index(), core::conformation::Residue::atom_type_set(), core::chemical::element::B, core::conformation::symmetry::SymmetryInfo::bb_is_independent(), core::pose::Pose::conformation(), core::pose::symmetry::is_symmetric(), core::conformation::Residue::natoms(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::Pose::size(), TR(), and core::pose::Pose::xyz().

Referenced by core::energy_methods::FiberDiffractionEnergy::setup_for_derivatives(), and core::energy_methods::FiberDiffractionEnergy::setup_for_scoring().

◆ setup_form_factors()

utility::vector0< utility::vector1< utility::vector1< core::Real > > > core::scoring::fiber_diffraction::setup_form_factors ( pose::Pose &  pose,
core::Size const &  lmax,
utility::vector0< utility::vector1< core::Real > >::iterator const &  layer_lines_R,
core::Real const &  c,
core::Real const &  B_factor,
core::Real const &  B_factor_solv,
core::Real const &  Ksolv 
)

References core::pose::Pose::data(), core::scoring::fiber_diffraction::KromerMann::f0(), core::pose::datacache::CacheableDataType::FIBER_DIFFRACTION_FA_SCATTERING, get_km(), core::scoring::fiber_diffraction::FAScatter::getValues(), retrieve_fa_scatter_from_pose(), and TR().

Referenced by calculate_chi2_free(), core::energy_methods::FiberDiffractionEnergy::setup_for_derivatives(), and core::energy_methods::FiberDiffractionEnergy::setup_for_scoring().

◆ square() [1/2]

core::Real core::scoring::fiber_diffraction::square ( core::Real  x)
inline

◆ square() [2/2]

float core::scoring::fiber_diffraction::square ( float  x)
inline

◆ TR() [1/3]

static basic::Tracer core::scoring::fiber_diffraction::TR ( "core.scoring.fiber_diffraction.FiberDiffraction"  )
static

Referenced by calculate_chi2_free(), find_pitch(), generate_shannon_points(), get_A(), get_km(), getFiberDiffractionData_legacy(), core::scoring::fiber_diffraction::FiberDiffraction::loadFiberDiffractionData(), setup_cylindrical_coords(), setup_form_factors(), core::scoring::fiber_diffraction::FiberDiffraction::setupBesselOrder(), and core::scoring::fiber_diffraction::FiberDiffraction::trimFiberDiffractionData().

◆ TR() [2/3]

static basic::Tracer core::scoring::fiber_diffraction::TR ( "core.scoring.fiber_diffraction.util"  )
static

◆ TR() [3/3]

static basic::Tracer core::scoring::fiber_diffraction::TR ( "core.scoring.fiber_diffraction.util_ndft"  )
static
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