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core::scoring::electron_density Namespace Reference

Namespaces

 SplineInterp
 

Classes

class  ElectronDensity
 
class  KromerMann
 
class  OneGaussianScattering
 
struct  poseCoord
 

Typedefs

typedef
utility::pointer::shared_ptr
< ElectronDensity
ElectronDensityOP
 
typedef
utility::pointer::shared_ptr
< ElectronDensity const > 
ElectronDensityCOP
 
typedef utility::vector1
< poseCoord
poseCoords
 

Functions

static basic::Tracer TR ("core.scoring.electron_density.ElectronDensity")
 
float d2r (float d)
 SHORT HELPER FUNCTIONS. More...
 
core::Real d2r (core::Real d)
 
float square (float x)
 
core::Real square (core::Real x)
 
int min_mod (int x, int y)
 
float min_mod (float x, float y)
 
core::Real min_mod (core::Real x, core::Real y)
 
static void swap4_aligned (void *v, long ndata)
 
ElectronDensitygetDensityMap (std::string const &filename="", bool force_reload=false)
 The EDM instance. More...
 
ElectronDensitygetDensityMap_legacy (std::string const &filename="", bool force_reload=false)
 The EDM instance. More...
 
int pos_mod (int x, int y)
 
float pos_mod (float x, float y)
 
core::Real pos_mod (core::Real x, core::Real y)
 
static basic::Tracer TR ("protocols.scoring.electron_density.util")
 
void add_dens_scores_from_cmdline_to_scorefxn (core::scoring::ScoreFunction &scorefxn)
 read density weights from the cmd line into the scorefunction More...
 
bool pose_has_nonzero_Bs (core::pose::Pose const &pose)
 helper function quickly guesses if a pose has non-zero B factors More...
 
bool pose_has_nonzero_Bs (poseCoords const &pose)
 
core::Real interp_spline (ObjexxFCL::FArray3D< core::Real > &coeffs, numeric::xyzVector< core::Real > const &idxX, bool mirrored)
 spline interpolation with periodic boundaries More...
 
numeric::xyzVector< core::Realinterp_dspline (ObjexxFCL::FArray3D< core::Real > &coeffs, numeric::xyzVector< core::Real > const &idxX, bool mirrored)
 spline interpolation with periodic boundaries More...
 
core::Real interp_spline (ObjexxFCL::FArray3D< float > &coeffs, numeric::xyzVector< core::Real > const &idxX, bool mirrored)
 spline interpolation with periodic boundaries, single precision More...
 
numeric::xyzVector< core::Realinterp_dspline (ObjexxFCL::FArray3D< float > &coeffs, numeric::xyzVector< core::Real > const &idxX, bool mirrored)
 spline interpolation with periodic boundaries, single precision More...
 
void spline_coeffs (ObjexxFCL::FArray3D< core::Real > const &data, ObjexxFCL::FArray3D< core::Real > &coeffs, bool mirrored=false)
 precompute spline coefficients (float array => core::Real coeffs) More...
 
void spline_coeffs (ObjexxFCL::FArray3D< float > const &data, ObjexxFCL::FArray3D< core::Real > &coeffs, bool mirrored=false)
 precompute spline coefficients (core::Real array => core::Real coeffs) More...
 
void conj_map_times (ObjexxFCL::FArray3D< std::complex< core::Real > > &map_product, ObjexxFCL::FArray3D< std::complex< core::Real > > const &mapA, ObjexxFCL::FArray3D< std::complex< core::Real > > const &mapB)
 
ObjexxFCL::FArray3D< core::Realconvolute_maps (ObjexxFCL::FArray3D< core::Real > const &mapA, ObjexxFCL::FArray3D< core::Real > const &mapB)
 
core::Real interp_spline (ObjexxFCL::FArray4D< core::Real > &coeffs, core::Real slab, numeric::xyzVector< core::Real > const &idxX)
 4D interpolants More...
 
void interp_dspline (ObjexxFCL::FArray4D< core::Real > &coeffs, numeric::xyzVector< core::Real > const &idxX, core::Real slab, numeric::xyzVector< core::Real > &gradX, core::Real &gradSlab)
 spline interpolation with periodic boundaries More...
 
void spline_coeffs (ObjexxFCL::FArray4D< core::Real > const &data, ObjexxFCL::FArray4D< core::Real > &coeffs)
 
void spline_coeffs (ObjexxFCL::FArray4D< float > const &data, ObjexxFCL::FArray4D< core::Real > &coeffs)
 
void calculate_density_nbr (pose::Pose &pose, std::map< Size, Real > &per_rsd_dens, std::map< Size, Real > &per_rsd_nbrdens, core::conformation::symmetry::SymmetryInfoCOP syminfo, bool mixed_sliding_window=false, Size sliding_window_size=3)
 Calculate the density and relative neighbor density score. Map must be initialized to number of calculation residues. More...
 
void calculate_rama (pose::Pose &pose, std::map< Size, Real > &rama, Size n_symm_subunit, Real weight=0.2)
 Calculate the geometry score using rama or sugar_bb Map must be initialized to number of calculation residues. More...
 
void calculate_geometry (pose::Pose &pose, std::map< Size, Real > &geometry, Size n_symm_subunit, Real weight=1.0)
 Calculate the geometry score using cartesian scoring. Map must be initialized to number of calculation residues. More...
 
void calc_per_rsd_score (pose::Pose &pose, scoring::ScoreType const &score_type, std::map< Size, Real > &per_rsd_score, Size n_symm_subunit, Real weight)
 Fill the weighted per-residue weighted score of a particular score type Note, does not decompose pair-energies, but does work with symmetry. More...
 
template<class S >
core::Real interp_linear (ObjexxFCL::FArray3D< S > const &data, numeric::xyzVector< core::Real > const &idxX)
 trilinear interpolation with periodic boundaries More...
 
template<class S , class T >
void resample (ObjexxFCL::FArray3D< S > const &density, ObjexxFCL::FArray3D< T > &newDensity, numeric::xyzVector< int > newDims)
 templated helper function to FFT resample a map More...
 
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)
 

Variables

const core::Real MAX_FLT = 1e37
 

Typedef Documentation

typedef utility::pointer::shared_ptr< ElectronDensity const > core::scoring::electron_density::ElectronDensityCOP

Function Documentation

void core::scoring::electron_density::add_dens_scores_from_cmdline_to_scorefxn ( core::scoring::ScoreFunction scorefxn)
void core::scoring::electron_density::calc_per_rsd_score ( pose::Pose pose,
scoring::ScoreType const &  score_type,
std::map< Size, Real > &  per_rsd_score,
Size  n_symm_subunit,
Real  weight 
)

Fill the weighted per-residue weighted score of a particular score type Note, does not decompose pair-energies, but does work with symmetry.

References core::pose::Pose::energies(), and core::scoring::Energies::residue_total_energies().

Referenced by calculate_geometry().

void core::scoring::electron_density::calculate_density_nbr ( pose::Pose pose,
std::map< Size, Real > &  per_rsd_dens,
std::map< Size, Real > &  per_rsd_nbrdens,
core::conformation::symmetry::SymmetryInfoCOP  symminfo,
bool  mixed_sliding_window,
Size  sliding_window_size 
)
void core::scoring::electron_density::calculate_geometry ( pose::Pose pose,
std::map< Size, Real > &  geometry,
Size  n_symm_subunit,
Real  weight 
)

Calculate the geometry score using cartesian scoring. Map must be initialized to number of calculation residues.

References calc_per_rsd_score(), and core::scoring::cart_bonded_angle.

Referenced by core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::compute_scores(), and protocols::hybridization::FragmentBiasAssigner::geometry().

void core::scoring::electron_density::calculate_rama ( pose::Pose pose,
std::map< Size, Real > &  rama,
Size  n_symm_subunit,
Real  weight 
)
void core::scoring::electron_density::conj_map_times ( ObjexxFCL::FArray3D< std::complex< core::Real > > &  map_product,
ObjexxFCL::FArray3D< std::complex< core::Real > > const &  mapA,
ObjexxFCL::FArray3D< std::complex< core::Real > > const &  mapB 
)

Referenced by convolute_maps().

ObjexxFCL::FArray3D< core::Real > core::scoring::electron_density::convolute_maps ( ObjexxFCL::FArray3D< core::Real > const &  mapA,
ObjexxFCL::FArray3D< core::Real > const &  mapB 
)

References conj_map_times().

float core::scoring::electron_density::d2r ( float  d)
inline
core::Real core::scoring::electron_density::d2r ( core::Real  d)
inline
bool core::scoring::electron_density::factorsLTE19 ( int  X)

Referenced by findSampling().

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

Referenced by findSampling5().

int core::scoring::electron_density::findSampling ( core::Real  MINSMP,
int  NMUL 
)
int core::scoring::electron_density::findSampling5 ( core::Real  MINSMP,
int  NMUL 
)
OneGaussianScattering core::scoring::electron_density::get_A ( std::string  elt)
KromerMann core::scoring::electron_density::get_km ( std::string  elt)

References TR().

ElectronDensity & core::scoring::electron_density::getDensityMap ( std::string const &  filename,
bool  force_reload 
)

The EDM instance.

ELECTRON DENSITY CLASS DEFINITIONS

References getDensityMap_legacy().

Referenced by protocols::electron_density::ScaleMapIntensities::apply(), protocols::electron_density::ReportFSC::apply(), protocols::task_operations::SelectByDensityFitOperation::apply(), protocols::electron_density::SetupForDensityScoringMover::apply(), protocols::electron_density::VoxelSpacingRefinementMover::apply(), protocols::electron_density::BfactorFittingMover::apply(), protocols::cryst::RecomputeDensityMapMover::apply(), protocols::cryst::LoadDensityMapMover::apply(), core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::calculate(), calculate_density_nbr(), protocols::loop_grower::LoopGrower::check_auto_stop(), protocols::hybridization::FragmentBiasAssigner::density(), protocols::electron_density::DockIntoDensityMover::density_grid_search(), protocols::electron_density::VoxelSpacingMultifunc::dfunc(), protocols::electron_density::BfactorMultifunc::dfunc(), core::energy_methods::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::energy_methods::ElecDensCenEnergy::eval_atom_derivative(), core::energy_methods::ElecDensEnergy::eval_atom_derivative(), core::energy_methods::FastDensEnergy::eval_residue_pair_derivatives(), protocols::viewer::triangleIterator::evalGradient(), protocols::electron_density::findLoopFromDensity(), protocols::electron_density::VoxelSpacingMultifunc::foldInChanges(), protocols::hybridization::MRMover::init(), protocols::electron_density::DockIntoDensityMover::map_from_spectrum(), protocols::rotamer_recovery::RRComparerElecDensDiff::measure_rotamer_recovery(), protocols::loop_grower::LoopGrower::modifieddensity(), protocols::electron_density::VoxelSpacingMultifunc::operator()(), protocols::electron_density::BfactorMultifunc::operator()(), protocols::loop_grower::DensSkeleton::path_length(), protocols::electron_density::DockIntoDensityMover::poseSphericalSamples(), protocols::electron_density::DockIntoDensityMover::predefine_search(), core::energy_methods::FastDensEnergy::residue_pair_energy(), core::energy_methods::ElecDensEnergy::residue_pair_energy(), protocols::electron_density::DockIntoDensityMover::select_points(), core::energy_methods::ElecDensAllAtomCenEnergy::setup_for_derivatives(), core::energy_methods::ElecDensEnergy::setup_for_derivatives(), core::energy_methods::ElecDensCenEnergy::setup_for_derivatives(), core::energy_methods::FastDensEnergy::setup_for_derivatives(), core::energy_methods::ElecDensEnergy::setup_for_scoring(), core::energy_methods::FastDensEnergy::setup_for_scoring(), core::energy_methods::ElecDensAllAtomCenEnergy::setup_for_scoring(), core::energy_methods::ElecDensCenEnergy::setup_for_scoring(), and protocols::electron_density::VoxelSpacingMultifunc::VoxelSpacingMultifunc().

ElectronDensity & core::scoring::electron_density::getDensityMap_legacy ( std::string const &  filename,
bool  force_reload 
)
numeric::xyzVector< core::Real > core::scoring::electron_density::interp_dspline ( ObjexxFCL::FArray3D< core::Real > &  coeffs,
numeric::xyzVector< core::Real > const &  idxX,
bool  mirrored 
)
numeric::xyzVector< core::Real > core::scoring::electron_density::interp_dspline ( ObjexxFCL::FArray3D< float > &  coeffs,
numeric::xyzVector< core::Real > const &  idxX,
bool  mirrored 
)

spline interpolation with periodic boundaries, single precision

void core::scoring::electron_density::interp_dspline ( ObjexxFCL::FArray4D< core::Real > &  coeffs,
numeric::xyzVector< core::Real > const &  idxX,
core::Real  slab,
numeric::xyzVector< core::Real > &  gradX,
core::Real gradSlab 
)

spline interpolation with periodic boundaries

References core::scoring::electron_density::SplineInterp::grad4().

template<class S >
core::Real core::scoring::electron_density::interp_linear ( ObjexxFCL::FArray3D< S > const &  data,
numeric::xyzVector< core::Real > const &  idxX 
)

trilinear interpolation with periodic boundaries

References core::chemical::element::S.

Referenced by core::scoring::PoissonBoltzmannPotential::get_potential().

core::Real core::scoring::electron_density::interp_spline ( ObjexxFCL::FArray3D< core::Real > &  coeffs,
numeric::xyzVector< core::Real > const &  idxX,
bool  mirrored 
)
core::Real core::scoring::electron_density::interp_spline ( ObjexxFCL::FArray3D< float > &  coeffs,
numeric::xyzVector< core::Real > const &  idxX,
bool  mirrored 
)

spline interpolation with periodic boundaries, single precision

spline interpolation with periodic boundaries

core::Real core::scoring::electron_density::interp_spline ( ObjexxFCL::FArray4D< core::Real > &  coeffs,
core::Real  slab,
numeric::xyzVector< core::Real > const &  idxX 
)

4D interpolants

4d interpolants

spline interpolation with periodic boundaries

References core::scoring::electron_density::SplineInterp::interp4().

int core::scoring::electron_density::min_mod ( int  x,
int  y 
)
inline
float core::scoring::electron_density::min_mod ( float  x,
float  y 
)
inline
core::Real core::scoring::electron_density::min_mod ( core::Real  x,
core::Real  y 
)
inline
int core::scoring::electron_density::pos_mod ( int  x,
int  y 
)
inline
float core::scoring::electron_density::pos_mod ( float  x,
float  y 
)
inline
core::Real core::scoring::electron_density::pos_mod ( core::Real  x,
core::Real  y 
)
inline
bool core::scoring::electron_density::pose_has_nonzero_Bs ( core::pose::Pose const &  pose)
bool core::scoring::electron_density::pose_has_nonzero_Bs ( poseCoords const &  pose)
template<class S , class T >
void core::scoring::electron_density::resample ( ObjexxFCL::FArray3D< S > const &  density,
ObjexxFCL::FArray3D< T > &  newDensity,
numeric::xyzVector< int >  newDims 
)

templated helper function to FFT resample a map

References protocols::mean_field::max(), and protocols::mean_field::min().

Referenced by core::scoring::electron_density::ElectronDensity::resize().

void core::scoring::electron_density::spline_coeffs ( ObjexxFCL::FArray3D< core::Real > const &  data,
ObjexxFCL::FArray3D< core::Real > &  coeffs,
bool  mirrored 
)
void core::scoring::electron_density::spline_coeffs ( ObjexxFCL::FArray3D< float > const &  data,
ObjexxFCL::FArray3D< core::Real > &  coeffs,
bool  mirrored 
)

precompute spline coefficients (core::Real array => core::Real coeffs)

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

void core::scoring::electron_density::spline_coeffs ( ObjexxFCL::FArray4D< core::Real > const &  data,
ObjexxFCL::FArray4D< core::Real > &  coeffs 
)
void core::scoring::electron_density::spline_coeffs ( ObjexxFCL::FArray4D< float > const &  data,
ObjexxFCL::FArray4D< core::Real > &  coeffs 
)
float core::scoring::electron_density::square ( float  x)
inline

Referenced by protocols::loops::loop_closure::ccd::compute_single_direction_deviation(), core::scoring::electron_density::ElectronDensity::computeCrystParams(), protocols::fldsgn::filters::InterlockingAromaFilter::contact_distance(), core::energy_methods::HybridVDW_Energy::eval_atom_derivative(), core::scoring::dna::DNA_DihedralPotential::eval_harmonic_backbone_torsion_score_and_deriv(), core::scoring::dna::DNA_DihedralPotential::eval_harmonic_sugar_pucker_dependent_chi_torsion_score_and_deriv(), core::scoring::dna::DNA_DihedralPotential::eval_sugar_torsion_score_and_deriv(), protocols::evolution::NucleotideMutation::find_neighbors(), core::conformation::find_neighbors_3dgrid(), core::conformation::find_neighbors_3dgrid_restricted(), core::conformation::find_neighbors_octree(), core::conformation::find_neighbors_octree_restricted(), protocols::pockets::PlaidFingerprint::fp_compare(), protocols::scoring::ImplicitFastClashCheck::init_clash_check(), core::scoring::electron_density::ElectronDensity::matchCentroidPose(), core::scoring::dna::DNA_DihedralPotential::parse_dna_geometry_log(), protocols::fldsgn::NcontactsCalculator::recompute(), protocols::fldsgn::potentials::AACompositionEnergy::residue_energy(), core::energy_methods::HybridVDW_Energy::residue_pair_energy(), protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::score(), protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::score(), protocols::cryst::Spacegroup::set_parameters(), and core::scoring::lkball::LK_BallEnergy::setup_d2_bounds().

core::Real core::scoring::electron_density::square ( core::Real  x)
inline
static void core::scoring::electron_density::swap4_aligned ( void *  v,
long  ndata 
)
static
static basic::Tracer core::scoring::electron_density::TR ( "protocols.scoring.electron_density.util"  )
static
static basic::Tracer core::scoring::electron_density::TR ( "core.scoring.electron_density.ElectronDensity"  )
static

Variable Documentation

const core::Real core::scoring::electron_density::MAX_FLT = 1e37