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core::scoring::electron_density Namespace Reference

Namespaces

 SplineInterp
 

Classes

class  ElecDensAllAtomCenEnergy
 
class  ElecDensAllAtomCenEnergyCreator
 
class  ElecDensCenEnergy
 
class  ElecDensCenEnergyCreator
 
class  ElecDensEnergy
 
class  ElecDensEnergyCreator
 
class  ElectronDensity
 
class  FastDensEnergy
 
class  FastDensEnergyCreator
 
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.methods.ElecDensEnergy")
 
core::Real SQ (core::Real N)
 
static basic::Tracer TR ("core.scoring.electron_density.ElecDensEnergy")
 
static basic::Tracer TR ("core.scoring.electron_density.ElecDensEnergy")
 
static basic::Tracer TR ("core.scoring.electron_density.FastDensEnergy")
 
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::scoring::electron_density::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensCenEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensEnergy::eval_atom_derivative(), core::scoring::electron_density::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::scoring::electron_density::FastDensEnergy::residue_pair_energy(), core::scoring::electron_density::ElecDensEnergy::residue_pair_energy(), protocols::electron_density::DockIntoDensityMover::select_points(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::setup_for_derivatives(), core::scoring::electron_density::ElecDensEnergy::setup_for_derivatives(), core::scoring::electron_density::ElecDensCenEnergy::setup_for_derivatives(), core::scoring::electron_density::FastDensEnergy::setup_for_derivatives(), core::scoring::electron_density::ElecDensEnergy::setup_for_scoring(), core::scoring::electron_density::FastDensEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::setup_for_scoring(), core::scoring::electron_density::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 
)
core::Real core::scoring::electron_density::SQ ( core::Real  N)
inline
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::scoring::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::scoring::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.FastDensEnergy"  )
static
static basic::Tracer core::scoring::electron_density::TR ( "core.scoring.electron_density.ElecDensEnergy"  )
static
static basic::Tracer core::scoring::electron_density::TR ( "core.scoring.methods.ElecDensEnergy"  )
static

Referenced by core::scoring::electron_density::ElectronDensity::calcRhoC(), calculate_density_nbr(), core::scoring::electron_density::ElectronDensity::compute_symm_rotations(), core::scoring::electron_density::ElectronDensity::computeCrystParams(), core::scoring::electron_density::ElectronDensity::computeGradients(), core::scoring::electron_density::ElectronDensity::dCCdB_fastRes(), core::scoring::electron_density::ElectronDensity::dCCdx_aacen(), core::scoring::electron_density::ElectronDensity::dCCdx_cen(), core::scoring::electron_density::ElectronDensity::dCCdx_fastRes(), core::scoring::electron_density::ElectronDensity::dCCdx_PointFast(), core::scoring::electron_density::ElectronDensity::dCCdx_res(), core::scoring::electron_density::ElectronDensity::ElectronDensity(), get_A(), get_km(), getDensityMap_legacy(), core::scoring::electron_density::ElectronDensity::getFSC(), core::scoring::electron_density::ElectronDensity::getIntensities(), core::scoring::electron_density::ElectronDensity::getPhaseError(), core::scoring::electron_density::ElectronDensity::getResolutionBins(), core::scoring::electron_density::ElectronDensity::initializeSymmOps(), core::scoring::electron_density::ElectronDensity::mapSphericalSamples(), core::scoring::electron_density::ElectronDensity::matchAtomFast(), core::scoring::electron_density::ElectronDensity::matchCentroidPose(), core::scoring::electron_density::ElectronDensity::matchPointFast(), core::scoring::electron_density::ElectronDensity::matchPose(), core::scoring::electron_density::ElectronDensity::matchRes(), core::scoring::electron_density::ElectronDensity::matchResFast(), core::scoring::electron_density::ElectronDensity::readMRCandResize(), core::scoring::electron_density::ElectronDensity::rescale_fastscoring_temp_bins(), core::scoring::electron_density::ElectronDensity::resize(), core::scoring::electron_density::ElectronDensity::scaleIntensities(), core::scoring::electron_density::ElectronDensity::set_voxel_spacing(), core::scoring::electron_density::ElectronDensity::setup_fastscoring_first_time(), core::scoring::electron_density::ElecDensEnergy::setup_for_derivatives(), core::scoring::electron_density::ElecDensEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::setup_for_scoring(), core::scoring::electron_density::FastDensEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensCenEnergy::setup_for_scoring(), and core::scoring::electron_density::ElectronDensity::writeMRC().

static basic::Tracer core::scoring::electron_density::TR ( "core.scoring.electron_density.ElecDensEnergy"  )
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