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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  ElectronDensityLoader
 
class  ElectronDensityLoaderCreator
 creator for the ElectronDensityLoader class More...
 
class  ElectronDensityOptions
 
class  ElectronDensityOptionsCreator
 creator for the ElectronDensityOptions class More...
 
class  FastDensEnergy
 
class  FastDensEnergyCreator
 
class  PattersonCorrEnergy
 
class  PattersonCorrEnergyCreator
 
class  KromerMann
 
class  OneGaussianScattering
 

Typedefs

typedef
utility::pointer::owning_ptr
< ElectronDensity > 		ElectronDensityOP
 
typedef
utility::pointer::owning_ptr
< ElectronDensity const > 		ElectronDensityCOP
 
typedef
utility::pointer::owning_ptr
< ElectronDensityLoader > 		ElectronDensityLoaderOP
 
typedef
utility::pointer::owning_ptr
< ElectronDensityLoader const > 		ElectronDensityLoaderCOP
 
typedef
utility::pointer::owning_ptr
< ElectronDensityOptions > 		ElectronDensityOptionsOP
 
typedef
utility::pointer::owning_ptr
< ElectronDensityOptions const > 		ElectronDensityOptionsCOP
 

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")
 
basic::Tracer TR ("core.scoring.electron_density.ElectronDensity")
 
float d2r (float d)
 
double d2r (double d)
 
float square (float x)
 
double square (double x)
 
int min_mod (int x, int y)
 
float min_mod (float x, float y)
 
double min_mod (double x, double y)
 
bool is_missing_density (numeric::xyzVector< core::Real > const &X)
 
static void swap4_aligned (void *v, long ndata)
 
ElectronDensity & getDensityMap ()
 The EDM instance. More...
 
ElectronDensity & getDensityMap_legacy ()
 The EDM instance. More...
 
float pos_mod (float x, float y)
 
int pos_mod (int x, int y)
 
double pos_mod (double x, double y)
 
static basic::Tracer TR ("core.scoring.electron_density.FastDensEnergy")
 
static basic::Tracer TR ("core.scoring.electron_density.PattersonCorrEnergy")
 
void add_dens_scores_from_cmdline_to_scorefxn (core::scoring::ScoreFunction &scorefxn)
 read density weights from the cmd line into the scorefunction More...
 
core::Real interp_spline (ObjexxFCL::FArray3D< double > &coeffs, numeric::xyzVector< core::Real > const &idxX)
 spline interpolation with periodic boundaries More...
 
void spline_coeffs (ObjexxFCL::FArray3D< double > &data, ObjexxFCL::FArray3D< double > &coeffs)
 precompute spline coefficients (float array => double coeffs) More...
 
void spline_coeffs (ObjexxFCL::FArray3D< float > &data, ObjexxFCL::FArray3D< double > &coeffs)
 precompute spline coefficients (double array => double coeffs) 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 (double MINSMP, int NMUL)
 
int findSampling (double MINSMP, int NMUL)
 

Variables

const int CCP4HDSIZE = 1024
 
const core::Real MAX_FLT = 1e37
 

Typedef Documentation

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

Definition at line 27 of file ElectronDensity.fwd.hh.

typedef utility::pointer::owning_ptr< ElectronDensityLoader const > core::scoring::electron_density::ElectronDensityLoaderCOP

Definition at line 26 of file ElectronDensityLoader.fwd.hh.

typedef utility::pointer::owning_ptr< ElectronDensityLoader > core::scoring::electron_density::ElectronDensityLoaderOP

Definition at line 24 of file ElectronDensityLoader.fwd.hh.

typedef utility::pointer::owning_ptr< ElectronDensity > core::scoring::electron_density::ElectronDensityOP

Definition at line 25 of file ElectronDensity.fwd.hh.

typedef utility::pointer::owning_ptr< ElectronDensityOptions const > core::scoring::electron_density::ElectronDensityOptionsCOP

Definition at line 26 of file ElectronDensityOptions.fwd.hh.

typedef utility::pointer::owning_ptr< ElectronDensityOptions > core::scoring::electron_density::ElectronDensityOptionsOP

Definition at line 24 of file ElectronDensityOptions.fwd.hh.

Function Documentation

void core::scoring::electron_density::add_dens_scores_from_cmdline_to_scorefxn ( core::scoring::ScoreFunction &  scorefxn)

read density weights from the cmd line into the scorefunction

update scorefxn with density scores from commandline

Definition at line 35 of file util.cc.

References core::scoring::elec_dens_fast, core::scoring::elec_dens_whole_structure_allatom, core::scoring::elec_dens_whole_structure_ca, core::scoring::elec_dens_window, core::scoring::patterson_cc, and core::scoring::ScoreFunction::set_weight().

Referenced by protocols::loop_build::LoopBuildMover::apply(), protocols::rbsegment_relax::RBSegmentRelax::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::rbsegment_relax::AutoRBMover::AutoRBMover(), protocols::electron_density::dockPoseIntoMap(), protocols::relax::generate_relax_from_cmd(), protocols::symmetric_docking::SymDockProtocol::set_default(), and protocols::electron_density::set_pose_and_scorefxn_for_edens_scoring().

float core::scoring::electron_density::d2r ( float  d)
inline

Definition at line 101 of file ElectronDensity.cc.

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

double core::scoring::electron_density::d2r ( double  d)
inline

Definition at line 102 of file ElectronDensity.cc.

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

Definition at line 256 of file xray_scattering.cc.

Referenced by findSampling().

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

Definition at line 247 of file xray_scattering.cc.

Referenced by findSampling5().

int core::scoring::electron_density::findSampling ( double  MINSMP,
int  NMUL 
)

Definition at line 284 of file xray_scattering.cc.

References factorsLTE19(), and protocols::forge::build::SegmentInsertConnectionScheme::N.

Referenced by core::scoring::electron_density::ElectronDensity::resize(), and core::scoring::electron_density::ElectronDensity::setup_fastscoring_first_time().

int core::scoring::electron_density::findSampling5 ( double  MINSMP,
int  NMUL 
)

Definition at line 270 of file xray_scattering.cc.

References factorsLTE5(), and protocols::forge::build::SegmentInsertConnectionScheme::N.

Referenced by core::scoring::electron_density::ElectronDensity::ElectronDensity(), and core::scoring::electron_density::ElectronDensity::setup_patterson_first_time().

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

Definition at line 60 of file xray_scattering.cc.

References TR().

Referenced by core::scoring::electron_density::ElectronDensity::ElectronDensity(), core::scoring::electron_density::ElectronDensity::matchPose(), core::scoring::electron_density::ElectronDensity::matchPoseToPatterson(), core::scoring::electron_density::ElectronDensity::matchRes(), core::scoring::electron_density::ElectronDensity::readMRCandResize(), core::scoring::electron_density::ElectronDensity::rematchResToPatterson(), core::scoring::electron_density::ElectronDensity::rotAlign2DPose(), core::scoring::electron_density::ElectronDensity::setup_fastscoring_first_time(), core::scoring::electron_density::ElectronDensity::setup_patterson_first_time(), and core::scoring::electron_density::ElectronDensity::updateCachedDensity().

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

Definition at line 92 of file xray_scattering.cc.

References TR().

ElectronDensity & core::scoring::electron_density::getDensityMap ( )

The EDM instance.

Definition at line 147 of file ElectronDensity.cc.

References getDensityMap_legacy().

Referenced by protocols::electron_density::SetupForDensityScoringMover::apply(), protocols::hybridization::CartesianSampler::compute_fragment_bias(), 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_pat(), core::scoring::electron_density::ElectronDensity::dCCdx_res(), protocols::electron_density::dockPoseIntoMap(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::ElecDensAllAtomCenEnergy(), core::scoring::electron_density::ElecDensCenEnergy::ElecDensCenEnergy(), core::scoring::electron_density::ElecDensEnergy::ElecDensEnergy(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::scoring::electron_density::PattersonCorrEnergy::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_atom_derivative(), protocols::viewer::triangleIterator::evalGradient(), protocols::electron_density::fast2DRotAlignPose(), core::scoring::electron_density::FastDensEnergy::FastDensEnergy(), protocols::electron_density::fastTransAlignPose(), protocols::electron_density::findLoopFromDensity(), protocols::electron_density::findLoopFromPatterson(), core::scoring::electron_density::PattersonCorrEnergy::PattersonCorrEnergy(), core::scoring::electron_density::ElecDensEnergy::residue_pair_energy(), core::scoring::electron_density::FastDensEnergy::residue_pair_energy(), core::scoring::electron_density::PattersonCorrEnergy::residue_pair_energy(), core::scoring::electron_density::PattersonCorrEnergy::setup_for_derivatives(), core::scoring::electron_density::ElecDensEnergy::setup_for_derivatives(), core::scoring::electron_density::FastDensEnergy::setup_for_derivatives(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::setup_for_derivatives(), core::scoring::electron_density::ElecDensCenEnergy::setup_for_derivatives(), core::scoring::electron_density::PattersonCorrEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensCenEnergy::setup_for_scoring(), and core::scoring::electron_density::PattersonCorrEnergy::update_residue_for_packing().

ElectronDensity & core::scoring::electron_density::getDensityMap_legacy ( )

The EDM instance.

Definition at line 162 of file ElectronDensity.cc.

References core::scoring::electron_density::ElectronDensity::isMapLoaded(), core::scoring::electron_density::ElectronDensity::readMRCandResize(), and TR().

Referenced by getDensityMap().

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

Definition at line 41 of file util.hh.

Referenced by core::scoring::PoissonBoltzmannPotential::get_potential(), core::scoring::electron_density::ElectronDensity::matchPoseToPatterson(), and core::scoring::electron_density::ElectronDensity::rotAlign2DPose().

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

spline interpolation with periodic boundaries

Definition at line 62 of file util.cc.

References core::scoring::electron_density::SplineInterp::interp3().

Referenced by core::scoring::electron_density::ElectronDensity::dCCdx_fastRes(), core::scoring::electron_density::ElectronDensity::dens_grad(), core::scoring::electron_density::ElectronDensity::matchPoseToPatterson(), and core::scoring::electron_density::ElectronDensity::matchResFast().

bool core::scoring::electron_density::is_missing_density ( numeric::xyzVector< core::Real > const &  X)
inline

Definition at line 124 of file ElectronDensity.cc.

Referenced by core::scoring::electron_density::ElectronDensity::ElectronDensity(), core::scoring::electron_density::ElectronDensity::matchCentroidPose(), core::scoring::electron_density::ElectronDensity::matchPose(), core::scoring::electron_density::ElectronDensity::matchPoseToPatterson(), core::scoring::electron_density::ElectronDensity::matchRes(), core::scoring::electron_density::ElectronDensity::rematchResToPatterson(), core::scoring::electron_density::ElectronDensity::rotAlign2DPose(), core::scoring::electron_density::ElectronDensity::setup_patterson_first_time(), and core::scoring::electron_density::ElectronDensity::updateCachedDensity().

int core::scoring::electron_density::min_mod ( int  x,
int  y 
)
inline

Definition at line 108 of file ElectronDensity.cc.

float core::scoring::electron_density::min_mod ( float  x,
float  y 
)
inline

Definition at line 112 of file ElectronDensity.cc.

double core::scoring::electron_density::min_mod ( double  x,
double  y 
)
inline

Definition at line 116 of file ElectronDensity.cc.

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

Definition at line 529 of file ElectronDensity.hh.

Referenced by core::scoring::electron_density::ElectronDensity::ElectronDensity(), core::scoring::electron_density::ElectronDensity::expandToUnitCell(), core::scoring::electron_density::ElectronDensity::matchCentroidPose(), core::scoring::electron_density::ElectronDensity::matchPose(), core::scoring::electron_density::ElectronDensity::matchPoseToPatterson(), core::scoring::electron_density::ElectronDensity::rotAlign2DPose(), and core::scoring::electron_density::ElectronDensity::setup_patterson_first_time().

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

Definition at line 525 of file ElectronDensity.hh.

double core::scoring::electron_density::pos_mod ( double  x,
double  y 
)
inline

Definition at line 533 of file ElectronDensity.hh.

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

Definition at line 88 of file util.hh.

Referenced by core::scoring::electron_density::ElectronDensity::resize(), and core::scoring::electron_density::ElectronDensity::setup_fastscoring_first_time().

void core::scoring::electron_density::spline_coeffs ( ObjexxFCL::FArray3D< double > &  data,
ObjexxFCL::FArray3D< double > &  coeffs 
)

precompute spline coefficients (float array => double coeffs)

Definition at line 71 of file util.cc.

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

Referenced by core::scoring::electron_density::ElectronDensity::computeGradients(), core::scoring::electron_density::ElectronDensity::matchPoseToPatterson(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::precompute_unweighted_score(), core::scoring::electron_density::ElectronDensity::setup_fastscoring_first_time(), and spline_coeffs().

void core::scoring::electron_density::spline_coeffs ( ObjexxFCL::FArray3D< float > &  data,
ObjexxFCL::FArray3D< double > &  coeffs 
)

precompute spline coefficients (double array => double coeffs)

Definition at line 79 of file util.cc.

References protocols::forge::build::SegmentInsertConnectionScheme::N, and spline_coeffs().

core::Real core::scoring::electron_density::SQ ( core::Real  N)
inline

Definition at line 85 of file ElecDensAllAtomCenEnergy.cc.

References protocols::forge::build::SegmentInsertConnectionScheme::N.

Referenced by core::scoring::electron_density::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensCenEnergy::eval_atom_derivative(), and core::scoring::electron_density::ElecDensEnergy::eval_atom_derivative().

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

Definition at line 103 of file ElectronDensity.cc.

Referenced by core::scoring::electron_density::ElectronDensity::computeCrystParams(), protocols::fldsgn::filters::InterlockingAromaFilter::contact_distance(), core::scoring::methods::HybridVDW_Energy::eval_atom_derivative(), protocols::loops::loop_closure::ccd::fast_ccd_loop_closure(), 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::electron_density::ElectronDensity::matchPoseToPatterson(), protocols::fldsgn::NcontactsCalculator::recompute(), core::scoring::electron_density::ElectronDensity::rematchResToPatterson(), protocols::fldsgn::potentials::AACompositionEnergy::residue_energy(), core::scoring::methods::HybridVDW_Energy::residue_pair_energy(), core::scoring::electron_density::ElectronDensity::rotAlign2DPose(), protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::score(), protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::score(), core::scoring::methods::LK_BallEnergy::setup_d2_bounds(), and core::scoring::electron_density::ElectronDensity::updateCachedDensity().

double core::scoring::electron_density::square ( double  x)
inline

Definition at line 104 of file ElectronDensity.cc.

static void core::scoring::electron_density::swap4_aligned ( void *  v,
long  ndata 
)
static

Definition at line 133 of file ElectronDensity.cc.

References protocols::forge::build::SegmentInsertConnectionScheme::N.

Referenced by core::io::silent::BinaryRNASilentStruct::init_from_lines(), core::io::silent::BinaryProteinSilentStruct::init_from_lines(), and core::scoring::electron_density::ElectronDensity::readMRCandResize().

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

Referenced by 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::computeStats(), 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_pat(), core::scoring::electron_density::ElectronDensity::dCCdx_res(), core::scoring::electron_density::ElecDensCenEnergy::ElecDensCenEnergy(), core::scoring::electron_density::ElecDensEnergy::ElecDensEnergy(), core::scoring::electron_density::ElectronDensity::ElectronDensity(), get_A(), get_km(), getDensityMap_legacy(), core::scoring::electron_density::ElectronDensity::initializeSymmOps(), core::scoring::electron_density::ElectronDensity::matchCentroidPose(), core::scoring::electron_density::ElectronDensity::matchPose(), core::scoring::electron_density::ElectronDensity::matchPoseToPatterson(), core::scoring::electron_density::ElectronDensity::matchRes(), core::scoring::electron_density::ElectronDensity::matchResFast(), core::scoring::electron_density::ElectronDensity::readMRCandResize(), core::scoring::electron_density::PattersonCorrEnergy::residue_pair_energy(), core::scoring::electron_density::ElectronDensity::resize(), core::scoring::electron_density::ElectronDensity::rotAlign2DPose(), core::scoring::electron_density::ElectronDensity::setup_fastscoring_first_time(), core::scoring::electron_density::ElecDensEnergy::setup_for_derivatives(), core::scoring::electron_density::PattersonCorrEnergy::setup_for_scoring(), 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(), core::scoring::electron_density::ElectronDensity::setup_patterson_first_time(), core::scoring::electron_density::ElectronDensity::showCachedScores(), and core::scoring::electron_density::ElectronDensity::writeMRC().

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.electron_density.PattersonCorrEnergy"  )
static

Variable Documentation

const int core::scoring::electron_density::CCP4HDSIZE = 1024

Definition at line 93 of file ElectronDensity.cc.

Referenced by core::scoring::electron_density::ElectronDensity::readMRCandResize(), and core::scoring::electron_density::ElectronDensity::writeMRC().

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

Definition at line 45 of file ElectronDensity.hh.

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

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