Utils for docking into density. More...

#include <protocols/electron_density/DockIntoDensityUtils.hh>
#include <protocols/simple_moves/SwitchResidueTypeSetMover.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <basic/options/keys/edensity.OptionKeys.gen.hh>
#include <core/chemical/AtomType.hh>
#include <core/chemical/AtomTypeSet.hh>
#include <core/conformation/Residue.hh>
#include <core/pose/util.hh>
#include <core/pose/PDBInfo.hh>
#include <core/scoring/electron_density/ElectronDensity.hh>
#include <core/scoring/electron_density/xray_scattering.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/id/AtomID.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/io/StructFileRep.hh>
#include <core/io/StructFileRepOptions.hh>
#include <core/io/silent/SilentFileOptions.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/BinarySilentStruct.hh>
#include <core/types.hh>
#include <utility/io/ozstream.hh>
#include <utility/vector1.hh>
#include <utility/exit.hh>
#include <numeric/fourier/SHT.hh>
#include <numeric/numeric.functions.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/xyzMatrix.hh>
#include <basic/Tracer.hh>

Namespaces
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.

	protocols::electron_density

Functions
static basic::Tracer	TR ("protocols.electron_density.DockIntoDensityUtils")

std::ostream &	protocols::electron_density::operator<< (std::ostream &out, const RBfitResult &result)

template<typename T >
void	protocols::electron_density::write_RBfitResultDB (RBfitResultDB fit_result_DB, T &outresults)
	FUNCTIONS. More...

template void	protocols::electron_density::write_RBfitResultDB< std::ofstream > (RBfitResultDB fit_result_DB, std::ofstream &outresults)

template void	protocols::electron_density::write_RBfitResultDB< std::stringstream > (RBfitResultDB fit_result_DB, std::stringstream &outresults)

template<typename T >
void	protocols::electron_density::dump_RefinementDB_to_silent (T resultDB, std::string const &outfile, std::string const &tag_prefix, std::string const &final_chain, bool const centroid_output, bool const append_to_outfile, utility::vector1< core::pose::PoseCOP > const &natives, DensitySymmInfo const &symminfo, bool const legacy_rms)

template void	protocols::electron_density::dump_RefinementDB_to_silent< RevRefinementResultDB > (RevRefinementResultDB resultDB, std::string const &outfile, std::string const &tag_prefix, std::string const &final_chain, bool const centroid_output, bool const append_to_outfile, utility::vector1< core::pose::PoseCOP > const &natives, DensitySymmInfo const &symminfo, bool const legacy_rms)

template void	protocols::electron_density::dump_RefinementDB_to_silent< RefinementResultDB > (RefinementResultDB resultDB, std::string const &outfile, std::string const &tag_prefix, std::string const &final_chain, bool const centroid_output, bool const append_to_outfile, utility::vector1< core::pose::PoseCOP > const &natives, DensitySymmInfo const &symminfo, bool const legacy_rms)

void	protocols::electron_density::compare_RBfitDB_to_native (RBfitResultDB resultDB, core::pose::Pose const &pose, core::pose::PoseCOPs const &natives, utility::vector1< numeric::xyzVector< core::Real > > const &native_coms, utility::vector1< numeric::xyzVector< core::Real > > const &native_middle_cas, DensitySymmInfo const &symminfo, bool const rot_middle_ca, core::Real const rms_cutoff)

core::Real	protocols::electron_density::get_rms (core::pose::Pose const &r1, core::pose::Pose const &r2, DensitySymmInfo const &d)

template<typename T >
void	protocols::electron_density::dump_and_raise_bad_pose_alignment (core::pose::Pose const &r1, char const r1_chain, core::Size const r1_resnum, core::Size const r1_posenum, core::pose::Pose const &r2, core::Size const r2_posenum, T &out)

template<typename T >
void	protocols::electron_density::dump_and_raise_no_pose_alignment (core::pose::Pose const &r1, core::pose::Pose const &r2, T &out)

core::Real	protocols::electron_density::get_rms (core::pose::Pose const &r1, core::pose::Pose const &r2, DensitySymmInfo const &d, bool const native)

core::Real	protocols::electron_density::get_rms (RefinementResult const &r1, RefinementResult const &r2, DensitySymmInfo const &d)

core::Real	protocols::electron_density::get_gdt (core::pose::Pose const &r1, core::pose::Pose const &r2, DensitySymmInfo const &d, bool native)

void	protocols::electron_density::apply_transform (core::pose::Pose &pose, RBfitResult const &transform)
	FUNCTIONS. More...

core::Real	protocols::electron_density::get_rot_angle (numeric::xyzMatrix< core::Real > const &R)

void	protocols::electron_density::pose_spherical_samples (core::pose::Pose const &pose, ObjexxFCL::FArray3D< core::Real > &sigR, ObjexxFCL::FArray3D< core::Real > &epsR, PoseSphericalSamplesOptions const &params)
	Step 0: map pose to spherically sampled density + mask. More...

core::Real	protocols::electron_density::get_radius (core::pose::Pose const &pose, numeric::xyzVector< core::Real > &com, bool const center_on_middle_ca)
	Get max extent of pose. More...

core::Real	protocols::electron_density::get_spectrum (core::pose::Pose const &pose, utility::vector1< core::Real > &pose_1dspec, core::Real const delR, core::Real const fragDens, bool const convolute_single_residue, bool const center_on_middle_ca)
	Get 1d power spectrum of a pose. More...

void	protocols::electron_density::map_from_spectrum (utility::vector1< core::Real > const &pose_1dspec, ObjexxFCL::FArray3D< core::Real > &rot, core::Real const delR)

utility::vector1< std::pair< numeric::xyzVector< core::Real >, core::Real > >	protocols::electron_density::create_and_sort_point_score_pairs (ObjexxFCL::FArray3D< float > const &densdata, ObjexxFCL::FArray3D< core::Real > const &rot, core::Size const grid_step)

void	protocols::electron_density::dump_points_to_search_to_pdb_or_txt (utility::vector1< numeric::xyzVector< core::Real > > const &points_to_search, std::string const &pdb_filename, std::string const &txt_filename)

utility::vector1< numeric::xyzVector< core::Real > >	protocols::electron_density::select_density_points (core::pose::Pose const &pose, SelectDensityPointsOptions const &params, core::Size &nRsteps)

void	protocols::electron_density::cluster_RefinementDB (RefinementResultDB &results, DensitySymmInfo const &symminfo, core::Real const cluster_radius, core::Size const target_size=0)
	cluster a RefinementResultDB based on a specific cluster_radius. If target_size is unset or More...

void	protocols::electron_density::do_filter (utility::vector1< core::pose::PoseOP > const &poses, RBfitResultDB &results, bool const rescore, DensitySymmInfo const &symminfo, core::Real const cluster_radius)

void	protocols::electron_density::cluster_RBfitResultDB_fast (RBfitResultDB &results, core::Size const delR, core::Size const nRsteps, core::Real const cluster_radius, core::Size const max_results, bool const include_distance, core::scoring::electron_density::ElectronDensity const &dens)

void	protocols::electron_density::density_grid_search (core::Size pose_idx, core::pose::Pose const &pose, RBfitResultDB &results, utility::vector1< numeric::xyzVector< core::Real > > const &points_to_search, DensityGridSearchOptions const &params)
	do the main search over the map More...

Detailed Description

Utils for docking into density.

Author: Frank DiMaio; Danny Farrell

Function Documentation

◆ TR()

static basic::Tracer TR ( "protocols.electron_density.DockIntoDensityUtils" )

static

Namespaces

Functions

Detailed Description

Function Documentation

◆ TR()