protocols::electron_density Namespace Reference

Classes
class	BfactorFittingMover
	mover to fit B factors More...
class	BfactorFittingMoverCreator
class	BfactorMultifunc
	Bfactor multifunc. More...
class	DensitySymmInfo
	scale density map intensities to match a pose's More...
class	DockIntoDensityMover
	The workhorse. More...
class	PointScoreComparator
class	RBfitResult
class	RBfitResultComparitor
class	RefinementResult
class	RefinementResultComparitor
class	ReportFSC
	scale density map intensities to match a pose's More...
class	ReportFSCCreator
class	ResultDB
class	ScaleMapIntensities
	scale density map intensities to match a pose's More...
class	ScaleMapIntensitiesCreator
struct	ScoredPoint
struct	ScoredPointCmptr
class	SetupForDensityScoringMover
class	SetupForDensityScoringMoverCreator
class	VoxelSpacingMultifunc
	Bfactor multifunc. More...
class	VoxelSpacingRefinementMover
	mover to fit B factors More...
class	VoxelSpacingRefinementMoverCreator

Typedefs
typedef ResultDB< RBfitResult, RBfitResultComparitor >	RBfitResultDB
typedef ResultDB < RefinementResult, RefinementResultComparitor >	RefinementResultDB
typedef utility::pointer::shared_ptr < DockIntoDensityMover >	DockIntoDensityMoverOP
typedef utility::pointer::shared_ptr < SetupForDensityScoringMover >	SetupForDensityScoringMoverOP

Functions
void	symmetrizeBfactors (core::pose::Pose &pose)
	helper function More...
static basic::Tracer	TR ("protocols.electron_density.DockIntoDensityMover")
core::Real	get_rms (core::pose::PoseOP r1, core::pose::PoseOP r2, DensitySymmInfo const &d)
core::Real	get_rms (RefinementResult r1, RefinementResult r2, DensitySymmInfo const &d)
core::Real	get_rot_angle (numeric::xyzMatrix< core::Real > R)
static basic::Tracer	TR ("protocols.electron_density.util")
void	set_pose_and_scorefxn_for_edens_scoring (core::pose::Pose &pose, core::scoring::ScoreFunction &scorefxn)
static basic::Tracer	TR ("protocols.electron_density.util")
protocols::loops::Loops	findLoopFromDensity (core::pose::Pose &pose, core::Real frac, int max_helix_melt, int max_strand_melt)
core::Real	dockPoseIntoMap (core::pose::Pose &pose, std::string const &align_in)

Typedef Documentation

typedef utility::pointer::shared_ptr< DockIntoDensityMover > protocols::electron_density::DockIntoDensityMoverOP

typedef ResultDB<RBfitResult,RBfitResultComparitor> protocols::electron_density::RBfitResultDB

typedef ResultDB<RefinementResult,RefinementResultComparitor> protocols::electron_density::RefinementResultDB

typedef utility::pointer::shared_ptr< SetupForDensityScoringMover > protocols::electron_density::SetupForDensityScoringMoverOP

Function Documentation

core::Real protocols::electron_density::dockPoseIntoMap	(	core::pose::Pose &	pose,
		std::string const &	align_in
	)

References core::scoring::electron_density::add_dens_scores_from_cmdline_to_scorefxn(), 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::pose::Pose::fold_tree(), core::kinematics::FoldTree::get_outgoing_edges(), core::scoring::get_score_function(), core::pose::symmetry::is_symmetric(), core::pose::symmetry::make_symmetric_movemap(), core::kinematics::FoldTree::root(), and TR().

Referenced by protocols::electron_density::SetupForDensityScoringMover::apply().

protocols::loops::Loops protocols::electron_density::findLoopFromDensity	(	core::pose::Pose &	pose,
		core::Real	frac,
		int	max_helix_melt,
		int	max_strand_melt
	)

References core::conformation::Residue::atom(), core::kinematics::FoldTree::cutpoints(), core::scoring::dssp::Dssp::dssp_reduced(), core::pose::Pose::fold_tree(), core::scoring::electron_density::getDensityMap(), core::kinematics::FoldTree::is_cutpoint(), core::conformation::Residue::is_polymer(), protocols::mean_field::max(), protocols::mean_field::min(), core::conformation::Residue::natoms(), protocols::loops::Loops::push_back(), core::pose::Pose::residue(), core::scoring::electron_density::ElectronDensity::set_nres(), core::pose::Pose::size(), and core::conformation::Atom::xyz().

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

References protocols::electron_density::DensitySymmInfo::min_symm_dist2(), core::chemical::element::N, and core::scoring::rms.

Referenced by protocols::electron_density::DockIntoDensityMover::apply_multi(), protocols::electron_density::DockIntoDensityMover::density_grid_search(), protocols::electron_density::DockIntoDensityMover::do_filter(), protocols::electron_density::DockIntoDensityMover::do_refinement(), get_rms(), and protocols::electron_density::DockIntoDensityMover::print_best_rms().

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

References get_rms(), and protocols::electron_density::RefinementResult::pose_.

core::Real protocols::electron_density::get_rot_angle

(

numeric::xyzMatrix< core::Real >

R

)

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

Referenced by protocols::electron_density::DockIntoDensityMover::do_filter().

void protocols::electron_density::set_pose_and_scorefxn_for_edens_scoring	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunction &	scorefxn
	)

References core::scoring::electron_density::add_dens_scores_from_cmdline_to_scorefxn(), and core::pose::addVirtualResAsRoot().

void protocols::electron_density::symmetrizeBfactors

(

core::pose::Pose &

pose

)

helper function

References core::chemical::aa_vrt, core::chemical::element::B, core::pose::Pose::conformation(), core::pose::symmetry::is_symmetric(), core::conformation::Residue::natoms(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by protocols::electron_density::BfactorFittingMover::apply().

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

static

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

static

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

static

Referenced by protocols::electron_density::ScaleMapIntensities::apply(), protocols::electron_density::ReportFSC::apply(), protocols::electron_density::BfactorFittingMover::apply(), protocols::electron_density::DockIntoDensityMover::apply_multi(), protocols::electron_density::DensitySymmInfo::autocorrelate(), protocols::electron_density::DockIntoDensityMover::density_grid_search(), protocols::electron_density::DensitySymmInfo::detect_axes(), protocols::electron_density::DockIntoDensityMover::do_filter(), protocols::electron_density::DockIntoDensityMover::do_refinement(), dockPoseIntoMap(), protocols::electron_density::DockIntoDensityMover::get_spectrum(), protocols::electron_density::SetupForDensityScoringMover::parse_my_tag(), protocols::electron_density::DockIntoDensityMover::poseSphericalSamples(), protocols::electron_density::DockIntoDensityMover::print_best_rms(), and protocols::electron_density::DockIntoDensityMover::select_points().