protocols::electron_density Namespace Reference

Classes
class	BfactorFittingMover
	mover to fit B factors More...
class	BfactorFittingMoverCreator
class	BfactorMultifunc
	Bfactor multifunc. More...
class	DensityMorphingMover
class	DensityMorphingMoverCreator
class	ReportFSC
	scale density map intensities to match a pose's More...
class	ReportFSCCreator
class	ScaleMapIntensities
	scale density map intensities to match a pose's More...
class	ScaleMapIntensitiesCreator
class	SetupForDensityScoringMover
class	SetupForDensityScoringMoverCreator

Typedefs
typedef utility::pointer::shared_ptr < SetupForDensityScoringMover >	SetupForDensityScoringMoverOP

Functions
void	symmetrizeBfactors (core::pose::Pose &pose)
	helper function More...
core::id::AtomID	find_best_anchor (core::pose::Pose &pose)
static thread_local basic::Tracer	TR ("protocols.electron_density.util")
void	set_pose_and_scorefxn_for_edens_scoring (core::pose::Pose &pose, core::scoring::ScoreFunction &scorefxn)
static thread_local basic::Tracer	TR ("protocols.electron_density.util")
protocols::loops::Loops	findLoopFromPatterson (core::pose::Pose &pose, core::Size N, core::Size nloops, bool allow_termini)
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 align_in)
core::Real	fastTransAlignPose (core::pose::Pose &pose)
core::Real	fast2DRotAlignPose (core::pose::Pose &pose, std::string axis)

Typedef Documentation

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

Function Documentation

core::Real protocols::electron_density::dockPoseIntoMap	(	core::pose::Pose &	pose,
		std::string	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, fast2DRotAlignPose(), fastTransAlignPose(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::get_outgoing_edges(), core::kinematics::Jump::get_rotation(), core::scoring::get_score_function(), core::scoring::electron_density::getDensityMap(), core::scoring::electron_density::ElectronDensity::getUseDensityInMinimizer(), core::pose::symmetry::is_symmetric(), core::pose::Pose::jump(), core::pose::symmetry::make_symmetric_movemap(), protocols::membrane::geometry::membrane_axis(), option, core::scoring::patterson_cc, protocols::geometry::random_reorientation_matrix(), core::kinematics::FoldTree::root(), rot(), core::pose::Pose::set_jump(), core::kinematics::Jump::set_rotation(), core::scoring::electron_density::ElectronDensity::setUseDensityInMinimizer(), core::scoring::symmetry::symmetrize_scorefunction(), and TR().

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

core::Real protocols::electron_density::fast2DRotAlignPose	(	core::pose::Pose &	pose,
		std::string	axis
	)

References core::chemical::aa_vrt, core::scoring::electron_density::getDensityMap(), core::pose::Pose::residue(), core::scoring::electron_density::ElectronDensity::rotAlign2DPose(), core::pose::Pose::set_xyz(), core::pose::Pose::total_residue(), TR(), core::conformation::Atom::xyz(), and core::pose::Pose::xyz().

Referenced by dockPoseIntoMap().

core::Real protocols::electron_density::fastTransAlignPose

(

core::pose::Pose &

pose

)

References core::chemical::aa_vrt, core::scoring::electron_density::ElectronDensity::getCoM(), core::scoring::electron_density::getDensityMap(), core::scoring::electron_density::ElectronDensity::idx2cart(), core::pose::Pose::residue(), core::pose::Pose::set_xyz(), core::pose::Pose::total_residue(), core::conformation::Atom::xyz(), and core::pose::Pose::xyz().

Referenced by dockPoseIntoMap().

core::id::AtomID protocols::electron_density::find_best_anchor

(

core::pose::Pose &

pose

)

References core::chemical::ResidueType::atom_index(), core::pose::Pose::conformation(), numeric::xyzVector< class >::distance_squared(), core::chemical::ResidueType::has(), core::pose::symmetry::is_symmetric(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

Referenced by protocols::electron_density::DensityMorphingMover::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(), core::conformation::Residue::natoms(), protocols::loops::Loops::push_back(), core::pose::Pose::residue(), core::scoring::electron_density::ElectronDensity::set_nres(), core::pose::Pose::total_residue(), and core::conformation::Atom::xyz().

protocols::loops::Loops protocols::electron_density::findLoopFromPatterson	(	core::pose::Pose &	pose,
		core::Size	N,
		core::Size	nloops,
		bool	allow_termini
	)

References core::scoring::electron_density::ElectronDensity::clearMask(), core::pose::Pose::fold_tree(), core::scoring::electron_density::getDensityMap(), core::kinematics::FoldTree::is_cutpoint(), core::conformation::Residue::is_protein(), core::scoring::electron_density::ElectronDensity::maskResidues(), core::scoring::electron_density::ElectronDensity::matchPoseToPatterson(), protocols::loops::Loops::push_back(), core::pose::Pose::residue(), runtime_assert, and core::pose::Pose::total_residue().

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, B, core::pose::Pose::conformation(), core::pose::symmetry::is_symmetric(), core::conformation::Residue::natoms(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), and core::pose::Pose::total_residue().

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

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

static

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

static

Referenced by protocols::electron_density::DensityMorphingMover::apply(), protocols::electron_density::ScaleMapIntensities::apply(), protocols::electron_density::ReportFSC::apply(), protocols::electron_density::BfactorFittingMover::apply(), dockPoseIntoMap(), fast2DRotAlignPose(), and protocols::electron_density::SetupForDensityScoringMover::parse_my_tag().