protocols::electron_density Namespace Reference

Classes
class	SetupForDensityScoringMover
class	SetupForDensityScoringMoverCreator

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

Functions
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	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::owning_ptr< SetupForDensityScoringMover > protocols::electron_density::SetupForDensityScoringMoverOP

Definition at line 70 of file SetupForDensityScoringMover.hh.

Function Documentation

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

Definition at line 268 of file util.cc.

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::electron_density::getDensityMap(), core::scoring::getScoreFunction(), core::scoring::electron_density::ElectronDensity::getUseDensityInMinimizer(), core::pose::symmetry::is_symmetric(), core::pose::Pose::jump(), core::pose::symmetry::make_symmetric_movemap(), 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(), and TR().

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

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

Definition at line 430 of file util.cc.

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)

Definition at line 388 of file util.cc.

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().

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

Definition at line 121 of file util.cc.

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(), and core::pose::Pose::total_residue().

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

Definition at line 72 of file util.cc.

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(), 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
	)

Definition at line 142 of file SetupForDensityScoringMover.cc.

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

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

static

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

static

Referenced by dockPoseIntoMap(), and fast2DRotAlignPose().