The workhorse. More...

#include <DockIntoDensityMover.hh>

Inheritance diagram for protocols::electron_density::DockIntoDensityMover:

Public Member Functions
	DockIntoDensityMover ()

void	setDelR (core::Real delR)

void	setNRsteps (core::Real nRsteps)

void	setB (core::Real B)

void	setTopN (core::Real topNtrans, core::Real topNfilter, core::Real topNfinal)

void	setGridStep (core::Size gridStep)

void	setDoRefine (bool do_refine)

void	setMinDist (core::Real mindist)

void	setMinBackbone (bool min_backbone)

void	setNCyc (core::Size ncyc)

void	setOutputSilent (std::string silent_out)

void	setClusterRadius (core::Real cluster_radius)

void	setPointRadius (core::Real point_radius)

void	setTag (std::string tag)

void	setFragDens (core::Real fragDens)

void	setPassThrough (bool passthrough)

void	setNormScores (bool normscores)

void	setClusterOversamp (core::Size cluster_oversample)

void	setMaxRotPerTrans (core::Size max_rot_per_trans)

void	setSymminfo (DensitySymmInfo const &symminfo)

void	setConvoluteSingleR (bool convolute_single_residue)

void	setLaplacianOffset (core::Real laplacian_offset)

void	predefine_search (utility::vector1< numeric::xyzVector< core::Real > > &pts_in)

void	setCenterOnMiddleCA (bool val)

void	setNative (core::pose::PoseOP native)

void	apply (core::pose::Pose &pose) override

void	apply_multi (utility::vector1< core::pose::PoseOP > &poses)

core::Real	get_radius (core::pose::Pose const &pose, numeric::xyzVector< core::Real > &com)

void	apply_transform (core::pose::Pose &pose, RBfitResult const &transform)

void	get_spectrum (core::pose::Pose const &pose, utility::vector1< core::Real > &pose_1dspec)

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

void	poseSphericalSamples (core::pose::Pose const &pose, ObjexxFCL::FArray3D< double > &sigR)
	step 0: map pose to spherically sampled density More...

void	select_points (core::pose::Pose &pose)
	step 1: select points over which to search (saved in class variable) More...

void	density_grid_search (core::Size pose_idx, core::pose::Pose &pose, RBfitResultDB &results)
	step 2: perform the grid search, storing these results More...

void	do_refinement (utility::vector1< core::pose::PoseOP > const &poses, RBfitResultDB &results_in, RefinementResultDB &results_out)
	step 3: local refinement of each hit empties the results_in DB More...

void	do_filter (utility::vector1< core::pose::PoseOP > const &poses, RBfitResultDB &results_in, bool rescore)
	step 4: filter similar hits (non-refined) More...

void	do_filter (RBfitResultDB &results_in)
	step 4: (fast) filter hits using rotation only More...

void	do_filter (RefinementResultDB &results_in)
	step 4: filter similar hits (refined) More...

void	print_best_rms (core::pose::Pose const &pose, RBfitResultDB const &results)
	debugging: add some stats More...

std::string	get_name () const override
	Each derived class must specify its name. The class name. More...

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

	~Mover () override

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

	Mover (std::string type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

	Mover (Mover const &other)

Mover &	operator= (Mover const &other)
	assignment operator More...

virtual core::Real	last_proposal_density_ratio ()

std::string const &	type () const

void	set_type (std::string const &setting)

std::string	get_current_tag () const
	A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...

virtual void	set_current_tag (std::string const &new_tag)

virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...

virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...

void	type (const std::string &type_in)

virtual MoverOP	clone () const
	Return a clone of the Mover object. More...

virtual void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

std::string	get_type () const

MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...

void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...

virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...

virtual Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

virtual bool	reinitialize_for_each_job () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...

virtual bool	reinitialize_for_new_input () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...

virtual MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. More...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

Private Attributes
core::Size	topNtrans_

core::Size	topNfilter_

core::Size	topNfinal_

core::Real	delR_

core::Real	dens_wt_

core::Real	cluster_radius_

core::Real	point_radius_

core::Real	fragDens_

core::Real	mindist_

core::Real	laplacian_offset_

core::Size	B_

core::Size	nRsteps_

core::Size	gridStep_

bool	center_on_middle_ca_

bool	points_defined_

bool	convolute_single_residue_

DensitySymmInfo	symminfo_

core::Size	cluster_oversample_

core::Size	max_rot_per_trans_

bool	do_refine_

bool	min_backbone_

core::Size	ncyc_

std::string	silent_

std::string	tag_

utility::vector1 < numeric::xyzVector < core::Real > >	points_to_search_

bool	normscores_

bool	passthrough_

core::pose::PoseOP	native_

numeric::xyzVector< core::Real >	native_com_

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef protocols::filters::Filters_map	Filters_map

typedef std::list< std::string >	Strings

Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()

static void	register_options ()
	Overload this static method if you access options within the mover. More...

Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Detailed Description

The workhorse.

Constructor & Destructor Documentation

protocols::electron_density::DockIntoDensityMover::DockIntoDensityMover ( )

inline

Member Function Documentation

void protocols::electron_density::DockIntoDensityMover::apply ( core::pose::Pose & pose )

overridevirtual

Implements protocols::moves::Mover.

References apply_multi().

void protocols::electron_density::DockIntoDensityMover::apply_multi ( utility::vector1< core::pose::PoseOP > & poses )

Referenced by apply().

void protocols::electron_density::DockIntoDensityMover::apply_transform	(	core::pose::Pose &	pose,
		RBfitResult const &	transform
	)

References core::pose::Pose::batch_set_xyz(), core::chemical::ResidueType::natoms(), protocols::electron_density::RBfitResult::post_trans_, protocols::electron_density::RBfitResult::pre_trans_, core::pose::Pose::residue_type(), protocols::electron_density::RBfitResult::rotation_, core::pose::Pose::size(), and core::pose::Pose::xyz().

Referenced by density_grid_search(), do_filter(), do_refinement(), and print_best_rms().

void protocols::electron_density::DockIntoDensityMover::density_grid_search	(	core::Size	pose_idx,
		core::pose::Pose &	pose,
		RBfitResultDB &	results
	)

step 2: perform the grid search, storing these results

References protocols::electron_density::ResultDB< T, Tcomp >::add_element(), core::pose::addVirtualResAsRoot(), apply_transform(), B_, delR_, do_filter(), get_radius(), protocols::electron_density::get_rms(), core::scoring::electron_density::getDensityMap(), core::scoring::electron_density::ElectronDensity::getGrid(), core::scoring::electron_density::ElectronDensity::idx2cart(), laplacian_offset_, core::scoring::electron_density::ElectronDensity::mapSphericalSamples(), max_rot_per_trans_, native_, native_com_, normscores_, nRsteps_, points_to_search_, protocols::electron_density::ResultDB< T, Tcomp >::pop(), poseSphericalSamples(), rot(), protocols::electron_density::RBfitResult::score_, protocols::electron_density::ResultDB< T, Tcomp >::size(), symminfo_, protocols::electron_density::ResultDB< T, Tcomp >::to_add_element(), protocols::electron_density::ResultDB< T, Tcomp >::top(), and protocols::electron_density::TR().

Referenced by apply_multi().

void protocols::electron_density::DockIntoDensityMover::do_filter	(	utility::vector1< core::pose::PoseOP > const &	poses,
		RBfitResultDB &	results_in,
		bool	rescore
	)

step 4: filter similar hits (non-refined)

References protocols::electron_density::ResultDB< T, Tcomp >::add_element(), core::pose::addVirtualResAsRoot(), apply_transform(), cluster_radius_, core::scoring::elec_dens_whole_structure_allatom, protocols::electron_density::get_rms(), protocols::electron_density::ResultDB< T, Tcomp >::pop(), protocols::electron_density::ResultDB< T, Tcomp >::size(), symminfo_, and protocols::electron_density::TR().

Referenced by apply_multi(), and density_grid_search().

void protocols::electron_density::DockIntoDensityMover::do_filter ( RBfitResultDB & results_in )

step 4: (fast) filter hits using rotation only

References protocols::electron_density::ResultDB< T, Tcomp >::add_element(), cluster_radius_, delR_, protocols::electron_density::get_rot_angle(), nRsteps_, protocols::electron_density::ResultDB< T, Tcomp >::pop(), and protocols::electron_density::ResultDB< T, Tcomp >::size().

void protocols::electron_density::DockIntoDensityMover::do_filter ( RefinementResultDB & results_in )

step 4: filter similar hits (refined)

References protocols::electron_density::ResultDB< T, Tcomp >::add_element(), cluster_radius_, protocols::electron_density::get_rms(), core::chemical::element::N, normscores_, protocols::electron_density::ResultDB< T, Tcomp >::pop(), protocols::electron_density::ResultDB< T, Tcomp >::size(), symminfo_, and protocols::electron_density::TR().

void protocols::electron_density::DockIntoDensityMover::do_refinement	(	utility::vector1< core::pose::PoseOP > const &	poses,
		RBfitResultDB &	results_in,
		RefinementResultDB &	results_out
	)

std::string protocols::electron_density::DockIntoDensityMover::get_name ( ) const

inlineoverridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

core::Real protocols::electron_density::DockIntoDensityMover::get_radius	(	core::pose::Pose const &	pose,
		numeric::xyzVector< core::Real > &	com
	)

References core::chemical::aa_vrt, center_on_middle_ca_, core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Atom::xyz().

Referenced by density_grid_search(), and get_spectrum().

void protocols::electron_density::DockIntoDensityMover::get_spectrum	(	core::pose::Pose const &	pose,
		utility::vector1< core::Real > &	pose_1dspec
	)

References core::chemical::aa_vrt, protocols::membrane::com(), convolute_single_residue_, delR_, fragDens_, get_radius(), core::conformation::Residue::is_virtual_residue(), nRsteps_, core::pose::Pose::residue(), core::pose::Pose::size(), and protocols::electron_density::TR().

Referenced by select_points().

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

References core::pack::interaction_graph::debug, delR_, core::scoring::electron_density::getDensityMap(), core::scoring::electron_density::ElectronDensity::idxoffset2cart(), rot(), and core::scoring::electron_density::ElectronDensity::writeMRC().

Referenced by select_points().

void protocols::electron_density::DockIntoDensityMover::poseSphericalSamples	(	core::pose::Pose const &	pose,
		ObjexxFCL::FArray3D< double > &	sigR
	)

void protocols::electron_density::DockIntoDensityMover::predefine_search ( utility::vector1< numeric::xyzVector< core::Real > > & pts_in )

References core::scoring::electron_density::ElectronDensity::cart2idx(), core::scoring::electron_density::getDensityMap(), points_defined_, and points_to_search_.

void protocols::electron_density::DockIntoDensityMover::print_best_rms	(	core::pose::Pose const &	pose,
		RBfitResultDB const &	results
	)

debugging: add some stats

References core::pose::addVirtualResAsRoot(), apply_transform(), protocols::electron_density::get_rms(), native_, protocols::electron_density::ResultDB< T, Tcomp >::pop(), protocols::electron_density::ResultDB< T, Tcomp >::size(), symminfo_, and protocols::electron_density::TR().

Referenced by apply_multi().

void protocols::electron_density::DockIntoDensityMover::select_points ( core::pose::Pose & pose )

step 1: select points over which to search (saved in class variable)

Referenced by apply_multi().

void protocols::electron_density::DockIntoDensityMover::setB ( core::Real B )

inline

References core::chemical::element::B, and B_.

void protocols::electron_density::DockIntoDensityMover::setCenterOnMiddleCA ( bool val )

inline

References center_on_middle_ca_, and protocols::hybridization::val.

void protocols::electron_density::DockIntoDensityMover::setClusterOversamp ( core::Size cluster_oversample )

inline

References cluster_oversample_.

void protocols::electron_density::DockIntoDensityMover::setClusterRadius ( core::Real cluster_radius )

inline

References cluster_radius_.

void protocols::electron_density::DockIntoDensityMover::setConvoluteSingleR ( bool convolute_single_residue )

inline

References convolute_single_residue_.

void protocols::electron_density::DockIntoDensityMover::setDelR ( core::Real delR )

inline

References delR_.

void protocols::electron_density::DockIntoDensityMover::setDoRefine ( bool do_refine )

inline

References do_refine_.

void protocols::electron_density::DockIntoDensityMover::setFragDens ( core::Real fragDens )

inline

References fragDens_.

void protocols::electron_density::DockIntoDensityMover::setGridStep ( core::Size gridStep )

inline

References gridStep_.

void protocols::electron_density::DockIntoDensityMover::setLaplacianOffset ( core::Real laplacian_offset )

inline

References laplacian_offset_.

void protocols::electron_density::DockIntoDensityMover::setMaxRotPerTrans ( core::Size max_rot_per_trans )

inline

References max_rot_per_trans_.

void protocols::electron_density::DockIntoDensityMover::setMinBackbone ( bool min_backbone )

inline

References min_backbone_.

void protocols::electron_density::DockIntoDensityMover::setMinDist ( core::Real mindist )

inline

References mindist_.

void protocols::electron_density::DockIntoDensityMover::setNative ( core::pose::PoseOP native )

References core::pose::addVirtualResAsRoot(), core::chemical::element::N, native_, and native_com_.

void protocols::electron_density::DockIntoDensityMover::setNCyc ( core::Size ncyc )

inline

References ncyc_.

void protocols::electron_density::DockIntoDensityMover::setNormScores ( bool normscores )

inline

References normscores_.

void protocols::electron_density::DockIntoDensityMover::setNRsteps ( core::Real nRsteps )

inline

References nRsteps_.

void protocols::electron_density::DockIntoDensityMover::setOutputSilent ( std::string silent_out )

inline

References silent_.

void protocols::electron_density::DockIntoDensityMover::setPassThrough ( bool passthrough )

inline

References passthrough_.

void protocols::electron_density::DockIntoDensityMover::setPointRadius ( core::Real point_radius )

inline

References point_radius_.

void protocols::electron_density::DockIntoDensityMover::setSymminfo ( DensitySymmInfo const & symminfo )

inline

References symminfo_.

void protocols::electron_density::DockIntoDensityMover::setTag ( std::string tag )

inline

References tag_.

void protocols::electron_density::DockIntoDensityMover::setTopN	(	core::Real	topNtrans,
		core::Real	topNfilter,
		core::Real	topNfinal
	)

inline

References topNfilter_, topNfinal_, and topNtrans_.

Member Data Documentation

core::Size protocols::electron_density::DockIntoDensityMover::B_

private

Referenced by density_grid_search(), poseSphericalSamples(), and setB().

bool protocols::electron_density::DockIntoDensityMover::center_on_middle_ca_

private

Referenced by get_radius(), poseSphericalSamples(), and setCenterOnMiddleCA().

core::Size protocols::electron_density::DockIntoDensityMover::cluster_oversample_

private

Referenced by apply_multi(), and setClusterOversamp().

core::Real protocols::electron_density::DockIntoDensityMover::cluster_radius_

private

Referenced by apply_multi(), do_filter(), and setClusterRadius().

bool protocols::electron_density::DockIntoDensityMover::convolute_single_residue_

private

Referenced by get_spectrum(), and setConvoluteSingleR().

core::Real protocols::electron_density::DockIntoDensityMover::delR_

private

Referenced by apply_multi(), density_grid_search(), do_filter(), get_spectrum(), map_from_spectrum(), poseSphericalSamples(), and setDelR().

core::Real protocols::electron_density::DockIntoDensityMover::dens_wt_

private

Referenced by do_refinement().

bool protocols::electron_density::DockIntoDensityMover::do_refine_

private

Referenced by do_refinement(), and setDoRefine().

core::Real protocols::electron_density::DockIntoDensityMover::fragDens_

private

Referenced by get_spectrum(), and setFragDens().

core::Size protocols::electron_density::DockIntoDensityMover::gridStep_

private

Referenced by select_points(), and setGridStep().

core::Real protocols::electron_density::DockIntoDensityMover::laplacian_offset_

private

Referenced by density_grid_search(), poseSphericalSamples(), and setLaplacianOffset().

core::Size protocols::electron_density::DockIntoDensityMover::max_rot_per_trans_

private

Referenced by density_grid_search(), and setMaxRotPerTrans().

bool protocols::electron_density::DockIntoDensityMover::min_backbone_

private

Referenced by do_refinement(), and setMinBackbone().

core::Real protocols::electron_density::DockIntoDensityMover::mindist_

private

Referenced by setMinDist().

core::pose::PoseOP protocols::electron_density::DockIntoDensityMover::native_

private

Referenced by apply_multi(), density_grid_search(), do_refinement(), print_best_rms(), select_points(), and setNative().

numeric::xyzVector< core::Real > protocols::electron_density::DockIntoDensityMover::native_com_

private

Referenced by density_grid_search(), select_points(), and setNative().

core::Size protocols::electron_density::DockIntoDensityMover::ncyc_

private

Referenced by do_refinement(), and setNCyc().

bool protocols::electron_density::DockIntoDensityMover::normscores_

private

Referenced by density_grid_search(), do_filter(), and setNormScores().

core::Size protocols::electron_density::DockIntoDensityMover::nRsteps_

private

Referenced by apply_multi(), density_grid_search(), do_filter(), get_spectrum(), poseSphericalSamples(), and setNRsteps().

bool protocols::electron_density::DockIntoDensityMover::passthrough_

private

Referenced by apply_multi(), and setPassThrough().

core::Real protocols::electron_density::DockIntoDensityMover::point_radius_

private

Referenced by select_points(), and setPointRadius().

bool protocols::electron_density::DockIntoDensityMover::points_defined_

private

Referenced by predefine_search(), and select_points().

utility::vector1< numeric::xyzVector<core::Real> > protocols::electron_density::DockIntoDensityMover::points_to_search_

private

Referenced by apply_multi(), density_grid_search(), predefine_search(), and select_points().

std::string protocols::electron_density::DockIntoDensityMover::silent_

private

Referenced by apply_multi(), and setOutputSilent().

DensitySymmInfo protocols::electron_density::DockIntoDensityMover::symminfo_

private

Referenced by apply_multi(), density_grid_search(), do_filter(), do_refinement(), print_best_rms(), select_points(), and setSymminfo().

std::string protocols::electron_density::DockIntoDensityMover::tag_

private

Referenced by apply_multi(), and setTag().

core::Size protocols::electron_density::DockIntoDensityMover::topNfilter_

private

Referenced by apply_multi(), and setTopN().

core::Size protocols::electron_density::DockIntoDensityMover::topNfinal_

private

Referenced by apply_multi(), and setTopN().

core::Size protocols::electron_density::DockIntoDensityMover::topNtrans_

private

3 stages, each with different filter numbers: 1: select points 2: select best by spharm rotation 3: select best after refinement

Referenced by select_points(), and setTopN().

The documentation for this class was generated from the following files:

src/protocols/electron_density/DockIntoDensityMover.hh
src/protocols/electron_density/DockIntoDensityMover.cc

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation