#include <MgScanner.hh>

Inheritance diagram for protocols::magnesium::MgScanner:

[legend]

Public Member Functions
	MgScanner ()

	~MgScanner () override

void	apply (core::pose::Pose &pose) override
	Main Method. More...

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

void	set_minimize (bool const &setting)

bool	minimize () const

void	set_hydrate (bool const &setting)

bool	hydrate () const

void	set_minimize_during_scoring (bool const &setting)

bool	minimize_during_scoring () const

void	set_tether_to_closest_res (bool const &setting)

bool	tether_to_closest_res () const

void	set_integration_test (bool const &setting)

bool	integration_test () const

void	set_score_cut (core::Real const &setting)

core::Real	score_cut () const

void	set_score_cut_PDB (core::Real const &setting)

core::Real	score_cut_PDB () const

void	set_xyz_step (core::Real const &setting)

core::Real	xyz_step () const

void	set_scorefxn (core::scoring::ScoreFunctionOP const &setting)

core::scoring::ScoreFunctionOP	scorefxn () const

void	set_silent_file (std::string const &setting)

std::string	silent_file () const

void	set_output_pdb (std::string const &setting)

std::string	output_pdb () const

void	set_input_scan_res (utility::vector1< core::Size > const &setting)

utility::vector1< core::Size >	input_scan_res () const

void	set_minimize_mg_coord_constraint_distance (core::Distance const &setting)

core::Distance	minimize_mg_coord_constraint_distance () const

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

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 const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

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...

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

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...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

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	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

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

jobdist::BasicJobCOP	get_current_job () const

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

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

virtual core::Real	last_proposal_density_ratio ()

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 void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Private Member Functions
void	scan_magnesiums (core::pose::Pose &pose)

core::Real	get_score (core::pose::Pose &pose, core::Vector const &mg_position, core::scoring::ScoreFunctionCOP scorefxn, bool const hydrate_magnesium=false, bool const keep_waters=false, bool const minimize=false)

void	cluster_mg ()

void	output_mg_to_silent_file (std::string const &silent_file)

void	output_mg_into_one_PDB (core::pose::Pose const &pose)

core::Size	get_unique_mg_res (core::pose::Pose const &mg_pose)

core::pose::PoseOP	get_single_mg_pose ()

core::Distance	distance_to_closest_magnesium (core::Vector const &mg_position, core::pose::Pose const &reference_pose)

Private Attributes
utility::vector1< core::pose::PoseOP >	mg_poses

bool	hydrate_

bool	minimize_

bool	minimize_during_scoring_

bool	tether_to_closest_res_

bool	integration_test_

core::Real	score_cut_

core::Real	score_cut_PDB_

core::Real	xyz_step_

std::string	silent_file_

std::string	output_pdb_

utility::vector1< core::Size >	input_scan_res_

core::Distance	minimize_mg_coord_constraint_distance_

core::scoring::ScoreFunctionOP	scorefxn_

utility::vector1< core::pose::PoseOP >	mg_poses_

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 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...

Constructor & Destructor Documentation

◆ MgScanner()

protocols::magnesium::MgScanner::MgScanner ( )

◆ ~MgScanner()

protocols::magnesium::MgScanner::~MgScanner ( )

overridedefault

Member Function Documentation

◆ apply()

void protocols::magnesium::MgScanner::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References cluster_mg(), mg_poses_, minimize_, protocols::magnesium::minimize_magnesium_and_hydration_shell(), minimize_mg_coord_constraint_distance_, output_mg_into_one_PDB(), output_mg_to_silent_file(), scan_magnesiums(), scorefxn_, and silent_file_.

◆ cluster_mg()

void protocols::magnesium::MgScanner::cluster_mg ( )

private

References core::sequence::end, get_unique_mg_res(), core::pose::getPoseExtraScore(), and mg_poses_.

Referenced by apply().

◆ distance_to_closest_magnesium()

Distance protocols::magnesium::MgScanner::distance_to_closest_magnesium	(	core::Vector const &	mg_position,
		core::pose::Pose const &	reference_pose
	)

private

References core::conformation::Residue::name3(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

Referenced by output_mg_to_silent_file().

◆ get_name()

std::string protocols::magnesium::MgScanner::get_name ( ) const

inlineoverridevirtual

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

Implements protocols::moves::Mover.

◆ get_score()

Real protocols::magnesium::MgScanner::get_score	(	core::pose::Pose &	pose,
		core::Vector const &	mg_position,
		core::scoring::ScoreFunctionCOP	scorefxn,
		bool const	hydrate_magnesium = `false`,
		bool const	keep_waters = `false`,
		bool const	minimize = `false`
	)

private

References protocols::magnesium::MgHydrater::apply(), minimize(), protocols::magnesium::minimize_magnesium_and_hydration_shell(), minimize_mg_coord_constraint_distance_, core::conformation::Residue::name3(), core::chemical::rings::q, core::pose::Pose::residue(), core::pose::Pose::residue_type(), protocols::hybridization::score, scorefxn(), protocols::magnesium::MgHydrater::set_excise_mini_pose(), core::pose::Pose::set_xyz(), core::pose::Pose::size(), core::pose::Pose::xyz(), and core::conformation::Residue::xyz().

Referenced by scan_magnesiums().

◆ get_single_mg_pose()

core::pose::PoseOP protocols::magnesium::MgScanner::get_single_mg_pose ( )

private

References protocols::magnesium::get_mg_rsd().

Referenced by output_mg_to_silent_file().

◆ get_unique_mg_res()

Size protocols::magnesium::MgScanner::get_unique_mg_res ( core::pose::Pose const & mg_pose )

private

References core::conformation::Residue::name3(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by cluster_mg(), output_mg_into_one_PDB(), and output_mg_to_silent_file().

◆ hydrate()

bool protocols::magnesium::MgScanner::hydrate ( ) const

inline

References hydrate_.

◆ input_scan_res()

utility::vector1< core::Size > protocols::magnesium::MgScanner::input_scan_res ( ) const

inline

References input_scan_res_.

◆ integration_test()

bool protocols::magnesium::MgScanner::integration_test ( ) const

inline

References integration_test_.

◆ minimize()

bool protocols::magnesium::MgScanner::minimize ( ) const

inline

References minimize_.

Referenced by get_score().

◆ minimize_during_scoring()

bool protocols::magnesium::MgScanner::minimize_during_scoring ( ) const

inline

References minimize_during_scoring_.

◆ minimize_mg_coord_constraint_distance()

core::Distance protocols::magnesium::MgScanner::minimize_mg_coord_constraint_distance ( ) const

inline

References minimize_mg_coord_constraint_distance_.

◆ output_mg_into_one_PDB()

void protocols::magnesium::MgScanner::output_mg_into_one_PDB ( core::pose::Pose const & pose )

private

References core::pose::Pose::append_residue_by_jump(), core::pose::Pose::dump_pdb(), protocols::magnesium::get_mg_rsd(), get_unique_mg_res(), core::pose::getPoseExtraScore(), mg_poses_, output_pdb_, score_cut_PDB_, core::pose::Pose::set_xyz(), and core::pose::Pose::size().

Referenced by apply().

◆ output_mg_to_silent_file()

void protocols::magnesium::MgScanner::output_mg_to_silent_file ( std::string const & silent_file )

private

References distance_to_closest_magnesium(), protocols::moves::Mover::get_native_pose(), get_single_mg_pose(), get_unique_mg_res(), hydrate_, mg_poses_, silent_file(), and core::io::silent::SilentFileData::write_silent_struct().

Referenced by apply().

◆ output_pdb()

std::string protocols::magnesium::MgScanner::output_pdb ( ) const

inline

References output_pdb_.

◆ scan_magnesiums()

void protocols::magnesium::MgScanner::scan_magnesiums ( core::pose::Pose & pose )

private

Referenced by apply().

◆ score_cut()

core::Real protocols::magnesium::MgScanner::score_cut ( ) const

inline

References score_cut_.

◆ score_cut_PDB()

core::Real protocols::magnesium::MgScanner::score_cut_PDB ( ) const

inline

References score_cut_PDB_.

◆ scorefxn()

core::scoring::ScoreFunctionOP protocols::magnesium::MgScanner::scorefxn ( ) const

inline

References scorefxn_.

Referenced by get_score().

◆ set_hydrate()

void protocols::magnesium::MgScanner::set_hydrate ( bool const & setting )

inline

References hydrate_.

◆ set_input_scan_res()

void protocols::magnesium::MgScanner::set_input_scan_res ( utility::vector1< core::Size > const & setting )

inline

References input_scan_res_.

◆ set_integration_test()

void protocols::magnesium::MgScanner::set_integration_test ( bool const & setting )

inline

References integration_test_.

◆ set_minimize()

void protocols::magnesium::MgScanner::set_minimize ( bool const & setting )

inline

References minimize_.

◆ set_minimize_during_scoring()

void protocols::magnesium::MgScanner::set_minimize_during_scoring ( bool const & setting )

inline

References minimize_during_scoring_.

◆ set_minimize_mg_coord_constraint_distance()

void protocols::magnesium::MgScanner::set_minimize_mg_coord_constraint_distance ( core::Distance const & setting )

inline

References minimize_mg_coord_constraint_distance_.

◆ set_output_pdb()

void protocols::magnesium::MgScanner::set_output_pdb ( std::string const & setting )

inline

References output_pdb_.

◆ set_score_cut()

void protocols::magnesium::MgScanner::set_score_cut ( core::Real const & setting )

inline

References score_cut_.

◆ set_score_cut_PDB()

void protocols::magnesium::MgScanner::set_score_cut_PDB ( core::Real const & setting )

inline

References score_cut_PDB_.

◆ set_scorefxn()

void protocols::magnesium::MgScanner::set_scorefxn ( core::scoring::ScoreFunctionOP const & setting )

inline

References scorefxn_.

◆ set_silent_file()

void protocols::magnesium::MgScanner::set_silent_file ( std::string const & setting )

inline

References silent_file_.

◆ set_tether_to_closest_res()

void protocols::magnesium::MgScanner::set_tether_to_closest_res ( bool const & setting )

inline

References tether_to_closest_res_.

◆ set_xyz_step()

void protocols::magnesium::MgScanner::set_xyz_step ( core::Real const & setting )

inline

References xyz_step_.

◆ silent_file()

std::string protocols::magnesium::MgScanner::silent_file ( ) const

inline

References silent_file_.

Referenced by output_mg_to_silent_file().

◆ tether_to_closest_res()

bool protocols::magnesium::MgScanner::tether_to_closest_res ( ) const

inline

References tether_to_closest_res_.

◆ xyz_step()

core::Real protocols::magnesium::MgScanner::xyz_step ( ) const

inline

References xyz_step_.

Member Data Documentation

◆ hydrate_

bool protocols::magnesium::MgScanner::hydrate_

private

Referenced by hydrate(), output_mg_to_silent_file(), scan_magnesiums(), and set_hydrate().

◆ input_scan_res_

utility::vector1< core::Size > protocols::magnesium::MgScanner::input_scan_res_

private

Referenced by input_scan_res(), scan_magnesiums(), and set_input_scan_res().

◆ integration_test_

bool protocols::magnesium::MgScanner::integration_test_

private

Referenced by integration_test(), scan_magnesiums(), and set_integration_test().

◆ mg_poses

utility::vector1< core::pose::PoseOP > protocols::magnesium::MgScanner::mg_poses

private

◆ mg_poses_

utility::vector1< core::pose::PoseOP > protocols::magnesium::MgScanner::mg_poses_

private

Referenced by apply(), cluster_mg(), output_mg_into_one_PDB(), output_mg_to_silent_file(), and scan_magnesiums().

◆ minimize_

bool protocols::magnesium::MgScanner::minimize_

private

Referenced by apply(), minimize(), and set_minimize().

◆ minimize_during_scoring_

bool protocols::magnesium::MgScanner::minimize_during_scoring_

private

Referenced by minimize_during_scoring(), scan_magnesiums(), and set_minimize_during_scoring().

◆ minimize_mg_coord_constraint_distance_

core::Distance protocols::magnesium::MgScanner::minimize_mg_coord_constraint_distance_

private

Referenced by apply(), get_score(), minimize_mg_coord_constraint_distance(), and set_minimize_mg_coord_constraint_distance().

◆ output_pdb_

std::string protocols::magnesium::MgScanner::output_pdb_

private

Referenced by output_mg_into_one_PDB(), output_pdb(), and set_output_pdb().

◆ score_cut_

core::Real protocols::magnesium::MgScanner::score_cut_

private

Referenced by scan_magnesiums(), score_cut(), and set_score_cut().

◆ score_cut_PDB_

core::Real protocols::magnesium::MgScanner::score_cut_PDB_

private

Referenced by output_mg_into_one_PDB(), score_cut_PDB(), and set_score_cut_PDB().

◆ scorefxn_

core::scoring::ScoreFunctionOP protocols::magnesium::MgScanner::scorefxn_

private

Referenced by apply(), scan_magnesiums(), scorefxn(), and set_scorefxn().

◆ silent_file_

std::string protocols::magnesium::MgScanner::silent_file_

private

Referenced by apply(), set_silent_file(), and silent_file().

◆ tether_to_closest_res_

bool protocols::magnesium::MgScanner::tether_to_closest_res_

private

Referenced by scan_magnesiums(), set_tether_to_closest_res(), and tether_to_closest_res().

◆ xyz_step_

core::Real protocols::magnesium::MgScanner::xyz_step_

private

Referenced by scan_magnesiums(), set_xyz_step(), and xyz_step().

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

src/protocols/magnesium/MgScanner.hh
src/protocols/magnesium/MgScanner.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ MgScanner()

◆ ~MgScanner()

Member Function Documentation

◆ apply()

◆ cluster_mg()

◆ distance_to_closest_magnesium()

◆ get_name()

◆ get_score()

◆ get_single_mg_pose()

◆ get_unique_mg_res()

◆ hydrate()

◆ input_scan_res()

◆ integration_test()

◆ minimize()

◆ minimize_during_scoring()

◆ minimize_mg_coord_constraint_distance()

◆ output_mg_into_one_PDB()

◆ output_mg_to_silent_file()

◆ output_pdb()

◆ scan_magnesiums()

◆ score_cut()

◆ score_cut_PDB()

◆ scorefxn()

◆ set_hydrate()

◆ set_input_scan_res()

◆ set_integration_test()

◆ set_minimize()

◆ set_minimize_during_scoring()

◆ set_minimize_mg_coord_constraint_distance()

◆ set_output_pdb()

◆ set_score_cut()

◆ set_score_cut_PDB()

◆ set_scorefxn()

◆ set_silent_file()

◆ set_tether_to_closest_res()

◆ set_xyz_step()

◆ silent_file()

◆ tether_to_closest_res()

◆ xyz_step()

Member Data Documentation

◆ hydrate_

◆ input_scan_res_

◆ integration_test_

◆ mg_poses

◆ mg_poses_

◆ minimize_

◆ minimize_during_scoring_

◆ minimize_mg_coord_constraint_distance_

◆ output_pdb_

◆ score_cut_

◆ score_cut_PDB_

◆ scorefxn_

◆ silent_file_

◆ tether_to_closest_res_

◆ xyz_step_