#include <AddConstraintsToCurrentConformationMover.hh>

Inheritance diagram for protocols::constraint_movers::AddConstraintsToCurrentConformationMover:

[legend]

Public Types
enum class	AtomSelector { ALL , CA_ONLY , BB_ONLY , SC_TIP_ONLY }

typedef core::pack::task::TaskFactoryOP	TaskFactoryOP

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

Public Member Functions
	AddConstraintsToCurrentConformationMover ()

	~AddConstraintsToCurrentConformationMover () override

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

virtual core::scoring::constraints::ConstraintCOPs	generate_constraints (Pose const &pose)

void	task_factory (TaskFactoryOP tf)

void	residue_selector (core::select::residue_selector::ResidueSelectorCOP selector)

moves::MoverOP	clone () const override
	Return a clone of the Mover object. More...

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

void	parse_my_tag (TagCOP, basic::datacache::DataMap &) override
	parse XML (specifically in the context of the parser/scripting scheme) More...

AtomSelector	atom_selector () const

void	set_atom_selector (AtomSelector const setting)

bool	CA_only () const

bool	bb_only () const

bool	sc_tip_only () const

bool &	use_distance_cst ()

bool &	use_harmonic_func ()

bool &	use_bounded_func ()

bool &	inter_chain ()

core::Real &	cst_weight ()

core::Real &	max_distance ()

core::Real &	coord_dev ()

core::Real &	bound_width ()

core::Size &	min_seq_sep ()

bool const &	use_distance_cst () const

bool const &	use_harmonic_func () const

bool const &	use_bounded_func () const

bool const &	inter_chain () const

core::Real const &	cst_weight () const

core::Real const &	max_distance () const

core::Real const &	coord_dev () const

core::Real const &	bound_width () const

core::Size const &	min_seq_sep () const

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 ()

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 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...

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

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...

Static Public Member Functions
static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

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...

Private Member Functions
core::Size	find_best_anchor (core::pose::Pose const &pose) const

virtual void	parse_task_operations (TagCOP, basic::datacache::DataMap const &)
	parse "task_operations" XML option (can be employed virtually by derived movers) More...

core::scoring::constraints::ConstraintCOPs	generate_coordinate_constraints (core::pose::Pose const &pose, core::select::residue_selector::ResidueSubset const &subset) const

core::scoring::constraints::ConstraintCOPs	generate_atom_pair_constraints (core::pose::Pose const &pose, core::select::residue_selector::ResidueSubset const &subset) const

Private Attributes
bool	use_distance_cst_

bool	use_harmonic_func_

AtomSelector	atom_sele_ = AtomSelector::CA_ONLY

bool	inter_chain_

core::Real	cst_weight_

core::Real	max_distance_

core::Real	coord_dev_

core::Real	bound_width_

core::Size	min_seq_sep_

core::select::residue_selector::ResidueSelectorCOP	selector_

bool	use_bounded_func_

Additional Inherited Members
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...

Member Typedef Documentation

◆ TaskFactoryOP

typedef core::pack::task::TaskFactoryOP protocols::constraint_movers::AddConstraintsToCurrentConformationMover::TaskFactoryOP

Member Enumeration Documentation

◆ AtomSelector

enum protocols::constraint_movers::AddConstraintsToCurrentConformationMover::AtomSelector

strong

Enumerator
ALL
CA_ONLY
BB_ONLY
SC_TIP_ONLY

Constructor & Destructor Documentation

◆ AddConstraintsToCurrentConformationMover()

protocols::constraint_movers::AddConstraintsToCurrentConformationMover::AddConstraintsToCurrentConformationMover ( )

◆ ~AddConstraintsToCurrentConformationMover()

protocols::constraint_movers::AddConstraintsToCurrentConformationMover::~AddConstraintsToCurrentConformationMover ( )

overridedefault

Member Function Documentation

◆ apply()

void protocols::constraint_movers::AddConstraintsToCurrentConformationMover::apply ( Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References core::pose::Pose::add_constraints(), generate_constraints(), protocols::TR(), use_bounded_func_, and use_harmonic_func_.

◆ atom_selector()

AtomSelector protocols::constraint_movers::AddConstraintsToCurrentConformationMover::atom_selector ( ) const

inline

References atom_sele_.

◆ bb_only()

bool protocols::constraint_movers::AddConstraintsToCurrentConformationMover::bb_only ( ) const

inline

References atom_sele_, and BB_ONLY.

Referenced by generate_coordinate_constraints(), and parse_my_tag().

◆ bound_width() [1/2]

core::Real& protocols::constraint_movers::AddConstraintsToCurrentConformationMover::bound_width ( )

inline

References bound_width_.

◆ bound_width() [2/2]

core::Real const& protocols::constraint_movers::AddConstraintsToCurrentConformationMover::bound_width ( ) const

inline

References bound_width_.

◆ CA_only()

bool protocols::constraint_movers::AddConstraintsToCurrentConformationMover::CA_only ( ) const

inline

References atom_sele_, and CA_ONLY.

Referenced by generate_atom_pair_constraints(), generate_coordinate_constraints(), and parse_my_tag().

◆ clone()

moves::MoverOP protocols::constraint_movers::AddConstraintsToCurrentConformationMover::clone ( ) const

overridevirtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

◆ coord_dev() [1/2]

core::Real& protocols::constraint_movers::AddConstraintsToCurrentConformationMover::coord_dev ( )

inline

References coord_dev_.

◆ coord_dev() [2/2]

core::Real const& protocols::constraint_movers::AddConstraintsToCurrentConformationMover::coord_dev ( ) const

inline

References coord_dev_.

◆ cst_weight() [1/2]

core::Real& protocols::constraint_movers::AddConstraintsToCurrentConformationMover::cst_weight ( )

inline

References cst_weight_.

◆ cst_weight() [2/2]

core::Real const& protocols::constraint_movers::AddConstraintsToCurrentConformationMover::cst_weight ( ) const

inline

References cst_weight_.

◆ find_best_anchor()

core::Size protocols::constraint_movers::AddConstraintsToCurrentConformationMover::find_best_anchor ( core::pose::Pose const & pose ) const

private

References core::chemical::ResidueType::atom_index(), core::chemical::ResidueType::has(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

Referenced by generate_coordinate_constraints().

◆ fresh_instance()

moves::MoverOP protocols::constraint_movers::AddConstraintsToCurrentConformationMover::fresh_instance ( ) const

overridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

◆ generate_atom_pair_constraints()

core::scoring::constraints::ConstraintCOPs protocols::constraint_movers::AddConstraintsToCurrentConformationMover::generate_atom_pair_constraints	(	core::pose::Pose const &	pose,
		core::select::residue_selector::ResidueSubset const &	subset
	)		const

private

◆ generate_constraints()

core::scoring::constraints::ConstraintCOPs protocols::constraint_movers::AddConstraintsToCurrentConformationMover::generate_constraints ( Pose const & pose )

virtual

References generate_atom_pair_constraints(), generate_coordinate_constraints(), selector_, and use_distance_cst_.

Referenced by apply().

◆ generate_coordinate_constraints()

core::scoring::constraints::ConstraintCOPs protocols::constraint_movers::AddConstraintsToCurrentConformationMover::generate_coordinate_constraints	(	core::pose::Pose const &	pose,
		core::select::residue_selector::ResidueSubset const &	subset
	)		const

private

◆ get_name()

std::string protocols::constraint_movers::AddConstraintsToCurrentConformationMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ inter_chain() [1/2]

bool& protocols::constraint_movers::AddConstraintsToCurrentConformationMover::inter_chain ( )

inline

References inter_chain_.

◆ inter_chain() [2/2]

bool const& protocols::constraint_movers::AddConstraintsToCurrentConformationMover::inter_chain ( ) const

inline

References inter_chain_.

◆ max_distance() [1/2]

core::Real& protocols::constraint_movers::AddConstraintsToCurrentConformationMover::max_distance ( )

inline

References max_distance_.

◆ max_distance() [2/2]

core::Real const& protocols::constraint_movers::AddConstraintsToCurrentConformationMover::max_distance ( ) const

inline

References max_distance_.

◆ min_seq_sep() [1/2]

core::Size& protocols::constraint_movers::AddConstraintsToCurrentConformationMover::min_seq_sep ( )

inline

References min_seq_sep_.

◆ min_seq_sep() [2/2]

core::Size const& protocols::constraint_movers::AddConstraintsToCurrentConformationMover::min_seq_sep ( ) const

inline

References min_seq_sep_.

◆ mover_name()

std::string protocols::constraint_movers::AddConstraintsToCurrentConformationMover::mover_name ( )

static

Referenced by get_name(), protocols::constraint_movers::AddConstraintsToCurrentConformationMoverCreator::keyname(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::constraint_movers::AddConstraintsToCurrentConformationMover::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &	datamap
	)

overridevirtual

parse XML (specifically in the context of the parser/scripting scheme)

Reimplemented from protocols::moves::Mover.

References ALL, BB_ONLY, bb_only(), bound_width_, CA_ONLY, CA_only(), coord_dev_, cst_weight_, inter_chain_, max_distance_, min_seq_sep_, core::select::residue_selector::parse_residue_selector(), parse_task_operations(), residue_selector(), SC_TIP_ONLY, sc_tip_only(), set_atom_selector(), protocols::TR(), use_bounded_func_, use_distance_cst_, and use_harmonic_func_.

◆ parse_task_operations()

void protocols::constraint_movers::AddConstraintsToCurrentConformationMover::parse_task_operations	(	TagCOP	tag,
		basic::datacache::DataMap const &	datamap
	)

privatevirtual

parse "task_operations" XML option (can be employed virtually by derived movers)

References core::pack::task::parse_task_operations(), and task_factory().

Referenced by parse_my_tag().

◆ provide_xml_schema()

void protocols::constraint_movers::AddConstraintsToCurrentConformationMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::select::residue_selector::attributes_for_parse_residue_selector(), core::pack::task::attributes_for_parse_task_operations(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::constraint_movers::AddConstraintsToCurrentConformationMoverCreator::provide_xml_schema().

◆ residue_selector()

void protocols::constraint_movers::AddConstraintsToCurrentConformationMover::residue_selector ( core::select::residue_selector::ResidueSelectorCOP selector )

References selector_.

Referenced by parse_my_tag(), and task_factory().