#include <JumpClaim.hh>

Inheritance diagram for protocols::environment::claims::JumpClaim:

Public Member Functions
	JumpClaim (ClientMoverOP owner, utility::tag::TagCOP tag, basic::datacache::DataMap const &)

	JumpClaim (ClientMoverOP owner, std::string const &label, LocalPosition const &pos1, LocalPosition const &pos2, LocalPosition const &cutp=core::environment::NO_POSITION)

void	yield_elements (core::environment::FoldTreeSketch const &fts, ResidueElements &elements) const override
	build ResidueElements that indicate the introduction of a new peptide edge into the fold tree. More...

void	yield_elements (core::environment::FoldTreeSketch const &fts, JumpElements &elements) const override
	build the JumpElements that represent the inclusion of a jump in the nascent FoldTree More...

void	yield_elements (core::environment::FoldTreeSketch const &fts, CutElements &elements) const override
	build and export the CutElements that represent the inclusion of a cut in the tree. More...

void	yield_elements (core::pose::Pose const &, DOFElements &elements) const override
	build and export DOFElements, which represent control over non-jump dofs (torsions, bond lengths, angles) final conformation. More...

void	set_atoms (std::string const &a1, std::string const &a2)
	set the two atom names to use as the start and beginning of the jump. Both must be set simultaneously because the FoldTree requires this. More...

void	strength (ControlStrength const &cstr, ControlStrength const &istr)

bool	physical () const

void	physical (bool setting)

void	create_vrt_if_necessary (bool setting)

void	create_vrt_if_necessary (bool setting_p1, bool setting_p2)
	configure this JumpClaim to create a virtual residue to be the jump point if label of the proposed jump point (i.e. pos1_.label()) does not already exist. More...

void	cut (LocalPosition const &)

void	stubs_intra_residue (bool setting)

bool	stubs_intra_residue () const

std::string const &	label () const

LocalPosition const &	pos1 () const

LocalPosition const &	pos2 () const

std::pair< std::string, std::string > const &	atoms () const

EnvClaimOP	clone () const override

std::string	type () const override

void	show (std::ostream &os) const override

Public Member Functions inherited from protocols::environment::claims::EnvClaim
	~EnvClaim () override
	Virtual destructor. More...

	EnvClaim (ClientMoverOP)

ClientMoverOP	owner () const
	A clone used by the EnvClaimFactory to instantiate new EnvClaims using an XML tag. More...

void	set_owner (ClientMoverOP owner)

void	annotate (core::pose::Pose const &, core::environment::SequenceAnnotationOP) const
	allow the claim to use any internally queued ResidueSelectors to create sequence annotations. More...

virtual void	yield_elements (FoldTreeSketch const &, CutBiasElements &) const
	build and export the CutElements that represent the inclusion of a cut in the tree. More...

Static Public Member Functions
static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

static std::string	class_name ()

Static Public Member Functions inherited from protocols::environment::claims::EnvClaim
static EnvClaimOP	make_claim (std::string const &name, ClientMoverOP owner, utility::tag::TagCOP tag, basic::datacache::DataMap &datamap)
	factory method for claims. More...

static bool	is_claim (std::string const &name)

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

static std::string	envclaim_ct_namer (std::string)

static std::string	envclaim_group_name ()

Protected Member Functions
LocalPosition const &	cut () const

void	validate () const

Protected Member Functions inherited from protocols::environment::claims::EnvClaim
virtual DOFElement	wrap_dof_id (core::id::DOF_ID const &id) const

ControlStrength	parse_ctrl_str (std::string const &str) const

void	queue_for_annotation (std::string const &label, ResidueSelectorCOP selector)

Private Types
typedef EnvClaim	Parent

typedef core::environment::LocalPosition	LocalPosition

typedef core::select::residue_selector::ResidueSelector	ResidueSelector

typedef core::select::residue_selector::ResidueSelectorCOP	ResidueSelectorCOP

Private Attributes
std::string	label_

LocalPosition	pos1_

LocalPosition	pos2_

LocalPosition	cut_

std::pair< std::string, std::string >	atoms_

bool	physical_cut_

bool	create_vrt_p1_

bool	create_vrt_p2_

bool	stubs_intra_residue_

ControlStrength	c_str_

ControlStrength	i_str_

Member Typedef Documentation

typedef core::environment::LocalPosition protocols::environment::claims::JumpClaim::LocalPosition

private

typedef EnvClaim protocols::environment::claims::JumpClaim::Parent

private

typedef core::select::residue_selector::ResidueSelector protocols::environment::claims::JumpClaim::ResidueSelector

private

typedef core::select::residue_selector::ResidueSelectorCOP protocols::environment::claims::JumpClaim::ResidueSelectorCOP

private

Constructor & Destructor Documentation

protocols::environment::claims::JumpClaim::JumpClaim	(	ClientMoverOP	owner,
		utility::tag::TagCOP	tag,
		basic::datacache::DataMap const &	datamap
	)

References cut(), label(), physical(), pos1(), pos2(), protocols::environment::claims::EnvClaim::queue_for_annotation(), set_atoms(), and validate().

protocols::environment::claims::JumpClaim::JumpClaim	(	ClientMoverOP	owner,
		std::string const &	label,
		LocalPosition const &	pos1,
		LocalPosition const &	pos2,
		LocalPosition const &	cutp = `core::environment::NO_POSITION`
	)

References validate().

Member Function Documentation

std::pair< std::string, std::string > const& protocols::environment::claims::JumpClaim::atoms ( ) const

inline

References atoms_.

Referenced by show(), and yield_elements().

std::string protocols::environment::claims::JumpClaim::class_name ( )

static

Referenced by protocols::environment::claims::EnvClaim::define_envclaim_schema_group(), and provide_xml_schema().

EnvClaimOP protocols::environment::claims::JumpClaim::clone ( ) const

overridevirtual

Implements protocols::environment::claims::EnvClaim.

void protocols::environment::claims::JumpClaim::create_vrt_if_necessary ( bool setting )

void protocols::environment::claims::JumpClaim::create_vrt_if_necessary	(	bool	setting_p1,
		bool	setting_p2
	)

configure this JumpClaim to create a virtual residue to be the jump point if label of the proposed jump point (i.e. pos1_.label()) does not already exist.

Parameters

set	this behavior for pos1()
set	this behavior for pos2()

References create_vrt_p1_, and create_vrt_p2_.

void protocols::environment::claims::JumpClaim::cut ( claims::LocalPosition const & p )

References cut_.

LocalPosition const & protocols::environment::claims::JumpClaim::cut ( ) const

protected

References cut_.

Referenced by JumpClaim(), and yield_elements().

std::string const & protocols::environment::claims::JumpClaim::label ( ) const

References label_.

Referenced by JumpClaim(), protocols::environment::claims::VirtResClaim::show(), and yield_elements().

bool protocols::environment::claims::JumpClaim::physical ( ) const

inline

References physical_cut_.

Referenced by JumpClaim(), protocols::environment::claims::VirtResClaim::VirtResClaim(), and yield_elements().

void protocols::environment::claims::JumpClaim::physical ( bool setting )

inline

References physical_cut_.

LocalPosition const & protocols::environment::claims::JumpClaim::pos1 ( ) const

References pos1_.

Referenced by JumpClaim(), show(), validate(), and yield_elements().

LocalPosition const & protocols::environment::claims::JumpClaim::pos2 ( ) const

References pos2_.

Referenced by JumpClaim(), show(), validate(), protocols::environment::claims::VirtResClaim::VirtResClaim(), and yield_elements().

void protocols::environment::claims::JumpClaim::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References class_name(), and protocols::environment::claims::EnvClaim::envclaim_ct_namer().

Referenced by protocols::environment::claims::EnvClaim::define_envclaim_schema_group().

void protocols::environment::claims::JumpClaim::set_atoms	(	std::string const &	a1,
		std::string const &	a2
	)

set the two atom names to use as the start and beginning of the jump. Both must be set simultaneously because the FoldTree requires this.

References atoms_.

Referenced by JumpClaim().

void protocols::environment::claims::JumpClaim::show ( std::ostream & os ) const

overridevirtual

Reimplemented from protocols::environment::claims::EnvClaim.

References atoms(), protocols::environment::claims::EnvClaim::owner(), pos1(), pos2(), and type().

void protocols::environment::claims::JumpClaim::strength	(	ControlStrength const &	cstr,
		ControlStrength const &	istr
	)

References c_str_, and i_str_.

Referenced by protocols::environment::claims::VirtResClaim::strength(), and protocols::environment::claims::VirtResClaim::VirtResClaim().

void protocols::environment::claims::JumpClaim::stubs_intra_residue ( bool setting )

inline

References stubs_intra_residue_.

bool protocols::environment::claims::JumpClaim::stubs_intra_residue ( ) const

inline

References stubs_intra_residue_.

Referenced by yield_elements().

std::string protocols::environment::claims::JumpClaim::type ( ) const

overridevirtual

Implements protocols::environment::claims::EnvClaim.

Referenced by show().

void protocols::environment::claims::JumpClaim::validate ( ) const

protected

References pos1(), and pos2().

Referenced by JumpClaim(), and yield_elements().

void protocols::environment::claims::JumpClaim::yield_elements	(	core::environment::FoldTreeSketch const &	,
		ResidueElements &
	)		const

overridevirtual

build ResidueElements that indicate the introduction of a new peptide edge into the fold tree.

Reimplemented from protocols::environment::claims::EnvClaim.

References protocols::environment::claims::ResidueElement::allow_duplicates, create_vrt_p1_, create_vrt_p2_, core::environment::LocalPosition::label(), protocols::environment::claims::ResidueElement::label, pos1(), and pos2().

Referenced by protocols::environment::claims::VirtResClaim::yield_elements().

void protocols::environment::claims::JumpClaim::yield_elements	(	core::environment::FoldTreeSketch const &	,
		JumpElements &
	)		const

overridevirtual

build the JumpElements that represent the inclusion of a jump in the nascent FoldTree

Reimplemented from protocols::environment::claims::EnvClaim.

References protocols::environment::claims::JumpElement::atom1, protocols::environment::claims::JumpElement::atom2, atoms(), protocols::environment::claims::JumpElement::force_stub_intra_residue, protocols::environment::claims::JumpElement::has_physical_cut, protocols::environment::claims::JumpElement::label, label(), protocols::environment::claims::JumpElement::p1, protocols::environment::claims::JumpElement::p2, physical(), pos1(), pos2(), stubs_intra_residue(), and validate().

void protocols::environment::claims::JumpClaim::yield_elements	(	core::environment::FoldTreeSketch const &	,
		CutElements &
	)		const

overridevirtual

build and export the CutElements that represent the inclusion of a cut in the tree.

Reimplemented from protocols::environment::claims::EnvClaim.

References cut(), core::environment::NO_POSITION, and protocols::environment::claims::CutElement::p.

void protocols::environment::claims::JumpClaim::yield_elements	(	core::pose::Pose const &	,
		DOFElements &
	)		const

overridevirtual

build and export DOFElements, which represent control over non-jump dofs (torsions, bond lengths, angles) final conformation.

Reimplemented from protocols::environment::claims::EnvClaim.

References protocols::environment::claims::DOFElement::c_str, c_str_, core::pose::Pose::conformation(), protocols::environment::claims::DOFElement::i_str, i_str_, protocols::environment::claims::DOFElement::id, core::conformation::Conformation::jump_atom_id(), label(), core::id::RB1, and core::id::RB6.

Member Data Documentation

std::pair< std::string, std::string > protocols::environment::claims::JumpClaim::atoms_

private

Referenced by atoms(), and set_atoms().

ControlStrength protocols::environment::claims::JumpClaim::c_str_

private

Referenced by strength(), and yield_elements().

bool protocols::environment::claims::JumpClaim::create_vrt_p1_

private

Referenced by create_vrt_if_necessary(), and yield_elements().

bool protocols::environment::claims::JumpClaim::create_vrt_p2_

private

Referenced by create_vrt_if_necessary(), and yield_elements().

LocalPosition protocols::environment::claims::JumpClaim::cut_

private

Referenced by cut().

ControlStrength protocols::environment::claims::JumpClaim::i_str_

private

Referenced by strength(), and yield_elements().

std::string protocols::environment::claims::JumpClaim::label_

private

Referenced by label().

bool protocols::environment::claims::JumpClaim::physical_cut_

private

Referenced by physical().

LocalPosition protocols::environment::claims::JumpClaim::pos1_

private

Referenced by pos1().

LocalPosition protocols::environment::claims::JumpClaim::pos2_

private

Referenced by pos2().

bool protocols::environment::claims::JumpClaim::stubs_intra_residue_

private

Referenced by stubs_intra_residue().

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

src/protocols/environment/claims/JumpClaim.hh
src/protocols/environment/claims/JumpClaim.cc

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Types

Private Attributes

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation