protocols::environment::claims::TorsionClaim Class Reference

#include <TorsionClaim.hh>

Inheritance diagram for protocols::environment::claims::TorsionClaim:

Public Types
typedef core::environment::LocalPosition	LocalPosition
typedef core::environment::LocalPositions	LocalPositions

Public Member Functions
	TorsionClaim (ClientMoverOP owner, utility::tag::TagCOP tag, basic::datacache::DataMap &)
	TorsionClaim (ClientMoverOP owner, core::select::residue_selector::ResidueSelectorCOP)
	TorsionClaim (ClientMoverOP owner, LocalPosition const &local_pos)
	TorsionClaim (ClientMoverOP owner, std::string const &label, std::pair< core::Size, core::Size > const &range)
	TorsionClaim (ClientMoverOP owner, LocalPositions const &positions)
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...
ControlStrength const &	ctrl_strength () const
void	claim_sidechain (bool in)
bool	claim_sidechain () const
void	claim_backbone (bool in)
bool	claim_backbone () const
void	strength (ControlStrength const &control_strength, ControlStrength const &initialization_strength)
	set the initialization and control strength of the TorsionClaim. More...
ControlStrength const &	init_strength () const
EnvClaimOP	clone () const override
std::string	type () const override
virtual ResidueSelectorCOP	selector () const
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 &, ResidueElements &) const
	build ResidueElements that indicate the introduction of a new peptide edge into the fold tree. More...
virtual void	yield_elements (FoldTreeSketch const &, JumpElements &) const
	build the JumpElements that represent the inclusion of a jump in the nascent FoldTree More...
virtual void	yield_elements (FoldTreeSketch const &, CutElements &) const
	build and export the CutElements that represent the inclusion of a cut in the tree. 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
DOFElement	wrap_dof_id (core::id::DOF_ID const &id) const override
void	insert_dof_element (core::conformation::Conformation const &conf, DOFElements &elements, core::Size seqpos, core::id::TorsionType type, core::Size torsion_number) const
Protected Member Functions inherited from protocols::environment::claims::EnvClaim
ControlStrength	parse_ctrl_str (std::string const &str) const
void	queue_for_annotation (std::string const &label, ResidueSelectorCOP selector)

Private Types
typedef core::environment::FoldTreeSketch	FoldTreeSketch
typedef EnvClaim	Parent
typedef core::select::residue_selector::ResidueSelectorCOP	ResidueSelectorCOP

Private Attributes
ResidueSelectorCOP	selector_
ControlStrength	c_str_
ControlStrength	i_str_
bool	claim_sidechain_
bool	claim_backbone_

Member Typedef Documentation

FoldTreeSketch

typedef core::environment::FoldTreeSketch protocols::environment::claims::TorsionClaim::FoldTreeSketch

private

LocalPosition

typedef core::environment::LocalPosition protocols::environment::claims::TorsionClaim::LocalPosition

LocalPositions

typedef core::environment::LocalPositions protocols::environment::claims::TorsionClaim::LocalPositions

Parent

typedef EnvClaim protocols::environment::claims::TorsionClaim::Parent

private

ResidueSelectorCOP

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

private

Constructor & Destructor Documentation

TorsionClaim() [1/5]

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

References claim_backbone_, claim_sidechain_, core::select::residue_selector::get_residue_selector(), selector_, protocols::environment::tr(), and type().

TorsionClaim() [2/5]

protocols::environment::claims::TorsionClaim::TorsionClaim	(	ClientMoverOP	owner,
		core::select::residue_selector::ResidueSelectorCOP	selector
	)

TorsionClaim() [3/5]

protocols::environment::claims::TorsionClaim::TorsionClaim	(	ClientMoverOP	owner,
		LocalPosition const &	local_pos
	)

TorsionClaim() [4/5]

protocols::environment::claims::TorsionClaim::TorsionClaim	(	ClientMoverOP	owner,
		std::string const &	label,
		std::pair< core::Size, core::Size > const &	range
	)

References protocols::sic_dock::range(), and selector_.

TorsionClaim() [5/5]

protocols::environment::claims::TorsionClaim::TorsionClaim	(	ClientMoverOP	owner,
		LocalPositions const &	positions
	)

Member Function Documentation

claim_backbone() [1/2]

bool protocols::environment::claims::TorsionClaim::claim_backbone ( ) const

inline

References claim_backbone_.

Referenced by yield_elements().

claim_backbone() [2/2]

void protocols::environment::claims::TorsionClaim::claim_backbone ( bool  in )

inline

References claim_backbone_, and core::conformation::membrane::in.

claim_sidechain() [1/2]

bool protocols::environment::claims::TorsionClaim::claim_sidechain ( ) const

inline

References claim_sidechain_.

Referenced by yield_elements().

claim_sidechain() [2/2]

void protocols::environment::claims::TorsionClaim::claim_sidechain ( bool  in )

inline

References claim_sidechain_, and core::conformation::membrane::in.

class_name()

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

static

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

clone()

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

overridevirtual

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

ctrl_strength()

ControlStrength const & protocols::environment::claims::TorsionClaim::ctrl_strength

(

)

const

References c_str_.

Referenced by show(), and wrap_dof_id().

init_strength()

ControlStrength const & protocols::environment::claims::TorsionClaim::init_strength

(

)

const

References i_str_.

Referenced by show(), and wrap_dof_id().

insert_dof_element()

void protocols::environment::claims::TorsionClaim::insert_dof_element ( core::conformation::Conformation const &  conf, DOFElements &  elements, core::Size  seqpos, core::id::TorsionType  type, core::Size  torsion_number  ) const

protected

References core::conformation::Conformation::dof_id_from_torsion_id(), protocols::environment::tr(), type(), core::id::DOF_ID::valid(), core::id::TorsionID::valid(), and wrap_dof_id().

Referenced by yield_elements().

provide_xml_schema()

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

static

References core::select::residue_selector::attributes_for_parse_residue_selector(), class_name(), and protocols::environment::claims::EnvClaim::envclaim_ct_namer().

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

selector()

virtual ResidueSelectorCOP protocols::environment::claims::TorsionClaim::selector ( ) const

inlinevirtual

References selector_.

Referenced by show().

show()

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

overridevirtual

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

References ctrl_strength(), init_strength(), protocols::environment::claims::EnvClaim::owner(), selector(), and type().

strength()

void protocols::environment::claims::TorsionClaim::strength	(	ControlStrength const &	control_strength,
		ControlStrength const &	initialization_strength
	)

set the initialization and control strength of the TorsionClaim.

References c_str_, protocols::environment::claims::DOES_NOT_CONTROL, protocols::environment::claims::EXCLUSIVE, and i_str_.

type()

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

overridevirtual

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

Referenced by insert_dof_element(), show(), and TorsionClaim().

wrap_dof_id()

DOFElement protocols::environment::claims::TorsionClaim::wrap_dof_id ( core::id::DOF_ID const &  id ) const

overrideprotectedvirtual

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

References protocols::environment::claims::DOFElement::c_str, ctrl_strength(), protocols::environment::claims::DOFElement::i_str, init_strength(), and protocols::environment::claims::EnvClaim::wrap_dof_id().

Referenced by insert_dof_element().

yield_elements()

void protocols::environment::claims::TorsionClaim::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 core::id::BB, core::chemical::rna::CHI, claim_backbone(), claim_sidechain(), core::pose::Pose::conformation(), insert_dof_element(), core::conformation::Residue::n_nus(), core::id::NU, core::conformation::Conformation::residue(), selector_, core::pose::Pose::size(), and protocols::environment::tr().

Member Data Documentation

c_str_

ControlStrength protocols::environment::claims::TorsionClaim::c_str_

private

Referenced by ctrl_strength(), and strength().

claim_backbone_

bool protocols::environment::claims::TorsionClaim::claim_backbone_

private

Referenced by claim_backbone(), and TorsionClaim().

claim_sidechain_

bool protocols::environment::claims::TorsionClaim::claim_sidechain_

private

Referenced by claim_sidechain(), and TorsionClaim().

i_str_

ControlStrength protocols::environment::claims::TorsionClaim::i_str_

private

Referenced by init_strength(), and strength().

selector_

ResidueSelectorCOP protocols::environment::claims::TorsionClaim::selector_

private

Referenced by selector(), TorsionClaim(), and yield_elements().

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

• src/protocols/environment/claims/TorsionClaim.hh
• src/protocols/environment/claims/TorsionClaim.cc