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protocols::environment::claims::JumpClaim Class Reference

#include <JumpClaim.hh>

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

Constructor & Destructor Documentation

protocols::environment::claims::JumpClaim::JumpClaim ( ClientMoverOP  owner,
utility::tag::TagCOP  tag,
basic::datacache::DataMap const &  datamap 
)
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
EnvClaimOP protocols::environment::claims::JumpClaim::clone ( ) const
overridevirtual
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
setthis behavior for pos1()
setthis 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
bool protocols::environment::claims::JumpClaim::physical ( ) const
inline
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
void protocols::environment::claims::JumpClaim::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
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
void protocols::environment::claims::JumpClaim::strength ( ControlStrength const &  cstr,
ControlStrength const &  istr 
)
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
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
void protocols::environment::claims::JumpClaim::yield_elements ( core::environment::FoldTreeSketch const &  ,
JumpElements  
) const
overridevirtual
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

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