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core::environment::FoldTreeSketch Class Reference

#include <FoldTreeSketch.hh>

Inheritance diagram for core::environment::FoldTreeSketch:
Inheritance graph
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Classes

class  Node
 

Public Types

typedef utility::pointer::shared_ptr< NodeNodeOP
 
typedef utility::pointer::shared_ptr< Node const > NodeCOP
 
typedef utility::pointer::weak_ptr< NodeNodeAP
 
typedef utility::pointer::weak_ptr< Node const > NodeCAP
 

Public Member Functions

 FoldTreeSketch ()
 
 FoldTreeSketch (core::Size const length)
 
 FoldTreeSketch (core::kinematics::FoldTree const &)
 
 FoldTreeSketch (FoldTreeSketch &&)=default
 
 FoldTreeSketch (FoldTreeSketch const &)=delete
 We (apparently) want this to be a deep copy, but that would require re-annotating the forward and backward pointers for the nodes. More...
 
FoldTreeSketchoperator= (FoldTreeSketch const &)=delete
 
FoldTreeSketchoperator= (FoldTreeSketch &&)=default
 For move assignment, we can just steal the existing Nodes. More...
 
void insert_jump (Size const p1, Size const p2)
 insert a jump between positions p1 and p2 in the graph More...
 
void insert_cut (Size const l)
 insert a cut after position l (i.e. between position l and l+1) More...
 
void append_peptide (Size const l)
 add a new (graph-detached) peptide-bonded strech of length l at the end of the sequence More...
 
void append_residue ()
 
bool has_cut (Size const) const
 
bool has_jump (Size const p1, Size const p2) const
 
utility::vector1< Size > const cycle (Size const start=1) const
 
std::set< Sizeremove_cycles ()
 
std::set< Sizeremove_cycles (utility::vector1< Real > const &bias)
 
core::kinematics::FoldTreeOP render () const
 wrapper for the other render() More...
 
void render (core::kinematics::FoldTree &ft) const
 build this graph into the FoldTree ft. The state of the graph must be valid here. More...
 
Size nres () const
 
Size num_jumps () const
 
int num_cuts () const
 
core::Size insert_cut (utility::vector1< Real > bias)
 randomly insert a cut using the bias passed in. More...
 

Private Member Functions

bool cuttable (utility::vector1< Size > const &cycle) const
 
void range_check (Size const seqpos) const
 
void visit (NodeCAP n, NodeCAP parent) const
 

Private Attributes

utility::vector1< NodeOPnodes_
 
core::Size n_jumps_
 
int n_cuts_
 

Member Typedef Documentation

◆ NodeAP

typedef utility::pointer::weak_ptr< Node > core::environment::FoldTreeSketch::NodeAP

◆ NodeCAP

typedef utility::pointer::weak_ptr< Node const > core::environment::FoldTreeSketch::NodeCAP

◆ NodeCOP

typedef utility::pointer::shared_ptr< Node const > core::environment::FoldTreeSketch::NodeCOP

◆ NodeOP

typedef utility::pointer::shared_ptr< Node > core::environment::FoldTreeSketch::NodeOP

Constructor & Destructor Documentation

◆ FoldTreeSketch() [1/5]

core::environment::FoldTreeSketch::FoldTreeSketch ( )

◆ FoldTreeSketch() [2/5]

core::environment::FoldTreeSketch::FoldTreeSketch ( core::Size const  length)

References append_peptide().

◆ FoldTreeSketch() [3/5]

core::environment::FoldTreeSketch::FoldTreeSketch ( core::kinematics::FoldTree const &  ft)

◆ FoldTreeSketch() [4/5]

core::environment::FoldTreeSketch::FoldTreeSketch ( FoldTreeSketch &&  )
default

◆ FoldTreeSketch() [5/5]

core::environment::FoldTreeSketch::FoldTreeSketch ( FoldTreeSketch const &  )
delete

We (apparently) want this to be a deep copy, but that would require re-annotating the forward and backward pointers for the nodes.

Member Function Documentation

◆ append_peptide()

void core::environment::FoldTreeSketch::append_peptide ( Size const  l)

add a new (graph-detached) peptide-bonded strech of length l at the end of the sequence

References n_cuts_, core::environment::FoldTreeSketch::Node::newNode(), and nodes_.

Referenced by append_residue(), and FoldTreeSketch().

◆ append_residue()

void core::environment::FoldTreeSketch::append_residue ( )
inline

◆ cuttable()

bool core::environment::FoldTreeSketch::cuttable ( utility::vector1< Size > const &  cycle) const
private

References cycle(), and nodes_.

Referenced by remove_cycles().

◆ cycle()

utility::vector1< Size > const core::environment::FoldTreeSketch::cycle ( core::Size const  start_resid = 1) const

◆ has_cut()

bool core::environment::FoldTreeSketch::has_cut ( Size const  p) const

References nodes_, nres(), and range_check().

Referenced by insert_cut().

◆ has_jump()

bool core::environment::FoldTreeSketch::has_jump ( Size const  p1,
Size const  p2 
) const

◆ insert_cut() [1/2]

void core::environment::FoldTreeSketch::insert_cut ( Size const  l)

◆ insert_cut() [2/2]

core::Size core::environment::FoldTreeSketch::insert_cut ( utility::vector1< Real bias)

randomly insert a cut using the bias passed in.

References has_cut(), insert_cut(), nres(), core::scoring::rg, core::simple_metrics::metrics::sum, and tr().

◆ insert_jump()

void core::environment::FoldTreeSketch::insert_jump ( Size const  p1,
Size const  p2 
)

insert a jump between positions p1 and p2 in the graph

References has_jump(), n_jumps_, nodes_, range_check(), and core::id::to_string().

Referenced by FoldTreeSketch(), and protocols::environment::EnvClaimBroker::process_elements().

◆ nres()

Size core::environment::FoldTreeSketch::nres ( ) const

◆ num_cuts()

int core::environment::FoldTreeSketch::num_cuts ( ) const

◆ num_jumps()

Size core::environment::FoldTreeSketch::num_jumps ( ) const

◆ operator=() [1/2]

FoldTreeSketch& core::environment::FoldTreeSketch::operator= ( FoldTreeSketch &&  )
default

For move assignment, we can just steal the existing Nodes.

◆ operator=() [2/2]

FoldTreeSketch& core::environment::FoldTreeSketch::operator= ( FoldTreeSketch const &  )
delete

◆ range_check()

void core::environment::FoldTreeSketch::range_check ( Size const  seqpos) const
private

◆ remove_cycles() [1/2]

std::set< core::Size > core::environment::FoldTreeSketch::remove_cycles ( )

References nres().

◆ remove_cycles() [2/2]

std::set< core::Size > core::environment::FoldTreeSketch::remove_cycles ( utility::vector1< Real > const &  bias)

◆ render() [1/2]

core::kinematics::FoldTreeOP core::environment::FoldTreeSketch::render ( ) const

◆ render() [2/2]

void core::environment::FoldTreeSketch::render ( core::kinematics::FoldTree ft) const

build this graph into the FoldTree ft. The state of the graph must be valid here.

References nodes_, core::id::to_string(), tr(), and core::kinematics::FoldTree::tree_from_jumps_and_cuts().

◆ visit()

void core::environment::FoldTreeSketch::visit ( NodeCAP  n,
NodeCAP  parent 
) const
private

Member Data Documentation

◆ n_cuts_

int core::environment::FoldTreeSketch::n_cuts_
private

◆ n_jumps_

core::Size core::environment::FoldTreeSketch::n_jumps_
private

Referenced by insert_jump(), and num_jumps().

◆ nodes_

utility::vector1< NodeOP > core::environment::FoldTreeSketch::nodes_
private

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