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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 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 Types

typedef
utility::pointer::shared_ptr
< Node
NodeOP
 
typedef
utility::pointer::shared_ptr
< Node const > 
NodeCOP
 
typedef
utility::pointer::weak_ptr
< Node
NodeAP
 
typedef
utility::pointer::weak_ptr
< Node const > 
NodeCAP
 

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

typedef utility::pointer::weak_ptr< Node > core::environment::FoldTreeSketch::NodeAP
private
typedef utility::pointer::weak_ptr< Node const > core::environment::FoldTreeSketch::NodeCAP
private
typedef utility::pointer::shared_ptr< Node const > core::environment::FoldTreeSketch::NodeCOP
private
typedef utility::pointer::shared_ptr< Node > core::environment::FoldTreeSketch::NodeOP
private

Constructor & Destructor Documentation

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

References append_peptide().

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

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().

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

References nodes_.

Referenced by remove_cycles().

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

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

Referenced by insert_cut().

bool core::environment::FoldTreeSketch::has_jump ( Size const  p1,
Size const  p2 
) const
void core::environment::FoldTreeSketch::insert_cut ( Size const  l)
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().

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().

Size core::environment::FoldTreeSketch::nres ( ) const
int core::environment::FoldTreeSketch::num_cuts ( ) const
Size core::environment::FoldTreeSketch::num_jumps ( ) const
FoldTreeSketch& core::environment::FoldTreeSketch::operator= ( FoldTreeSketch const &  )
delete
FoldTreeSketch& core::environment::FoldTreeSketch::operator= ( FoldTreeSketch &&  )
default

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

void core::environment::FoldTreeSketch::range_check ( Size const  seqpos) const
private
std::set< core::Size > core::environment::FoldTreeSketch::remove_cycles ( )

References nres().

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

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

Member Data Documentation

int core::environment::FoldTreeSketch::n_cuts_
private
core::Size core::environment::FoldTreeSketch::n_jumps_
private

Referenced by insert_jump(), and num_jumps().

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

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