Rosetta Core  2014.35
Classes | Public Member Functions | Private Types | Private Member Functions | Private Attributes | List of all members
core::environment::FoldTreeSketch Class Reference

#include <FoldTreeSketch.hh>

Classes

class  Node
 

Public Member Functions

 FoldTreeSketch ()
 
 FoldTreeSketch (core::Size const length)
 
 FoldTreeSketch (core::kinematics::FoldTree const &)
 
 FoldTreeSketch (FoldTreeSketch const &)
 copy the FoldTreeSketch 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 (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
 
Size num_cuts () const
 
core::Size insert_cut (utility::vector1< Real > const &bias)
 randomly insert a cut using the bias passed in. More...
 

Private Types

typedef
utility::pointer::owning_ptr
< Node
NodeOP
 
typedef
utility::pointer::owning_ptr
< Node const > 
NodeCOP
 
typedef
utility::pointer::access_ptr
< Node
NodeAP
 
typedef
utility::pointer::access_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_
 
core::Size n_cuts_
 

Member Typedef Documentation

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 const &  rhs)

copy the FoldTreeSketch

Warning
This is not a full deep copy. It doesn't copy the Node pointers deeply, which means

References n_jumps_, and 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_, and nodes_.

Referenced by append_residue(), and FoldTreeSketch().

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

References append_peptide().

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

References nodes_, range_check(), and start.

Referenced by remove_cycles().

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

References nodes_, and range_check().

Referenced by insert_jump().

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

insert a cut after position l (i.e. between position l and l+1)

References has_cut(), n_cuts_, nodes_, range_check(), and utility::to_string().

Referenced by FoldTreeSketch(), and insert_cut().

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

randomly insert a cut using the bias passed in.

References insert_cut(), nres(), RG, ss, sum(), tr, and numeric::random::RandomGenerator::uniform().

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 utility::to_string().

Referenced by FoldTreeSketch().

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

References nodes_.

Referenced by has_cut(), insert_cut(), range_check(), and remove_cycles().

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

References n_cuts_.

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

References n_jumps_.

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

wrapper for the other render()

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 jumps, nodes_, utility::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

core::Size core::environment::FoldTreeSketch::n_cuts_
private
core::Size core::environment::FoldTreeSketch::n_jumps_
private
utility::vector1< NodeOP > core::environment::FoldTreeSketch::nodes_
private

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