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 &)
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< Size >	remove_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

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< NodeOP >	nodes_
core::Size	n_jumps_

Member Typedef Documentation

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

private

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

private

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

private

typedef utility::pointer::owning_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

)

References append_peptide(), core::kinematics::FoldTree::cutpoints(), core::kinematics::FoldTree::downstream_jump_residue(), insert_cut(), insert_jump(), core::kinematics::FoldTree::nres(), core::kinematics::FoldTree::num_jump(), and core::kinematics::FoldTree::upstream_jump_residue().

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 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(), nodes_, range_check(), and utility::to_string().

Referenced by FoldTreeSketch().

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(), range_check(), and remove_cycles().

Size core::environment::FoldTreeSketch::num_jumps

(

)

const

References n_jumps_.

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

private

References nres(), and utility::to_string().

Referenced by cycle(), has_cut(), has_jump(), insert_cut(), and insert_jump().

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

(

utility::vector1< Real > const &

bias

)

References cuttable(), cycle(), nodes_, nres(), RG, sum(), utility::to_string(), tr, and numeric::random::RandomGenerator::uniform().

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(), 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_jumps_

private

Referenced by insert_jump(), and num_jumps().

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

private

Referenced by append_peptide(), cuttable(), cycle(), has_cut(), has_jump(), insert_cut(), insert_jump(), nres(), remove_cycles(), and render().

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

• symlinks/rosetta/src/core/environment/FoldTreeSketch.hh
• symlinks/rosetta/src/core/environment/FoldTreeSketch.cc