#include <FoldTreeSketch.hh>

Inheritance diagram for core::environment::FoldTreeSketch:

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...

FoldTreeSketch &	operator= (FoldTreeSketch const &)=delete

FoldTreeSketch &	operator= (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< Size >	remove_cycles ()

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

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< NodeOP >	nodes_

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 )

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().

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

References append_peptide().

Referenced by protocols::environment::EnvClaimBroker::process_elements().

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 protocols::loops::start.

Referenced by remove_cycles(), and protocols::environment::EnvClaimBroker::render_fold_tree().

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(), protocols::environment::introduce_datamap_cuts(), protocols::environment::EnvClaimBroker::process_elements(), and protocols::environment::EnvClaimBroker::render_fold_tree().

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 core::id::to_string().

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

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

References nodes_.

Referenced by has_cut(), insert_cut(), protocols::environment::introduce_datamap_cuts(), protocols::environment::EnvClaimBroker::process_elements(), range_check(), and remove_cycles().

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

References n_cuts_.

Referenced by protocols::environment::EnvClaimBroker::render_fold_tree().

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

References n_jumps_.

Referenced by protocols::environment::EnvClaimBroker::render_fold_tree().

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

References nres(), and core::id::to_string().

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

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 )

References cuttable(), cycle(), nodes_, nres(), core::scoring::rg, core::simple_metrics::metrics::sum, core::id::to_string(), and tr().

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

wrapper for the other render()

Referenced by protocols::environment::EnvClaimBroker::render_fold_tree().

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

Referenced by append_peptide(), insert_cut(), and num_cuts().

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().

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

src/core/environment/FoldTreeSketch.hh
src/core/environment/FoldTreeSketch.cc

Classes

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation