#include <FoldGraph.hh>

Inheritance diagram for protocols::denovo_design::components::FoldGraph:

Public Types
typedef std::stack< core::Size >	NodeStack

typedef std::set< core::Size >	NodeSet

typedef utility::vector1< NodeSet >	Solution

typedef utility::vector1 < Solution >	Solutions

typedef std::map< core::Size, std::string >	NodeToSegmentMap

typedef std::map< std::string, core::Size >	SegmentToNodeMap

typedef std::map< core::Size, SegmentNameList >	MovableGroupToSegmentNameListMap

Public Member Functions
	FoldGraph (StructureData const &perm)
	FOLDGRAPH CLASS METHODS. More...

virtual	~FoldGraph ()

core::kinematics::FoldTree	fold_tree (SegmentNames const &start_segment) const
	gives a fold tree based on the segments in the given permutation More...

core::Size	nodeidx (std::string const &segment) const
	given a segment name, returns the associated graph node index More...

std::string const &	segment (core::Size const nodeidx) const
	given a node index, returns the associated segment More...

Solution	compute_best_solution (SegmentNames const &staple_loops) const
	generates a solution of movable segments to be used in remodel, based on the foldgraph More...

protocols::loops::LoopsOP	create_loops (SegmentNames const &staple_loops) const
	generates a loops object to be used in remodel, based on the foldgraph More...

protocols::loops::LoopsOP	create_loops (Solution const &solution) const

StructureData const &	sd () const
	const access to StructureData More...

Private Member Functions
void	add_edge (std::string const &seg1, std::string const &seg2)
	adds an non-peptide edge to the foldgraph to indicate a non-covalent interaction More...

void	add_peptide_edge (std::string const &seg1, std::string const &seg2)
	adds a peptide edge to the foldgraph, indicating a direct covalent interaction More...

bool	has_peptide_edge (std::string const &seg1, std::string const &seg2) const
	returns true if there is a peptide edge between the two given segments More...

bool	has_edge (std::string const &seg1, std::string const &seg2) const
	returns true if there is a non-peptide edge between the two given segments More...

void	build_seg2node ()
	populates segment to node number map using the StructureData object More...

void	build_node2seg (SegmentToNodeMap const &seg2node)
	populates node number to segment map using a segment to node number map More...

void	find_cutpoints ()
	propagaes the internal set of cutpoint-containing segments More...

void	fold_tree_rec (core::kinematics::FoldTree &ft, NodeSet &visited, NodeStack &node_stack, std::string const &segment_name, core::Size const parent_resid, int const parent_direction, bool const polymer_only) const
	recursive function to traverse graphs and build fold tree More...

void	create_loops_dfs (Solution &solutions, NodeSet &visited, core::Size const current_node) const
	recursive inner function that traverses the foldgraph to create loops objects More...

bool	has_peptide_edge (core::Size const n1, core::Size const n2) const
	returns true if there is a peptide edge between the two given nodes More...

bool	has_edge (core::Size const n1, core::Size const n2) const
	returns true if there is a non-peptide edge between the two given nodes More...

void	add_combined_solutions (Solutions &solutions) const
	checks to see whether solutions found by DFS search can be combined. More...

void	add_non_polymeric_connections (Solutions &solutions) const

Solution const &	select_best_solution (Solutions const &solutions) const

void	sort_solutions (Solutions &solutions) const
	sorts solutions such that the ones maximizing segments w/ same MG are fixed. More...

bool	check_solution (Solution const &solution) const
	checks a solution to ensure that covalently bound segments are not found both inside and outside of loops More...

int	find_cutpoint_in_range (int const min_res, int const max_res) const

Private Attributes
StructureDataCOP	sd_

SegmentToNodeMap	seg2node_

NodeToSegmentMap	node2seg_

NodeSet	cutpoints_

utility::graph::Graph	g_

utility::graph::Graph	gpeptide_

Member Typedef Documentation

typedef std::map< core::Size, SegmentNameList > protocols::denovo_design::components::FoldGraph::MovableGroupToSegmentNameListMap

typedef std::set< core::Size > protocols::denovo_design::components::FoldGraph::NodeSet

typedef std::stack< core::Size > protocols::denovo_design::components::FoldGraph::NodeStack

typedef std::map< core::Size, std::string > protocols::denovo_design::components::FoldGraph::NodeToSegmentMap

typedef std::map< std::string, core::Size > protocols::denovo_design::components::FoldGraph::SegmentToNodeMap

typedef utility::vector1< NodeSet > protocols::denovo_design::components::FoldGraph::Solution

typedef utility::vector1< Solution > protocols::denovo_design::components::FoldGraph::Solutions

Constructor & Destructor Documentation

protocols::denovo_design::components::FoldGraph::FoldGraph ( StructureData const & perm )

FOLDGRAPH CLASS METHODS.

protocols::denovo_design::components::FoldGraph::~FoldGraph ( )

virtual

Member Function Documentation

void protocols::denovo_design::components::FoldGraph::add_combined_solutions ( Solutions & solutions ) const

private

checks to see whether solutions found by DFS search can be combined.

checks to see whether sets within solutions can be combined.

References core::sequence::end, gpeptide_, and protocols::TR().

Referenced by compute_best_solution().

void protocols::denovo_design::components::FoldGraph::add_edge	(	std::string const &	seg1,
		std::string const &	seg2
	)

private

adds an non-peptide edge to the foldgraph to indicate a non-covalent interaction

References g_, nodeidx(), and protocols::TR().

Referenced by add_peptide_edge(), and FoldGraph().

void protocols::denovo_design::components::FoldGraph::add_non_polymeric_connections ( Solutions & solutions ) const

private

References protocols::denovo_design::components::StructureData::covalent_bonds_begin(), protocols::denovo_design::components::StructureData::covalent_bonds_end(), nodeidx(), sd(), and segment().

Referenced by compute_best_solution().

void protocols::denovo_design::components::FoldGraph::add_peptide_edge	(	std::string const &	seg1,
		std::string const &	seg2
	)

private

adds a peptide edge to the foldgraph, indicating a direct covalent interaction

References add_edge(), gpeptide_, nodeidx(), and protocols::TR().

Referenced by FoldGraph().

void protocols::denovo_design::components::FoldGraph::build_node2seg ( SegmentToNodeMap const & seg2node )

private

populates node number to segment map using a segment to node number map

References node2seg_, and seg2node_.

Referenced by FoldGraph().

void protocols::denovo_design::components::FoldGraph::build_seg2node ( )

private

populates segment to node number map using the StructureData object

References core::kinematics::distance(), sd(), seg2node_, protocols::denovo_design::components::StructureData::segments_end(), and protocols::TR().

Referenced by FoldGraph().

bool protocols::denovo_design::components::FoldGraph::check_solution ( Solution const & solution ) const

private

checks a solution to ensure that covalently bound segments are not found both inside and outside of loops

References core::pack::dunbrack::c, protocols::denovo_design::components::StructureData::connected_segments(), gpeptide_, protocols::denovo_design::components::insert_mg(), core::scoring::mg, protocols::denovo_design::components::Segment::movable_group(), protocols::denovo_design::components::StructureData::non_polymer_bond_exists(), sd(), segment(), protocols::denovo_design::components::StructureData::segment(), protocols::denovo_design::components::StructureData::segments_end(), and protocols::TR().

Referenced by select_best_solution().

FoldGraph::Solution protocols::denovo_design::components::FoldGraph::compute_best_solution ( SegmentNames const & staple_loops ) const

generates a solution of movable segments to be used in remodel, based on the foldgraph

References add_combined_solutions(), add_non_polymeric_connections(), core::pack::dunbrack::c, create_loops_dfs(), cutpoints_, nodeidx(), sd(), select_best_solution(), sort_solutions(), protocols::hybridization::t, and protocols::TR().

Referenced by create_loops().

protocols::loops::LoopsOP protocols::denovo_design::components::FoldGraph::create_loops ( SegmentNames const & staple_loops ) const

generates a loops object to be used in remodel, based on the foldgraph

References compute_best_solution().

Referenced by protocols::denovo_design::movers::BuildDeNovoBackboneMover::create_loops().

protocols::loops::LoopsOP protocols::denovo_design::components::FoldGraph::create_loops ( Solution const & solution ) const

References find_cutpoint_in_range(), protocols::denovo_design::components::Segment::lower(), sd(), segment(), protocols::denovo_design::components::StructureData::segment(), protocols::loops::start, protocols::loops::stop, protocols::TR(), and protocols::denovo_design::components::Segment::upper().

void protocols::denovo_design::components::FoldGraph::create_loops_dfs	(	Solution &	solutions,
		NodeSet &	visited,
		core::Size const	current_node
	)		const

private

recursive inner function that traverses the foldgraph to create loops objects

References cutpoints_, gpeptide_, segment(), and protocols::TR().

Referenced by compute_best_solution().

int protocols::denovo_design::components::FoldGraph::find_cutpoint_in_range	(	int const	min_res,
		int const	max_res
	)		const

private

References core::pack::dunbrack::c, protocols::denovo_design::components::Segment::cutpoint(), cutpoints_, sd(), segment(), protocols::denovo_design::components::StructureData::segment(), and protocols::TR().

Referenced by create_loops().

void protocols::denovo_design::components::FoldGraph::find_cutpoints ( )

private

propagaes the internal set of cutpoint-containing segments

References protocols::denovo_design::components::Segment::cutpoint(), cutpoints_, nodeidx(), sd(), protocols::denovo_design::components::StructureData::segment(), and protocols::denovo_design::components::StructureData::segments_end().

Referenced by FoldGraph().

core::kinematics::FoldTree protocols::denovo_design::components::FoldGraph::fold_tree ( SegmentNames const & start_segment ) const

gives a fold tree based on the segments in the given permutation

gives a fold tree based on the segments in the SD

References core::kinematics::FoldTree::begin(), core::kinematics::FoldTree::end(), protocols::denovo_design::components::StructureData::find_non_polymer_bond(), fold_tree_rec(), g_, nodeidx(), core::kinematics::Edge::PEPTIDE, protocols::denovo_design::components::StructureData::pose_residue(), protocols::denovo_design::components::Segment::safe(), sd(), seg2node_, segment(), protocols::denovo_design::components::StructureData::segment(), and protocols::TR().

Referenced by protocols::denovo_design::components::ExtendedPoseBuilder::apply(), and protocols::denovo_design::movers::FoldTreeFromFoldGraphMover::apply().

void protocols::denovo_design::components::FoldGraph::fold_tree_rec	(	core::kinematics::FoldTree &	ft,
		NodeSet &	visited,
		NodeStack &	node_stack,
		std::string const &	segment_name,
		core::Size const	parent_resid,
		int const	parent_direction,
		bool const	polymer_only
	)		const

private

recursive function to traverse graphs and build fold tree

Parameters

parent_direction]	-1 if the previous edge is a peptide edge going backward, 1 if the previous edge is going forward, and 0 if the previous edge is a jump
parent_resid]	parent residue
parent_direction]	-1 if the previous edge is a peptide edge going backward, 1 if the previous edge is going forward, and 0 if the previous edge is a jump

References core::kinematics::FoldTree::add_edge(), g_, gpeptide_, protocols::denovo_design::components::Segment::lower(), nodeidx(), core::kinematics::FoldTree::num_jump(), core::kinematics::Edge::PEPTIDE, protocols::denovo_design::components::Segment::safe(), sd(), segment(), protocols::denovo_design::components::StructureData::segment(), protocols::TR(), and protocols::denovo_design::components::Segment::upper().