core::kinematics::Edge Class Reference

single edge of the fold_tree More...

#include <Edge.hh>

Public Member Functions
int	start () const
	start vertex, return by value More...
int &	start ()
	start vertex, return by reference More...
int	stop () const
	stop vertex, return by value More...
int &	stop ()
	stop vertex, return by reference More...
std::string	start_atom () const
	start_atom, return by value More...
std::string &	start_atom ()
	start atom, return by reference More...
std::string	stop_atom () const
	stop_atom, return by value More...
std::string &	stop_atom ()
	stop_atom, return by reference More...
std::string	upstream_atom () const
	start-atom, alt name, return by value More...
std::string &	upstream_atom ()
	start-atom, alt name, return by reference More...
std::string	downstream_atom () const
	stop-atom, alt name, return by value More...
std::string &	downstream_atom ()
	stop-atom, alt name, return by reference More...
int	label () const
	label (edge type), return by value More...
int &	label ()
	label (edge type), return by reference More...
bool	is_jump () const
	edge is a jump? More...
bool	is_chemical_bond () const
bool	is_polymer () const
	Edge is peptide edge? More...
bool	is_peptide () const
	Edge is peptide edge? deprecated. More...
bool	has_atom_info () const
	edge has start and stop atoms? More...
bool	keep_stub_in_residue () const
bool &	keep_stub_in_residue ()
int	polymer_direction () const
	direction for a continuous-segement edge. 1 if start residue number < stop residue number and -1 otherwise More...
bool	valid () const
	Is this edge valid (false for default-constructed edges) More...
	Edge ()
	default constructor More...
	Edge (int const start_in, int const stop_in, int const label_in)
	constructor without atomno info More...
	Edge (int const start_in, int const stop_in, std::string const &start_atom, std::string const &stop_atom)
	CHEMICAL Edge constructor (requires atomno info) – note: a chemical edge may be built from any constructor, this one is for convenience only. More...
	Edge (int const start_in, int const stop_in, int label, std::string const &start_atom, std::string const &stop_atom, bool bKeepStubInResidue)
	JUMP Edge constructor (requires atomno info) – note: a chemical edge may be built from any constructor, this one is for convenience only. More...

Static Public Attributes
static int const	PEPTIDE = -1
	APL – CODE DUPLICATION – FIX THIS IN A BETTER WAY TO RESOLVE THE CIRCULAR DEPENDENCY. More...
static int const	CHEMICAL = -2

Private Attributes
int	start_
	start vertex (residue) More...
int	stop_
	stop vertex (residue) More...
int	label_
	type of the edge, continuous segement(-1) or rigid-body jump(1,2,...) More...
std::string	start_atom_
	start atom More...
std::string	stop_atom_
	stop atom More...
bool	bKeepStubInResidue_
	STUB Info for jumps. More...

Friends
std::istream &	operator>> (std::istream &is, Edge &e)
	input operator More...
std::ostream &	operator<< (std::ostream &os, const Edge &e)
	output operator More...
bool	operator< (Edge const &a, Edge const &b)
	less than operator More...
bool	operator== (Edge const &a, Edge const &b)
	equal to operator More...
bool	operator!= (Edge const &a, Edge const &b)
	not equal to operator More...

Detailed Description

single edge of the fold_tree

an edge is a path between two vertices(start and end residues). it can be either a continuous segment like a normal piece of polymer ("PEPTIDE" edge, index label as "-1"), a chemical connection between two residues ("CHEMICAL edge), or a rigid-body transformation between two residues ("JUMP" edge, index label as "1", "2",...). The edge is the basic unit of the fold tree as it stores info on how to build coordinates of the end residue given that of the starting residue and degrees of freedom between these two vertices.

Constructor & Destructor Documentation

core::kinematics::Edge::Edge ( )

inline

default constructor

core::kinematics::Edge::Edge ( int const  start_in, int const  stop_in, int const  label_in  )

inline

constructor without atomno info

core::kinematics::Edge::Edge ( int const  start_in, int const  stop_in, std::string const &  start_atom, std::string const &  stop_atom  )

inline

CHEMICAL Edge constructor (requires atomno info) – note: a chemical edge may be built from any constructor, this one is for convenience only.

core::kinematics::Edge::Edge ( int const  start_in, int const  stop_in, int  label, std::string const &  start_atom, std::string const &  stop_atom, bool  bKeepStubInResidue  )

inline

JUMP Edge constructor (requires atomno info) – note: a chemical edge may be built from any constructor, this one is for convenience only.

Member Function Documentation

std::string core::kinematics::Edge::downstream_atom ( ) const

inline

stop-atom, alt name, return by value

References stop_atom_.

Referenced by core::kinematics::FoldTree::downstream_atom(), core::conformation::get_anchor_and_root_atoms(), and core::kinematics::FoldTree::set_jump_atoms().

std::string& core::kinematics::Edge::downstream_atom ( )

inline

stop-atom, alt name, return by reference

References stop_atom_.

bool core::kinematics::Edge::has_atom_info ( ) const

inline

edge has start and stop atoms?

References start_atom_, and stop_atom_.

Referenced by core::kinematics::FoldTree::downstream_atom(), core::conformation::get_anchor_and_root_atoms(), core::kinematics::operator<<(), and core::kinematics::FoldTree::upstream_atom().

bool core::kinematics::Edge::is_chemical_bond ( ) const

inline

References CHEMICAL, and label_.

Referenced by core::conformation::get_anchor_and_root_atoms(), and core::kinematics::FoldTree::new_chemical_bond().

bool core::kinematics::Edge::is_jump ( ) const

inline

edge is a jump?

References label_.

Referenced by core::conformation::build_jump_edge(), core::kinematics::FoldTree::delete_jump_seqpos(), core::conformation::get_anchor_and_root_atoms(), core::kinematics::FoldTree::get_jump_that_builds_residue(), core::kinematics::FoldTree::get_parent_residue(), core::kinematics::FoldTree::insert_fold_tree_by_jump(), core::kinematics::operator<<(), core::kinematics::operator>>(), core::kinematics::FoldTree::partition_by_jump(), core::conformation::promote_sameresidue_child_of_jump_atom(), core::kinematics::FoldTree::reassign_atoms_for_intra_residue_stubs(), core::conformation::replace_residue_in_atom_tree(), and core::import_pose::set_reasonable_fold_tree().

bool core::kinematics::Edge::is_peptide ( ) const

inline

Edge is peptide edge? deprecated.

References label_, and PEPTIDE.

bool core::kinematics::Edge::is_polymer ( ) const

inline

Edge is peptide edge?

References label_, and PEPTIDE.

Referenced by core::kinematics::FoldTree::delete_jump_seqpos(), and core::conformation::get_anchor_and_root_atoms().

bool core::kinematics::Edge::keep_stub_in_residue ( ) const

inline

References bKeepStubInResidue_.

Referenced by core::kinematics::operator<<(), core::conformation::replace_residue_in_atom_tree(), and core::kinematics::FoldTree::set_jump_atoms().

bool& core::kinematics::Edge::keep_stub_in_residue ( )

inline

References bKeepStubInResidue_.

int core::kinematics::Edge::label ( ) const

inline

label (edge type), return by value

References label_.

Referenced by core::kinematics::FoldTree::delete_edge(), core::kinematics::FoldTree::delete_jump_seqpos(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensCenEnergy::eval_atom_derivative(), core::scoring::electron_density::FastDensEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensEnergy::eval_atom_derivative(), core::kinematics::FoldTree::get_jump_that_builds_residue(), core::kinematics::FoldTree::insert_fold_tree_by_jump(), core::kinematics::operator!=(), core::kinematics::operator<(), core::kinematics::operator<<(), core::kinematics::operator==(), core::kinematics::operator>>(), core::kinematics::FoldTree::partition_by_jump(), and core::import_pose::set_reasonable_fold_tree().

int& core::kinematics::Edge::label ( )

inline

label (edge type), return by reference

References label_.

int core::kinematics::Edge::polymer_direction ( ) const

inline

direction for a continuous-segement edge. 1 if start residue number < stop residue number and -1 otherwise

References label_, PEPTIDE, start_, and stop_.

Referenced by core::conformation::build_polymer_edge(), core::kinematics::FoldTree::delete_jump_seqpos(), core::conformation::get_anchor_and_root_atoms(), and core::conformation::get_residue_connections().

int core::kinematics::Edge::start ( ) const

inline

start vertex, return by value

References start_.

Referenced by core::kinematics::FoldTree::boundary_left(), core::conformation::build_chemical_edge(), core::conformation::build_jump_edge(), core::kinematics::ShortestPathInFoldTree::build_jumpres_distmap(), core::conformation::build_polymer_edge(), core::kinematics::FoldTree::delete_edge(), core::kinematics::FoldTree::delete_jump_seqpos(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensCenEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensEnergy::eval_atom_derivative(), core::scoring::electron_density::FastDensEnergy::eval_atom_derivative(), core::io::silent::BinarySilentStruct::fill_pose(), core::conformation::get_anchor_and_root_atoms(), core::conformation::symmetry::get_asymm_unit_fold_tree(), core::kinematics::FoldTree::get_parent_residue(), core::conformation::symmetry::SymmetricConformation::get_upstream_vrt(), core::kinematics::FoldTree::insert_fold_tree_by_jump(), core::kinematics::operator!=(), core::kinematics::operator<(), core::kinematics::operator<<(), core::kinematics::operator==(), core::kinematics::FoldTree::partition_by_jump(), core::kinematics::FoldTree::partition_by_residue(), core::conformation::promote_sameresidue_child_of_jump_atom(), core::kinematics::FoldTree::reassign_atoms_for_intra_residue_stubs(), core::kinematics::FoldTree::reorder(), core::kinematics::FoldTree::set_jump_atoms(), core::scoring::electron_density::PattersonCorrEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensEnergy::setup_for_scoring(), core::scoring::electron_density::FastDensEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensCenEnergy::setup_for_scoring(), core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy::setup_for_scoring(), core::kinematics::simple_visualize_fold_tree(), core::kinematics::simple_visualize_fold_tree_and_movemap(), core::kinematics::simple_visualize_fold_tree_and_movemap_bb_chi(), and core::pose::transfer_jumps().

int& core::kinematics::Edge::start ( )

inline

start vertex, return by reference

References start_.

std::string core::kinematics::Edge::start_atom ( ) const

inline

start_atom, return by value

References start_atom_.

Referenced by core::kinematics::operator<(), core::kinematics::operator<<(), core::kinematics::operator==(), and core::kinematics::FoldTree::reorder().

std::string& core::kinematics::Edge::start_atom ( )

inline

start atom, return by reference

References start_atom_.

int core::kinematics::Edge::stop ( ) const

inline

stop vertex, return by value

References stop_.

Referenced by core::optimization::symmetry::SymMinimizerMap::asymmetric_dof(), core::kinematics::FoldTree::boundary_right(), core::conformation::build_chemical_edge(), core::conformation::build_jump_edge(), core::kinematics::ShortestPathInFoldTree::build_jumpres_distmap(), core::conformation::build_polymer_edge(), core::kinematics::FoldTree::delete_edge(), core::kinematics::FoldTree::delete_jump_seqpos(), core::io::silent::BinarySilentStruct::fill_pose(), core::conformation::get_anchor_and_root_atoms(), core::kinematics::FoldTree::get_parent_residue(), core::kinematics::FoldTree::insert_fold_tree_by_jump(), core::kinematics::operator!=(), core::kinematics::operator<(), core::kinematics::operator<<(), core::kinematics::operator==(), core::kinematics::FoldTree::partition_by_jump(), core::kinematics::FoldTree::partition_by_residue(), core::conformation::promote_sameresidue_child_of_jump_atom(), core::kinematics::FoldTree::reassign_atoms_for_intra_residue_stubs(), core::kinematics::FoldTree::reorder(), core::kinematics::FoldTree::set_jump_atoms(), core::import_pose::set_reasonable_fold_tree(), core::kinematics::simple_visualize_fold_tree(), core::kinematics::simple_visualize_fold_tree_and_movemap(), core::kinematics::simple_visualize_fold_tree_and_movemap_bb_chi(), and core::pose::transfer_jumps().

int& core::kinematics::Edge::stop ( )

inline

stop vertex, return by reference

References stop_.

std::string core::kinematics::Edge::stop_atom ( ) const

inline

stop_atom, return by value

References stop_atom_.

Referenced by core::kinematics::operator<(), core::kinematics::operator<<(), core::kinematics::operator==(), and core::kinematics::FoldTree::reorder().

std::string& core::kinematics::Edge::stop_atom ( )

inline

stop_atom, return by reference

References stop_atom_.

std::string core::kinematics::Edge::upstream_atom ( ) const

inline

start-atom, alt name, return by value

References start_atom_.

Referenced by core::conformation::get_anchor_and_root_atoms(), core::kinematics::FoldTree::set_jump_atoms(), and core::kinematics::FoldTree::upstream_atom().

std::string& core::kinematics::Edge::upstream_atom ( )

inline

start-atom, alt name, return by reference

References start_atom_.

bool core::kinematics::Edge::valid ( ) const

inline

Is this edge valid (false for default-constructed edges)

References label_, start_, and stop_.

Referenced by core::kinematics::FoldTree::delete_jump_seqpos().

Friends And Related Function Documentation

bool operator!= ( Edge const &  a, Edge const &  b  )

friend

not equal to operator

when any of start residue number, stop residue number and label index number is not equal

bool operator< ( Edge const &  a, Edge const &  b  )

friend

less than operator

compare start residue number first, then stop residue number, then label index number, then start_atom, then stop_atom

std::ostream& operator<< ( std::ostream &  os, const Edge &  e  )

friend

output operator

bool operator== ( Edge const &  a, Edge const &  b  )

friend

equal to operator

when start residue number, stop residue number and label index number are all equal

std::istream& operator>> ( std::istream &  is, Edge &  e  )

friend

input operator

Member Data Documentation

bool core::kinematics::Edge::bKeepStubInResidue_

private

STUB Info for jumps.

Referenced by keep_stub_in_residue(), and core::kinematics::operator>>().

int const core::kinematics::Edge::CHEMICAL = -2

static

Referenced by core::conformation::build_tree(), is_chemical_bond(), core::kinematics::operator<<(), and core::kinematics::operator>>().

int core::kinematics::Edge::label_

private

type of the edge, continuous segement(-1) or rigid-body jump(1,2,...)

Referenced by is_chemical_bond(), is_jump(), is_peptide(), is_polymer(), label(), core::kinematics::operator>>(), polymer_direction(), and valid().

int const core::kinematics::Edge::PEPTIDE = -1

static

APL – CODE DUPLICATION – FIX THIS IN A BETTER WAY TO RESOLVE THE CIRCULAR DEPENDENCY.

Referenced by core::conformation::build_tree(), is_peptide(), is_polymer(), and polymer_direction().

int core::kinematics::Edge::start_

private

start vertex (residue)

Referenced by core::kinematics::operator>>(), polymer_direction(), start(), and valid().

std::string core::kinematics::Edge::start_atom_

private

start atom

Referenced by has_atom_info(), core::kinematics::operator>>(), start_atom(), and upstream_atom().

int core::kinematics::Edge::stop_

private

stop vertex (residue)

Referenced by core::kinematics::operator>>(), polymer_direction(), stop(), and valid().

std::string core::kinematics::Edge::stop_atom_

private

stop atom

Referenced by downstream_atom(), has_atom_info(), core::kinematics::operator>>(), and stop_atom().

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

• src/core/kinematics/Edge.hh