Rosetta 3.4
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core::kinematics::Edge Class Reference

single edge of the fold_tree More...

#include <Edge.hh>

Collaboration diagram for core::kinematics::Edge:
Collaboration graph
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List of all members.

Public Member Functions

int start () const
 start vertex, return by value
intstart ()
 start vertex, return by reference
int stop () const
 stop vertex, return by value
intstop ()
 stop vertex, return by reference
std::string start_atom () const
 start_atom, return by value
std::string & start_atom ()
 start atom, return by reference
std::string stop_atom () const
 stop_atom, return by value
std::string & stop_atom ()
 stop_atom, return by reference
std::string upstream_atom () const
 start-atom, alt name, return by value
std::string & upstream_atom ()
 start-atom, alt name, return by reference
std::string downstream_atom () const
 stop-atom, alt name, return by value
std::string & downstream_atom ()
 stop-atom, alt name, return by reference
int label () const
 label (edge type), return by value
intlabel ()
 label (edge type), return by reference
bool is_jump () const
 edge is a jump?
bool is_chemical_bond () const
bool is_polymer () const
 Edge is peptide edge?
bool is_peptide () const
 Edge is peptide edge? deprecated.
bool has_atom_info () const
 edge has start and stop atoms?
bool keep_stub_in_residue () const
boolkeep_stub_in_residue ()
int polymer_direction () const
 direction for a continuous-segement edge. 1 if start residue number < stop residue number and -1 otherwise
bool valid () const
 Is this edge valid (false for default-constructed edges)
 Edge ()
 default constructor
 Edge (int const start_in, int const stop_in, int const label_in)
 constructor without atomno info
 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.
 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.

Static Public Attributes

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

Friends

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

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 segement 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 te 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]
std::string& core::kinematics::Edge::downstream_atom ( ) [inline]

stop-atom, alt name, return by reference

bool core::kinematics::Edge::has_atom_info ( ) const [inline]
bool core::kinematics::Edge::is_chemical_bond ( ) const [inline]
bool core::kinematics::Edge::is_jump ( ) const [inline]
bool core::kinematics::Edge::is_peptide ( ) const [inline]

Edge is peptide edge? deprecated.

References PEPTIDE.

bool core::kinematics::Edge::is_polymer ( ) const [inline]

Edge is peptide edge?

References PEPTIDE.

Referenced by core::conformation::get_anchor_and_root_atoms().

bool core::kinematics::Edge::keep_stub_in_residue ( ) const [inline]
bool& core::kinematics::Edge::keep_stub_in_residue ( ) [inline]
int core::kinematics::Edge::label ( ) const [inline]
int& core::kinematics::Edge::label ( ) [inline]

label (edge type), return by reference

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 PEPTIDE.

Referenced by core::conformation::build_polymer_edge(), 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

Referenced by protocols::protein_interface_design::movers::BackrubDDMover::apply(), core::kinematics::FoldTree::boundary_left(), core::conformation::build_chemical_edge(), core::conformation::build_jump_edge(), core::conformation::build_polymer_edge(), core::kinematics::FoldTree::delete_edge(), core::conformation::get_anchor_and_root_atoms(), core::conformation::symmetry::get_asymm_unit_fold_tree(), core::kinematics::FoldTree::insert_fold_tree_by_jump(), core::kinematics::operator!=(), core::kinematics::operator<(), core::kinematics::operator<<(), core::kinematics::operator==(), protocols::forge::methods::order(), 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_atomwise::ElecDensAtomwiseEnergy::setup_for_scoring(), core::scoring::electron_density::PattersonCorrEnergy::setup_for_scoring(), core::scoring::electron_density::FastDensEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensCenEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::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

std::string core::kinematics::Edge::start_atom ( ) const [inline]
std::string& core::kinematics::Edge::start_atom ( ) [inline]

start atom, return by reference

int& core::kinematics::Edge::stop ( ) [inline]

stop vertex, return by reference

int core::kinematics::Edge::stop ( ) const [inline]
std::string& core::kinematics::Edge::stop_atom ( ) [inline]

stop_atom, return by reference

std::string core::kinematics::Edge::stop_atom ( ) const [inline]
std::string& core::kinematics::Edge::upstream_atom ( ) [inline]

start-atom, alt name, return by reference

std::string core::kinematics::Edge::upstream_atom ( ) const [inline]
bool core::kinematics::Edge::valid ( ) const [inline]

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


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

int const core::kinematics::Edge::PEPTIDE = -1 [static]

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