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core::kinematics::Edge Class Reference

single edge of the fold_tree More...

#include <Edge.hh>

Public Member Functions

core::Size start () const
 start vertex, return by value More...
 
core::Sizestart ()
 start vertex, return by reference More...
 
core::Size stop () const
 stop vertex, return by value More...
 
core::Sizestop ()
 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
 
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 More...
 
bool valid () const
 Is this edge valid (false for default-constructed edges) More...
 
 Edge ()
 default constructor More...
 
 Edge (core::Size const start_in, core::Size const stop_in, int const label_in)
 constructor without atomno info More...
 
 Edge (core::Size const start_in, core::Size 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 (core::Size const start_in, core::Size 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 const int PEPTIDE {-1}
 APL – CODE DUPLICATION – FIX THIS IN A BETTER WAY TO RESOLVE THE CIRCULAR DEPENDENCY. More...
 
static const int CHEMICAL {-2}
 

Private Attributes

core::Size start_
 start vertex (residue) More...
 
core::Size 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 ( core::Size const  start_in,
core::Size const  stop_in,
int const  label_in 
)
inline

constructor without atomno info

core::kinematics::Edge::Edge ( core::Size const  start_in,
core::Size 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 ( core::Size const  start_in,
core::Size 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

References stop_atom_.

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 label_, and PEPTIDE.

bool core::kinematics::Edge::is_polymer ( ) const
inline
bool core::kinematics::Edge::keep_stub_in_residue ( ) const
inline
bool& core::kinematics::Edge::keep_stub_in_residue ( )
inline

References bKeepStubInResidue_.

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

core::Size core::kinematics::Edge::start ( ) const
inline

start vertex, return by value

References start_.

Referenced by protocols::ligand_docking::MinimizeBackbone::add_cut_points(), protocols::seeded_abinitio::CoordinateCst::apply(), protocols::protein_interface_design::movers::SpinMover::apply(), protocols::topology_broker::RigidBodyRandomTMHMover::apply(), protocols::metal_interface::ZincHeterodimerMover::apply(), protocols::cryst::UpdateCrystInfo::apply(), 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_residue_pair_derivatives(), core::io::silent::BinarySilentStruct::fill_pose(), protocols::topology_broker::MembraneTopologyClaimer::generate_claims(), 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(), protocols::denovo_design::insert_peptide_edges(), protocols::simple_filters::JumpEvaluator::JumpEvaluator(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::make_cutpoints_coherent_to_foldtree(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::make_final_tree(), protocols::topology_broker::TMHTopologySamplerClaimer::move_spans(), core::kinematics::operator!=(), core::kinematics::operator<(), core::kinematics::operator<<(), core::kinematics::operator==(), protocols::forge::methods::order(), core::kinematics::FoldTree::partition_by_residue(), core::scoring::electron_density::FastDensEnergy::pose_is_setup_for_density_scoring(), core::conformation::promote_sameresidue_child_of_jump_atom(), core::kinematics::FoldTree::reassign_atoms_for_intra_residue_stubs(), core::kinematics::FoldTree::reorder(), protocols::moves::PyMOLMover::send_foldtree(), core::kinematics::FoldTree::set_jump_atoms(), core::pose::set_reasonable_fold_tree(), core::scoring::electron_density::ElecDensEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::setup_for_scoring(), core::scoring::electron_density::FastDensEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensCenEnergy::setup_for_scoring(), core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy::setup_for_scoring(), protocols::fold_from_loops::movers::DisplayPoseLabelsMover::simple_visualize_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(), core::kinematics::FoldTree::slide_jump(), and core::pose::transfer_jumps().

core::Size& core::kinematics::Edge::start ( )
inline

start vertex, return by reference

References start_.

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

start atom, return by reference

References start_atom_.

core::Size core::kinematics::Edge::stop ( ) const
inline

stop vertex, return by value

References stop_.

Referenced by protocols::ligand_docking::MinimizeBackbone::add_cut_points(), protocols::seeded_abinitio::CoordinateCst::apply(), protocols::protein_interface_design::movers::SpinMover::apply(), protocols::topology_broker::RigidBodyRandomTMHMover::apply(), protocols::metal_interface::ZincHeterodimerMover::apply(), protocols::denovo_design::movers::RotateSegmentMover::apply(), 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(), protocols::hybridization::downstream_residues_from_jump(), core::io::silent::BinarySilentStruct::fill_pose(), protocols::topology_broker::MembraneTopologyClaimer::generate_claims(), core::conformation::get_anchor_and_root_atoms(), protocols::antibody::AntibodyInfo::get_FoldTree_AllCDRs_LHDock(), core::kinematics::FoldTree::get_parent_residue(), protocols::denovo_design::insert_peptide_edges(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::make_cutpoints_coherent_to_foldtree(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::make_final_tree(), protocols::topology_broker::TMHTopologySamplerClaimer::move_spans(), core::kinematics::operator!=(), core::kinematics::operator<(), core::kinematics::operator<<(), core::kinematics::operator==(), protocols::forge::methods::order(), 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(), protocols::moves::PyMOLMover::send_foldtree(), core::kinematics::FoldTree::set_jump_atoms(), core::pose::set_reasonable_fold_tree(), protocols::fold_from_loops::movers::DisplayPoseLabelsMover::simple_visualize_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().

core::Size& core::kinematics::Edge::stop ( )
inline

stop vertex, return by reference

References stop_.

std::string core::kinematics::Edge::stop_atom ( ) const
inline
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
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>>().

const int core::kinematics::Edge::CHEMICAL {-2}
static
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().

const int core::kinematics::Edge::PEPTIDE {-1}
static

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

Referenced by protocols::simple_moves::ResetFoldTree::apply(), protocols::pose_length_moves::PossibleLoop::assign_phi_psi_omega_from_lookback(), protocols::fold_from_loops::utils::attach_n_and_c_unfolded_poses_to_pose(), core::conformation::build_tree(), protocols::ligand_docking::MinimizeBackbone::create_fold_tree_with_cutpoints(), protocols::ligand_docking::MinimizeBackbone::create_fold_tree_with_ligand_jumps_from_attach_pts(), protocols::pose_length_moves::NearNativeLoopCloser::create_maximum_length_pose(), protocols::loop_modeling::LoopBuilder::do_apply(), protocols::star::Extender::extend_unaligned(), protocols::pose_length_moves::InsertResMover::extendRegion(), protocols::pose_length_moves::PossibleLoop::extendRegion(), protocols::pose_length_moves::NearNativeLoopCloser::extendRegion(), protocols::denovo_design::components::FoldGraph::fold_tree(), protocols::denovo_design::components::FoldGraph::fold_tree_rec(), protocols::antibody::GraftedStemOptimizer::get_Cstem_foldtree(), protocols::antibody::AntibodyInfo::get_FoldTree_AllCDRs_LHDock(), core::kinematics::get_foldtree_which_partitions(), protocols::antibody::GraftedStemOptimizer::get_N_C_stems_foldtree(), protocols::antibody::GraftedStemOptimizer::get_Nstem_foldtree(), protocols::rna::denovo::get_rnp_docking_fold_tree(), protocols::denovo_design::insert_peptide_edges(), protocols::grafting::insert_pose_into_pose(), is_peptide(), is_polymer(), protocols::pose_length_moves::PossibleLoop::kic_closure(), protocols::denovo_design::linear_chainbreak(), protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::make_disjointed_foldtree(), protocols::pose_length_moves::PossibleLoop::minimize_loop(), protocols::protein_interface_design::MinimizeInterface(), protocols::protein_interface_design::movers::PlaceStubMover::place_stub(), polymer_direction(), protocols::relax::RepeatProteinRelax::seal_jumps(), protocols::grafting::setup_single_loop_double_arm_remodeling_foldtree(), protocols::grafting::setup_single_loop_single_arm_remodeling_foldtree(), protocols::antibody::simple_fold_tree(), protocols::antibody::simple_one_loop_fold_tree(), protocols::protein_interface_design::star_fold_tree(), protocols::comparative_modeling::steal_ligands(), protocols::denovo_design::symmetric_fold_tree(), protocols::legacy_sewing::Assembly::to_pose(), and protocols::hybridization::HybridizeFoldtreeDynamic::update().

core::Size 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
core::Size 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

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