Rosetta 3.4
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protocols::loops::Loops Class Reference

#include <Loops.hh>

Inheritance diagram for protocols::loops::Loops:
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List of all members.

Public Types

typedef utility::vector1< LoopLoopList
typedef utility::vector1
< SerializedLoop
SerializedLoopList
typedef LoopList::iterator iterator
typedef LoopList::const_iterator const_iterator

Public Member Functions

bool empty () const
core::Size num_loop () const
const_iterator begin () const
const_iterator end () const
iterator v_begin ()
iterator v_end ()
 Loops ()
 Loops (const Loops &src)
 Loops (SerializedLoopList const &src)
 Loops (std::string const &loop_file_name)
 Loops (bool setup_loops_from_options_system)
Loopsoperator= (Loops const &src)
 ~Loops ()
void read_loops_options ()
void write_loops_to_file (std::string const &filename, std::string token="LOOP") const
void write_loops_to_stream (std::ostream &data, std::string token) const
void add_loop (Loop loop, core::Size minimal_gap=0)
void add_loop (core::Size const start, core::Size const stop, core::Size const cut=0, core::Real skip_rate=0.0, bool const extended=false)
void add_loop (const const_iterator &it)
void add_loop (const iterator &it)
void push_back (Loop loop)
void push_back (core::Size const start, core::Size const stop, core::Size const cut=0, core::Real skip_rate=0.0, bool const extended=false)
void add_overlap_loop (Loops loops)
void add_overlap_loop (const Loop loop)
void delete_loop (core::Size const start, core::Size const stop)
const_iterator one_random_loop () const
core::Size loop_size (core::Size const loop_num) const
core::Size loop_size () const
 return number of residues in all loops of this definition -- sum_i( loop_size( i ) )
core::Size size () const
core::Size nr_residues () const
void sequential_order ()
void clear ()
LoopList const & loops () const
LoopsFileIOOP get_loop_file_reader () const
bool is_loop_residue (core::Size const seqpos, int const offset=0) const
 Is seqpos contained in any of my loops?
bool has (core::Size const seqpos, int const offset=0) const
 is seqpos a residue in this Loops container ?
void set_extended (bool input)
void make_sequence_shift (int shift)
bool loop_of_residue (core::Size const seqpos, Loop &loop) const
 yield the Loop which contains the residue seqpos, returns false if seqpos is not in any residue.
Loops invert (core::Size num_residues) const
 Given the total number of residues, returns the inverse of this selection.
void switch_movemap (core::kinematics::MoveMap &movemap, core::id::TorsionType, bool allow_moves=true) const
 switch DOF_Type for residues in loop. id::CHI, id::BB --- don't use with id::JUMP
core::Size loop_index_of_residue (core::Size const seqpos) const
void auto_choose_cutpoints (core::pose::Pose const &pose)
void choose_cutpoints (core::pose::Pose const &pose)
void verify_against (core::pose::Pose const &pose) const
void remove_terminal_loops (core::pose::Pose const &pose)
void grow_all_loops (core::Size nres, core::Real magnitude)
 Extend a loop.
void grow_all_loops (core::pose::Pose const &pose, core::Real magnitude)
 Extend a loop (don't extend across cutpoints)
void grow_loop (core::pose::Pose const &pose, Loop &loop, core::Real magnitude)
 Extend a loop (don't extend across cutpoints)
void grow_loop_away_from_sheets (core::pose::Pose const &pose, Loop &loop, core::Real magnitude)
 if possible grows loop will not cross cutpoints or if possible into sheets
void grow_loop (core::Size nres, Loop &loop, core::Real magnitude)
 Extend a loop.
void grow_loop (core::Size nres, Loop &loop, core::Real mag_left, core::Real mag_right)
 Extend a loop unequally in both dirs.
std::string const & loop_file_name ()
void set_loop_file_name_and_reset (std::string const &loop_filename)
bool strict_looprelax_checks ()
void set_strict_looprelax_checks (bool const check)
std::string const & file_reading_token ()
void set_file_reading_token (std::string const &token)
void center_of_mass (const core::pose::Pose &pose, numeric::xyzVector< core::Real > *center) const
 Computes the center of mass of the Ca atoms specified by this instance, writing the result to

. Assumes there is no missing backbone density.

template<class T >
void transfer_to_residue_vector (utility::vector1< T > &, T val)
 set each loop-residue in the vector to val. input vector of nres length ( if shorter last residues of loop are ignored )
void get_residues (utility::vector1< Size > &selection) const
 add all residues within this loop definition into selection
const Loopoperator[] (core::Size const i) const
Loopoperator[] (core::Size const i)
bool operator== (Loops const &other) const
bool operator!= (Loops const &other) const

Friends

std::ostream & operator<< (std::ostream &os, const Loops &loops)

Member Typedef Documentation

typedef LoopList::const_iterator protocols::loops::Loops::const_iterator
typedef LoopList::iterator protocols::loops::Loops::iterator

Constructor & Destructor Documentation

protocols::loops::Loops::Loops ( )
protocols::loops::Loops::Loops ( const Loops src)

References loops().

protocols::loops::Loops::Loops ( SerializedLoopList const &  src)
protocols::loops::Loops::Loops ( std::string const &  loop_file_name)
protocols::loops::Loops::Loops ( bool  setup_loops_from_options_system)
protocols::loops::Loops::~Loops ( )

Member Function Documentation

void protocols::loops::Loops::add_loop ( loops::Loop  loop,
core::Size  minimal_gap = 0 
)

References protocols::loops::Loop::cut(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), and protocols::loops::tr().

Referenced by protocols::loops::add_loop(), add_loop(), protocols::loops::addScoresForLoopParts(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply(), protocols::loops::compute_ss_regions(), protocols::loops::define_scorable_core_from_secondary_structure(), protocols::loops::extract_secondary_structure_chunks(), protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::fascore(), protocols::abinitio::IterativeBase::gen_resample_fragments(), protocols::loophash::LoopHashLibrary::get_all(), protocols::abinitio::get_core(), protocols::loophash::LoopHashLibrary::graft_loop(), protocols::toolbox::pose_manipulation::insert_pose_into_pose(), protocols::forge::methods::intervals_to_confirmation_loops(), protocols::forge::methods::intervals_to_loops(), invert(), protocols::loops::loopfinder(), protocols::loophash::LocalInserter_SimpleMin::make_local_bb_change(), protocols::loophash::LocalInserter_SimpleMin::make_local_bb_change_include_cut(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::forge::build::BuildManager::modify(), protocols::seeded_abinitio::SwapSegment::parse_my_tag(), protocols::seeded_abinitio::parse_seeds(), protocols::antibody::Antibody::populate_all_cdrs(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::process_fragments(), push_back(), protocols::loops::remove_short_chunks(), protocols::loops::remove_small_gaps(), protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::select_final_loop(), protocols::loops::select_loop_residues(), protocols::abinitio::KinematicTaskControl::set_extended_torsions_and_idealize_loops(), protocols::loops::set_extended_torsions_and_idealize_loops(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::set_movemap_from_kic_segment(), protocols::forge::methods::set_single_loop_fold_tree(), protocols::antibody2::Ab_Info::setup_CDR_loops(), protocols::comparative_modeling::hybridize::FoldTreeHybridize::setup_foldtree(), protocols::loops::split_by_ca_ca_dist(), protocols::loops::split_by_resSeq(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::update_allow_sc_vectors(), and protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::update_movemap_vectors().

void protocols::loops::Loops::add_loop ( core::Size const  start,
core::Size const  stop,
core::Size const  cut = 0,
core::Real  skip_rate = 0.0,
bool const  extended = false 
)

References add_loop().

void protocols::loops::Loops::add_loop ( const const_iterator it)

References add_loop().

void protocols::loops::Loops::add_loop ( const iterator it)

References add_loop().

void protocols::loops::Loops::add_overlap_loop ( Loops  loops)

References begin(), and end().

void protocols::loops::Loops::add_overlap_loop ( const Loop  loop)
void protocols::loops::Loops::auto_choose_cutpoints ( core::pose::Pose const &  pose)
Loops::const_iterator protocols::loops::Loops::begin ( ) const

Referenced by add_overlap_loop(), protocols::abinitio::LoopJumpFoldCst::add_rigidity_jumps(), protocols::antibody2::Ab_Info::all_cdr_fold_tree(), protocols::antibody::Antibody::all_cdr_fold_tree(), protocols::antibody2::Ab_ModelCDRH3::all_cdr_VL_VH_fold_tree(), protocols::antibody::AntibodyModeler::all_cdr_VL_VH_fold_tree(), protocols::topology_broker::RigidChunkClaimer::allow_claim(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::loops::ccd_close_loops(), protocols::simple_moves::WobbleMover::ccd_closure(), center_of_mass(), protocols::medal::chunk_probabilities(), protocols::topology_broker::copy_internal_coords(), protocols::loops::extract_secondary_structure_chunks(), protocols::forge::methods::fill_non_loop_cst_set(), protocols::loops::filter_loop_neighbors_by_distance(), protocols::loops::fix_with_coord_cst(), protocols::forge::methods::fold_tree_from_loops(), protocols::canonical_sampling::CanonicalSamplingMover::get_ABGEO_string(), protocols::topology_broker::RigidChunkClaimer::initialize_dofs(), protocols::toolbox::pose_manipulation::insert_pose_into_pose(), protocols::toolbox::KClusterData::KClusterData(), protocols::loops::loop_local_rmsd(), protocols::loops::loop_rmsd(), protocols::comparative_modeling::ThreadingJob::loops(), protocols::loops::loops_set_move_map(), protocols::loops::operator<<(), OPT_1GRP_KEY(), protocols::topology_broker::RigidChunkClaimer::receive_message(), protocols::loops::remove_short_chunks(), protocols::antibody::AntibodyModeler::repulsive_ramp(), protocols::loops::select_loop_residues(), protocols::topology_broker::RigidChunkClaimer::select_parts(), protocols::abinitio::KinematicTaskControl::set_extended_torsions_and_idealize_loops(), protocols::loops::set_extended_torsions_and_idealize_loops(), protocols::nonlocal::StarTreeBuilder::set_up(), protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops(), protocols::antibody::AntibodyModeler::snugfit_mcm_protocol(), protocols::loops::split_by_ca_ca_dist(), protocols::loops::split_by_resSeq(), protocols::fibril::superimpose_pose_on_subset_bb(), switch_movemap(), protocols::topology_broker::RigidChunkClaimer::switch_to_fullatom(), transfer_to_residue_vector(), verify_against(), and write_loops_to_stream().

void protocols::loops::Loops::center_of_mass ( const core::pose::Pose pose,
numeric::xyzVector< core::Real > *  center 
) const

Computes the center of mass of the Ca atoms specified by this instance, writing the result to

. Assumes there is no missing backbone density.

Note: if this method is called on an instance without any Loop's, returns (0,0,0).

References begin(), end(), and core::pose::Pose::xyz().

Referenced by protocols::nonlocal::StarTreeBuilder::set_up().

void protocols::loops::Loops::choose_cutpoints ( core::pose::Pose const &  pose)

References v_begin(), and v_end().

void protocols::loops::Loops::clear ( )
void protocols::loops::Loops::delete_loop ( core::Size const  start,
core::Size const  stop 
)

Referenced by add_overlap_loop().

bool protocols::loops::Loops::empty ( ) const
Loops::const_iterator protocols::loops::Loops::end ( ) const

Referenced by add_overlap_loop(), protocols::abinitio::LoopJumpFoldCst::add_rigidity_jumps(), protocols::antibody2::Ab_Info::all_cdr_fold_tree(), protocols::antibody::Antibody::all_cdr_fold_tree(), protocols::antibody2::Ab_ModelCDRH3::all_cdr_VL_VH_fold_tree(), protocols::antibody::AntibodyModeler::all_cdr_VL_VH_fold_tree(), protocols::topology_broker::RigidChunkClaimer::allow_claim(), protocols::loops::ccd_close_loops(), center_of_mass(), protocols::medal::chunk_probabilities(), protocols::topology_broker::copy_internal_coords(), protocols::loops::extract_secondary_structure_chunks(), protocols::forge::methods::fill_non_loop_cst_set(), protocols::loops::filter_loop_neighbors_by_distance(), protocols::loops::fix_with_coord_cst(), protocols::forge::methods::fold_tree_from_loops(), protocols::canonical_sampling::CanonicalSamplingMover::get_ABGEO_string(), protocols::topology_broker::RigidChunkClaimer::initialize_dofs(), protocols::toolbox::KClusterData::KClusterData(), protocols::loops::loop_local_rmsd(), protocols::loops::loop_rmsd(), protocols::comparative_modeling::ThreadingJob::loops(), protocols::loops::loops_set_move_map(), one_random_loop(), protocols::loops::operator<<(), OPT_1GRP_KEY(), protocols::loops::remove_short_chunks(), protocols::antibody::AntibodyModeler::repulsive_ramp(), protocols::loops::select_loop_residues(), protocols::topology_broker::RigidChunkClaimer::select_parts(), protocols::abinitio::KinematicTaskControl::set_extended_torsions_and_idealize_loops(), protocols::loops::set_extended_torsions_and_idealize_loops(), protocols::nonlocal::StarTreeBuilder::set_up(), protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops(), protocols::antibody::AntibodyModeler::snugfit_mcm_protocol(), protocols::loops::split_by_ca_ca_dist(), protocols::loops::split_by_resSeq(), protocols::fibril::superimpose_pose_on_subset_bb(), switch_movemap(), protocols::topology_broker::RigidChunkClaimer::switch_to_fullatom(), transfer_to_residue_vector(), verify_against(), and write_loops_to_stream().

std::string const & protocols::loops::Loops::file_reading_token ( )
LoopsFileIOOP protocols::loops::Loops::get_loop_file_reader ( ) const
void protocols::loops::Loops::get_residues ( utility::vector1< Size > &  selection) const
void protocols::loops::Loops::grow_all_loops ( core::Size  nres,
core::Real  magnitude 
)
void protocols::loops::Loops::grow_all_loops ( core::pose::Pose const &  pose,
core::Real  magnitude 
)

Extend a loop (don't extend across cutpoints)

References grow_loop(), and size().

void protocols::loops::Loops::grow_loop ( core::pose::Pose const &  pose,
Loop loop,
core::Real  magnitude 
)

Extend a loop (don't extend across cutpoints)

Extend a loop .. don't extend across cutpoints in the pose.

References core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_cutpoint(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), and core::pose::Pose::total_residue().

Referenced by grow_all_loops(), grow_loop(), and grow_loop_away_from_sheets().

void protocols::loops::Loops::grow_loop ( core::Size  nres,
Loop loop,
core::Real  magnitude 
)

Extend a loop.

References grow_loop().

void protocols::loops::Loops::grow_loop ( core::Size  nres,
Loop loop,
core::Real  mag_left,
core::Real  mag_right 
)
void protocols::loops::Loops::grow_loop_away_from_sheets ( core::pose::Pose const &  pose,
Loop loop,
core::Real  magnitude 
)
bool protocols::loops::Loops::has ( core::Size const  seqpos,
int const  offset = 0 
) const

is seqpos a residue in this Loops container ?

References is_loop_residue().

Loops protocols::loops::Loops::invert ( core::Size  num_residues) const

Given the total number of residues, returns the inverse of this selection.

Given the total number of residues, inverts this set of loops. Note: the inline comments are geared toward comparative modeling, but are not specific to it. Think of "unaligned" as this, "aligned" as its inverse.

References add_loop(), num_loop(), sequential_order(), protocols::loops::Loop::start(), and protocols::loops::Loop::stop().

Referenced by protocols::relax::add_coordinate_constraints_to_pose(), protocols::loops::add_coordinate_constraints_to_pose(), protocols::loops::define_scorable_core_from_secondary_structure(), protocols::topology_broker::RigidChunkClaimer::read_tag(), and protocols::topology_broker::RigidChunkClaimer::select_parts().

bool protocols::loops::Loops::is_loop_residue ( core::Size const  seqpos,
int const  offset = 0 
) const
std::string const & protocols::loops::Loops::loop_file_name ( )
Size protocols::loops::Loops::loop_index_of_residue ( core::Size const  seqpos) const
bool protocols::loops::Loops::loop_of_residue ( core::Size const  seqpos,
Loop loop 
) const

yield the Loop which contains the residue seqpos, returns false if seqpos is not in any residue.

Size protocols::loops::Loops::loop_size ( core::Size const  loop_num) const
Size protocols::loops::Loops::loop_size ( ) const

return number of residues in all loops of this definition -- sum_i( loop_size( i ) )

References size().

Referenced by nr_residues().

Loops::LoopList const & protocols::loops::Loops::loops ( ) const
void protocols::loops::Loops::make_sequence_shift ( int  shift)
core::Size protocols::loops::Loops::nr_residues ( ) const
core::Size protocols::loops::Loops::num_loop ( ) const
Loops::const_iterator protocols::loops::Loops::one_random_loop ( ) const
bool protocols::loops::Loops::operator!= ( Loops const &  other) const
Loops & protocols::loops::Loops::operator= ( Loops const &  src)
bool protocols::loops::Loops::operator== ( Loops const &  other) const

References size().

const Loop & protocols::loops::Loops::operator[] ( core::Size const  i) const
Loop & protocols::loops::Loops::operator[] ( core::Size const  i)
void protocols::loops::Loops::push_back ( core::Size const  start,
core::Size const  stop,
core::Size const  cut = 0,
core::Real  skip_rate = 0.0,
bool const  extended = false 
)

References add_loop().

void protocols::loops::Loops::push_back ( Loop  loop)
void protocols::loops::Loops::read_loops_options ( )
void protocols::loops::Loops::remove_terminal_loops ( core::pose::Pose const &  pose)
void protocols::loops::Loops::sequential_order ( )
void protocols::loops::Loops::set_extended ( bool  input)

References v_begin(), and v_end().

void protocols::loops::Loops::set_file_reading_token ( std::string const &  token)
void protocols::loops::Loops::set_loop_file_name_and_reset ( std::string const &  loop_filename)

Referenced by read_loops_options().

void protocols::loops::Loops::set_strict_looprelax_checks ( bool const  check)
core::Size protocols::loops::Loops::size ( ) const

Referenced by protocols::seeded_abinitio::add_dist_constraints(), protocols::abinitio::LoopJumpFoldCst::add_rigidity_jumps(), protocols::loops::addScoresForLoopParts(), protocols::simple_moves::ScoreMover::apply(), protocols::rbsegment_relax::AutoRBMover::apply(), protocols::nonlocal::combine_and_trim(), protocols::abinitio::IterativeBase::gen_resample_fragments(), protocols::topology_broker::FragmentClaimer::generate_claims(), protocols::comparative_modeling::hybridize::ChunkTrialMover::get_alignment_from_chunk_mapping(), grow_all_loops(), protocols::rbsegment_relax::guess_rbsegs_from_pose(), protocols::comparative_modeling::hybridize::HybridizeProtocol::initialize_and_sample_loops(), protocols::loops::loop_rmsd_with_superimpose_core(), loop_size(), protocols::forge::methods::make_star_foldtree(), protocols::loops::native_loop_core_CA_rmsd(), protocols::abinitio::LoopJumpFoldCst::new_kinematics(), protocols::abinitio::DoubleLayerKinematicAbinitio::new_kinematics(), one_random_loop(), operator==(), protocols::seeded_abinitio::SwapSegment::parse_my_tag(), protocols::rbsegment_relax::read_RBSegment_file(), protocols::topology_broker::RigidChunkClaimer::receive_message(), protocols::abinitio::DoubleLayerKinematicAbinitio::select_core_loops(), protocols::abinitio::LoopJumpFoldCst::select_loops(), protocols::topology_broker::RigidChunkClaimer::select_parts(), protocols::rbsegment_relax::select_RBsegments(), protocols::abinitio::KinematicTaskControl::set_extended_torsions_and_idealize_loops(), protocols::seeded_abinitio::SeedFoldTree::set_foldtree(), protocols::star::setup_constraints(), and protocols::topology_broker::CoordConstraintClaimer::superimpose().

bool protocols::loops::Loops::strict_looprelax_checks ( )
void protocols::loops::Loops::switch_movemap ( core::kinematics::MoveMap movemap,
core::id::TorsionType  id,
bool  allow_moves = true 
) const
template<class T >
void protocols::loops::Loops::transfer_to_residue_vector ( utility::vector1< T > &  vector,
val 
)

set each loop-residue in the vector to val. input vector of nres length ( if shorter last residues of loop are ignored )

References begin(), and end().

Referenced by protocols::topology_broker::ConstraintClaimer::add_constraints(), and protocols::topology_broker::RigidChunkClaimer::manipulate_cut_bias().

Loops::iterator protocols::loops::Loops::v_begin ( )
Loops::iterator protocols::loops::Loops::v_end ( )
void protocols::loops::Loops::verify_against ( core::pose::Pose const &  pose) const
void protocols::loops::Loops::write_loops_to_file ( std::string const &  filename,
std::string  token = "LOOP" 
) const
void protocols::loops::Loops::write_loops_to_stream ( std::ostream &  data,
std::string  token 
) const

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  os,
const Loops loops 
) [friend]

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