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core::conformation::symmetry::SymmData Class Reference

#include <SymmData.hh>

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Public Types

typedef numeric::xyzVector
< core::Real > 		Vector
 
typedef numeric::xyzMatrix
< core::Real > 		Matrix
 

Public Member Functions

 SymmData ()
 
 SymmData (core::Size nres, core::Size njump)
 
 SymmData (SymmData const &)
 
SymmDataOP clone () const
 
virtual ~SymmData ()
 
void read_symmetry_info_from_pdb (std::string filename)
 
void read_symmetry_data_from_file (std::string filename)
 
void read_symmetry_data_from_stream (std::istream &infile)
 
void sanity_check ()
 
void show ()
 
std::string const & get_symmetry_name () const
 
std::string const & get_symmetry_type () const
 
core::Size get_subunits () const
 
core::Size get_num_components () const
 
core::Size get_interfaces () const
 
core::Size get_score_subunit () const
 
std::string const & get_anchor_residue () const
 
bool get_recenter () const
 
core::Size get_root () const
 
utility::vector1< Size > const & get_score_multiply_subunit () const
 
utility::vector1< Size > const & get_include_subunit () const
 
utility::vector1< Size > const & get_output_subunit () const
 
std::vector
< numeric::xyzMatrix
< core::Real > > const & 		get_rotation_matrix () const
 
std::vector
< numeric::xyzMatrix
< core::Real > > const & 		get_translation_matrix () const
 
std::map< std::string,
VirtualCoordinate > const & 		get_virtual_coordinates () const
 
core::Size get_num_virtual () const
 
std::map< Size, SymDof > const & get_dofs () const
 
std::map< Size, WtedClones >
const & 		get_jump_clones () const
 
std::map< std::string, Size >
const & 		get_jump_string_to_jump_num () const
 
std::map< std::string, Size >
const & 		get_virtual_id_to_num () const
 
std::map< std::string, Size >
const & 		get_virt_id_to_subunit_num () const
 
std::map< std::string, char >
const & 		get_virt_id_to_subunit_chain () const
 
std::map< std::string,
std::string > const & 		get_virt_id_to_subunit_residue () const
 
std::map< Size, std::string >
const & 		get_subunit_num_to_virt_id () const
 
std::map< Size, std::string >
const & 		get_virtual_num_to_id () const
 
std::map< std::string,
std::pair< std::string,
std::string > > const & 		get_virtual_connects () const
 
SymSlideInfo const & get_slide_info () const
 
core::Real get_cell_a () const
 
core::Real get_cell_b () const
 
core::Real get_cell_c () const
 
core::Real get_cell_alfa () const
 
core::Real get_cell_beta () const
 
core::Real get_cell_gamma () const
 
void set_symmetry_name (std::string symm_name)
 
void set_symmetry_type (std::string symm_type)
 
void set_subunits (core::Size num_subunits)
 
void set_interfaces (core::Size interfaces)
 
void set_anchor_residue (std::string anchor)
 
void set_score_multiply_subunit (utility::vector1< Size > &score_multiply_vector)
 
void set_slide_info (SymSlideInfo slide_info)
 
void set_rotation_matrix (std::vector< numeric::xyzMatrix< core::Real > > rotation_matrices)
 
void set_translation_matrix (std::vector< numeric::xyzMatrix< core::Real > > translation_matrices)
 
void set_symm_transforms (std::vector< std::vector< std::string > > symm_transforms)
 
void set_cell_a (core::Real cell_a)
 
void set_cell_b (core::Real cell_b)
 
void set_cell_c (core::Real cell_c)
 
void set_cell_alfa (core::Real cell_alfa)
 
void set_cell_beta (core::Real cell_beta)
 
void get_cell_gamma (core::Real cell_gamma)
 
utility::vector1< char > const & get_components () const
 
std::map< std::string, char >
const & 		get_subunit_name_to_component () const
 
std::map< std::string,
utility::vector1< char >
> const & 		get_jump_name_to_components () const
 
std::map< std::string,
utility::vector1< Size >
> const & 		get_jump_name_to_subunits () const
 
std::string const & get_parent_jump (std::string const &jname) const
 
std::string const & get_parent_virtual (std::string const &vname) const
 
bool is_ancestor_virtual (std::string const &ancestor, std::string const &child) const
 
std::string const & get_least_common_ancertor_jump (std::string const &jname1, std::string const &jname2) const
 
std::string const & get_least_common_ancertor_virtual (std::string const &vname1, std::string const &vname2) const
 
utility::vector1< char > components_moved_by_jump (std::string const &jname) const
 
utility::vector1< Size > subunits_moved_by_jump (std::string const &jname) const
 

Private Types

typedef utility::vector1
< std::pair< Size, Real > > 		WtedClones
 

Private Member Functions

utility::vector1< std::string > leaves_of_jump (std::string const &jname) const
 

Private Attributes

std::string symmetry_name_
 
std::string symmetry_type_
 
core::Size subunits_
 
core::Size num_components_
 
core::Size interfaces_
 
core::Size score_subunit_
 
std::string anchor_residue_
 
bool recenter_
 
core::Size root_
 
SymSlideInfo slide_info_
 
std::vector< std::string > slide_order_string_
 
std::vector< std::vector
< std::string > > 		symm_transforms_
 
std::vector
< numeric::xyzMatrix
< core::Real > > 		rotation_matrices_
 
std::vector
< numeric::xyzMatrix
< core::Real > > 		translation_matrices_
 
std::map< std::string,
VirtualCoordinate > 		virtual_coordinates_
 
std::map< std::string,
std::pair< std::string,
std::string > > 		jump_string_to_virtual_pair_
 
std::map< std::string, Size > jump_string_to_jump_num_
 
std::map< std::string, Size > virt_id_to_virt_num_
 
std::map< std::string, Size > virt_id_to_subunit_num_
 
std::map< std::string, char > virt_id_to_subunit_chain_
 
std::map< std::string,
std::string > 		virt_id_to_subunit_residue_
 
std::map< Size, std::string > virt_num_to_virt_id_
 
std::map< Size, std::string > subunit_num_to_virt_id_
 
std::map< Size, WtedClones > jump_clones_
 
std::map< Size, SymDof > dofs_
 
std::vector< Size > allow_virtual_
 
utility::vector1< Size > score_multiply_subunit_
 
utility::vector1< Size > include_subunit_
 
utility::vector1< Size > output_subunit_
 
core::Real cell_a_
 
core::Real cell_b_
 
core::Real cell_c_
 
core::Real cell_alfa_
 
core::Real cell_beta_
 
core::Real cell_gamma_
 
utility::vector1< char > components_
 
std::map< std::string, char > name2component_
 
std::map< std::string,
utility::vector1< char > > 		jname2components_
 
std::map< std::string,
utility::vector1< Size > > 		jname2subunits_
 

Friends

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

Detailed Description

Definition at line 44 of file SymmData.hh.

Member Typedef Documentation

typedef numeric::xyzMatrix< core::Real > core::conformation::symmetry::SymmData::Matrix

Definition at line 117 of file SymmData.hh.

typedef numeric::xyzVector< core::Real > core::conformation::symmetry::SymmData::Vector

Definition at line 116 of file SymmData.hh.

typedef utility::vector1< std::pair<Size,Real> > core::conformation::symmetry::SymmData::WtedClones
private

Definition at line 48 of file SymmData.hh.

Constructor & Destructor Documentation

core::conformation::symmetry::SymmData::SymmData ( )

Definition at line 75 of file SymmData.cc.

Referenced by clone().

core::conformation::symmetry::SymmData::SymmData ( core::Size  nres,
core::Size  njump 
)

Definition at line 93 of file SymmData.cc.

core::conformation::symmetry::SymmData::SymmData ( SymmData const &  src)

Definition at line 114 of file SymmData.cc.

core::conformation::symmetry::SymmData::~SymmData ( )
virtual

Definition at line 504 of file SymmData.cc.

Member Function Documentation

SymmDataOP core::conformation::symmetry::SymmData::clone ( ) const

Definition at line 161 of file SymmData.cc.

References SymmData().

vector1< char > core::conformation::symmetry::SymmData::components_moved_by_jump ( std::string const &  jname) const

Definition at line 1623 of file SymmData.cc.

References leaves_of_jump(), and virt_id_to_subunit_chain_.

Referenced by read_symmetry_data_from_stream(), and core::conformation::symmetry::setup_symmetric_conformation().

string const & core::conformation::symmetry::SymmData::get_anchor_residue ( ) const

Definition at line 217 of file SymmData.cc.

References anchor_residue_.

Referenced by read_symmetry_data_from_stream(), core::conformation::symmetry::recenter(), protocols::fibril::reorient_extended_fibril(), and core::conformation::symmetry::set_fold_tree_from_symm_data().

core::Real core::conformation::symmetry::SymmData::get_cell_a ( ) const

Definition at line 343 of file SymmData.cc.

References cell_a_.

core::Real core::conformation::symmetry::SymmData::get_cell_alfa ( ) const

Definition at line 361 of file SymmData.cc.

References cell_alfa_.

core::Real core::conformation::symmetry::SymmData::get_cell_b ( ) const

Definition at line 349 of file SymmData.cc.

References cell_b_.

core::Real core::conformation::symmetry::SymmData::get_cell_beta ( ) const

Definition at line 367 of file SymmData.cc.

References cell_beta_.

core::Real core::conformation::symmetry::SymmData::get_cell_c ( ) const

Definition at line 355 of file SymmData.cc.

References cell_c_.

core::Real core::conformation::symmetry::SymmData::get_cell_gamma ( ) const

Definition at line 373 of file SymmData.cc.

References cell_gamma_.

void core::conformation::symmetry::SymmData::get_cell_gamma ( core::Real  cell_gamma)

Definition at line 496 of file SymmData.cc.

References cell_gamma_.

utility::vector1< char > const & core::conformation::symmetry::SymmData::get_components ( ) const

Definition at line 1525 of file SymmData.cc.

References components_.

Referenced by core::conformation::symmetry::setup_symmetric_conformation().

map< Size, SymDof > const & core::conformation::symmetry::SymmData::get_dofs ( ) const

Definition at line 277 of file SymmData.cc.

References dofs_.

Referenced by core::conformation::symmetry::SymmetryInfo::SymmetryInfo().

vector1< Size > const & core::conformation::symmetry::SymmData::get_include_subunit ( ) const

Definition at line 241 of file SymmData.cc.

References include_subunit_.

core::Size core::conformation::symmetry::SymmData::get_interfaces ( ) const

Definition at line 205 of file SymmData.cc.

References interfaces_.

Referenced by core::conformation::symmetry::SymmetryInfo::SymmetryInfo().

map< Size, WtedClones > const & core::conformation::symmetry::SymmData::get_jump_clones ( ) const

Definition at line 283 of file SymmData.cc.

References jump_clones_.

Referenced by core::conformation::symmetry::SymmetryInfo::SymmetryInfo().

std::map< std::string, utility::vector1< char > > const & core::conformation::symmetry::SymmData::get_jump_name_to_components ( ) const

Definition at line 1534 of file SymmData.cc.

References jname2components_.

Referenced by core::conformation::symmetry::setup_symmetric_conformation().

std::map< std::string, utility::vector1< Size > > const & core::conformation::symmetry::SymmData::get_jump_name_to_subunits ( ) const

Definition at line 1539 of file SymmData.cc.

References jname2subunits_.

Referenced by core::conformation::symmetry::setup_symmetric_conformation().

map< string, Size > const & core::conformation::symmetry::SymmData::get_jump_string_to_jump_num ( ) const

Definition at line 289 of file SymmData.cc.

References jump_string_to_jump_num_.

Referenced by core::conformation::symmetry::SymmetryInfo::SymmetryInfo().

std::string const & core::conformation::symmetry::SymmData::get_least_common_ancertor_jump ( std::string const &  jname1,
std::string const &  jname2 
) const

Definition at line 1578 of file SymmData.cc.

References get_parent_jump(), and core::conformation::symmetry::NOPARENT.

std::string const & core::conformation::symmetry::SymmData::get_least_common_ancertor_virtual ( std::string const &  vname1,
std::string const &  vname2 
) const

Definition at line 1594 of file SymmData.cc.

References get_parent_virtual(), and core::conformation::symmetry::NOPARENT.

core::Size core::conformation::symmetry::SymmData::get_num_components ( ) const

Definition at line 199 of file SymmData.cc.

References num_components_.

Referenced by core::conformation::symmetry::set_fold_tree_from_symm_data(), core::conformation::symmetry::setup_symmetric_conformation(), and core::conformation::symmetry::SymmetryInfo::SymmetryInfo().

core::Size core::conformation::symmetry::SymmData::get_num_virtual ( ) const

Definition at line 271 of file SymmData.cc.

References virtual_coordinates_.

Referenced by core::conformation::symmetry::SymmetryInfo::SymmetryInfo().

vector1< Size > const & core::conformation::symmetry::SymmData::get_output_subunit ( ) const

Definition at line 247 of file SymmData.cc.

References output_subunit_.

std::string const & core::conformation::symmetry::SymmData::get_parent_jump ( std::string const &  jname) const

Definition at line 1544 of file SymmData.cc.

References jump_string_to_virtual_pair_, and core::conformation::symmetry::NOPARENT.

Referenced by get_least_common_ancertor_jump().

std::string const & core::conformation::symmetry::SymmData::get_parent_virtual ( std::string const &  vname) const

Definition at line 1556 of file SymmData.cc.

References jump_string_to_virtual_pair_, and core::conformation::symmetry::NOPARENT.

Referenced by get_least_common_ancertor_virtual(), and is_ancestor_virtual().

bool core::conformation::symmetry::SymmData::get_recenter ( ) const

Definition at line 223 of file SymmData.cc.

References recenter_.

Referenced by core::conformation::symmetry::setup_symmetric_conformation().

core::Size core::conformation::symmetry::SymmData::get_root ( ) const

Definition at line 229 of file SymmData.cc.

References root_.

Referenced by core::conformation::symmetry::setup_symmetric_conformation().

vector< numeric::xyzMatrix< core::Real > > const & core::conformation::symmetry::SymmData::get_rotation_matrix ( ) const

Definition at line 253 of file SymmData.cc.

References rotation_matrices_.

vector1< Size > const & core::conformation::symmetry::SymmData::get_score_multiply_subunit ( ) const

Definition at line 235 of file SymmData.cc.

References score_multiply_subunit_.

Referenced by core::conformation::symmetry::SymmetryInfo::SymmetryInfo().

core::Size core::conformation::symmetry::SymmData::get_score_subunit ( ) const

Definition at line 211 of file SymmData.cc.

References score_subunit_.

Referenced by core::conformation::symmetry::SymmetryInfo::SymmetryInfo().

SymSlideInfo const & core::conformation::symmetry::SymmData::get_slide_info ( ) const

Definition at line 337 of file SymmData.cc.

References slide_info_.

Referenced by core::conformation::symmetry::SymmetryInfo::SymmetryInfo().

std::map< std::string, char > const & core::conformation::symmetry::SymmData::get_subunit_name_to_component ( ) const

Definition at line 1530 of file SymmData.cc.

References name2component_.

Referenced by core::conformation::symmetry::setup_symmetric_conformation().

map< Size, string > const & core::conformation::symmetry::SymmData::get_subunit_num_to_virt_id ( ) const

Definition at line 319 of file SymmData.cc.

References subunit_num_to_virt_id_.

core::Size core::conformation::symmetry::SymmData::get_subunits ( ) const

Definition at line 193 of file SymmData.cc.

References subunits_.

Referenced by core::conformation::symmetry::set_fold_tree_from_symm_data(), core::conformation::symmetry::setup_symmetric_conformation(), and core::conformation::symmetry::SymmetryInfo::SymmetryInfo().

string const & core::conformation::symmetry::SymmData::get_symmetry_name ( ) const

Definition at line 181 of file SymmData.cc.

References symmetry_name_.

string const & core::conformation::symmetry::SymmData::get_symmetry_type ( ) const

Definition at line 187 of file SymmData.cc.

References symmetry_type_.

vector< numeric::xyzMatrix< core::Real > > const & core::conformation::symmetry::SymmData::get_translation_matrix ( ) const

Definition at line 259 of file SymmData.cc.

References translation_matrices_.

map< string, char > const & core::conformation::symmetry::SymmData::get_virt_id_to_subunit_chain ( ) const

Definition at line 307 of file SymmData.cc.

References virt_id_to_subunit_chain_.

Referenced by core::conformation::symmetry::set_fold_tree_from_symm_data().

map< string, Size > const & core::conformation::symmetry::SymmData::get_virt_id_to_subunit_num ( ) const

Definition at line 301 of file SymmData.cc.

References virt_id_to_subunit_num_.

Referenced by core::conformation::symmetry::set_fold_tree_from_symm_data().

map< string, string > const & core::conformation::symmetry::SymmData::get_virt_id_to_subunit_residue ( ) const

Definition at line 313 of file SymmData.cc.

References virt_id_to_subunit_residue_.

Referenced by core::conformation::symmetry::set_fold_tree_from_symm_data().

map< string, pair< string, string > > const & core::conformation::symmetry::SymmData::get_virtual_connects ( ) const

Definition at line 331 of file SymmData.cc.

References jump_string_to_virtual_pair_.

Referenced by core::conformation::symmetry::set_fold_tree_from_symm_data(), and core::conformation::symmetry::setup_symmetric_conformation().

map< string, VirtualCoordinate > const & core::conformation::symmetry::SymmData::get_virtual_coordinates ( ) const

Definition at line 265 of file SymmData.cc.

References virtual_coordinates_.

Referenced by core::conformation::symmetry::set_fold_tree_from_symm_data(), and core::conformation::symmetry::setup_symmetric_conformation().

map< string, Size > const & core::conformation::symmetry::SymmData::get_virtual_id_to_num ( ) const

Definition at line 295 of file SymmData.cc.

References virt_id_to_virt_num_.

Referenced by core::conformation::symmetry::set_fold_tree_from_symm_data().

map< Size, string > const & core::conformation::symmetry::SymmData::get_virtual_num_to_id ( ) const

Definition at line 325 of file SymmData.cc.

References virt_num_to_virt_id_.

Referenced by core::conformation::symmetry::set_fold_tree_from_symm_data(), core::conformation::symmetry::setup_symmetric_conformation(), and core::conformation::symmetry::show_foldtree().

bool core::conformation::symmetry::SymmData::is_ancestor_virtual ( std::string const &  ancestor,
std::string const &  child 
) const

Definition at line 1565 of file SymmData.cc.

References get_parent_virtual(), and core::conformation::symmetry::NOPARENT.

Referenced by leaves_of_jump().

vector1< string > core::conformation::symmetry::SymmData::leaves_of_jump ( std::string const &  jname) const
private

Definition at line 1610 of file SymmData.cc.

References is_ancestor_virtual(), jump_string_to_virtual_pair_, and virt_id_to_subunit_num_.

Referenced by components_moved_by_jump(), and subunits_moved_by_jump().

void core::conformation::symmetry::SymmData::read_symmetry_data_from_file ( std::string  filename)

Definition at line 605 of file SymmData.cc.

References read_symmetry_data_from_stream().

Referenced by protocols::simple_moves::symmetry::DetectSymmetry::apply().

void core::conformation::symmetry::SymmData::read_symmetry_data_from_stream ( std::istream &  infile)

Definition at line 619 of file SymmData.cc.

References core::conformation::symmetry::VirtualCoordinate::add_coordinate_from_string(), core::conformation::symmetry::SymDof::add_dof_from_string(), anchor_residue_, core::conformation::symmetry::CEN_DOCK_SCORE, components_, components_moved_by_jump(), core::conformation::symmetry::CONTACTS, dofs_, core::conformation::symmetry::FA_REP_SCORE, get_anchor_residue(), core::conformation::symmetry::VirtualCoordinate::get_origin(), core::conformation::symmetry::VirtualCoordinate::get_x(), core::conformation::symmetry::VirtualCoordinate::get_y(), include_subunit_, interfaces_, jname2components_, jname2subunits_, jump_clones_, jump_string_to_jump_num_, jump_string_to_virtual_pair_, protocols::forge::build::SegmentInsertConnectionScheme::N, name2component_, num_components_, core::conformation::symmetry::ORDERED_SEQUENTIAL, output_subunit_, core::conformation::symmetry::RANDOM, recenter_, root_, sanity_check(), score_subunit_, core::conformation::symmetry::SEQUENTIAL, set_score_multiply_subunit(), core::conformation::symmetry::SymSlideInfo::set_slide_order(), core::conformation::symmetry::SymSlideInfo::set_slide_type(), core::conformation::symmetry::SymSlideInfo::set_SlideCriteriaType(), core::conformation::symmetry::SymSlideInfo::set_SlideCriteriaVal(), show(), slide_info_, slide_order_string_, core::io::pdb::split(), protocols::kinmatch::str(), subunit_num_to_virt_id_, subunits_, subunits_moved_by_jump(), symmetry_name_, core::conformation::symmetry::TR(), trans(), virt_id_to_subunit_chain_, virt_id_to_subunit_num_, virt_id_to_subunit_residue_, virt_id_to_virt_num_, virt_num_to_virt_id_, and virtual_coordinates_.

Referenced by read_symmetry_data_from_file().

void core::conformation::symmetry::SymmData::read_symmetry_info_from_pdb ( std::string  filename)

Definition at line 509 of file SymmData.cc.

References cell_a_, cell_alfa_, cell_b_, cell_beta_, cell_c_, cell_gamma_, and core::io::pdb::split().

void core::conformation::symmetry::SymmData::sanity_check ( )

Definition at line 1404 of file SymmData.cc.

References interfaces_, jump_string_to_virtual_pair_, num_components_, score_multiply_subunit_, subunits_, virt_id_to_subunit_chain_, and virtual_coordinates_.

Referenced by read_symmetry_data_from_stream().

void core::conformation::symmetry::SymmData::set_anchor_residue ( std::string  anchor)

Definition at line 422 of file SymmData.cc.

References anchor_residue_.

void core::conformation::symmetry::SymmData::set_cell_a ( core::Real  cell_a)

Definition at line 461 of file SymmData.cc.

References cell_a_.

void core::conformation::symmetry::SymmData::set_cell_alfa ( core::Real  cell_alfa)

Definition at line 482 of file SymmData.cc.

References cell_alfa_.

void core::conformation::symmetry::SymmData::set_cell_b ( core::Real  cell_b)

Definition at line 468 of file SymmData.cc.

References cell_b_.

void core::conformation::symmetry::SymmData::set_cell_beta ( core::Real  cell_beta)

Definition at line 489 of file SymmData.cc.

References cell_beta_.

void core::conformation::symmetry::SymmData::set_cell_c ( core::Real  cell_c)

Definition at line 475 of file SymmData.cc.

References cell_c_.

void core::conformation::symmetry::SymmData::set_interfaces ( core::Size  interfaces)

Definition at line 415 of file SymmData.cc.

References interfaces_.

void core::conformation::symmetry::SymmData::set_rotation_matrix ( std::vector< numeric::xyzMatrix< core::Real > >  rotation_matrices)

Definition at line 440 of file SymmData.cc.

References rotation_matrices_.

void core::conformation::symmetry::SymmData::set_score_multiply_subunit ( utility::vector1< Size > &  score_multiply_vector)

Definition at line 428 of file SymmData.cc.

References score_multiply_subunit_.

Referenced by read_symmetry_data_from_stream().

void core::conformation::symmetry::SymmData::set_slide_info ( SymSlideInfo  slide_info)

Definition at line 434 of file SymmData.cc.

References slide_info_.

void core::conformation::symmetry::SymmData::set_subunits ( core::Size  num_subunits)

Definition at line 408 of file SymmData.cc.

References subunits_.

void core::conformation::symmetry::SymmData::set_symm_transforms ( std::vector< std::vector< std::string > >  symm_transforms)

Definition at line 454 of file SymmData.cc.

References symm_transforms_.

void core::conformation::symmetry::SymmData::set_symmetry_name ( std::string  symm_name)

Definition at line 394 of file SymmData.cc.

References symmetry_name_.

void core::conformation::symmetry::SymmData::set_symmetry_type ( std::string  symm_type)

Definition at line 401 of file SymmData.cc.

References symmetry_type_.

void core::conformation::symmetry::SymmData::set_translation_matrix ( std::vector< numeric::xyzMatrix< core::Real > >  translation_matrices)

Definition at line 447 of file SymmData.cc.

References translation_matrices_.

void core::conformation::symmetry::SymmData::show ( )

Definition at line 1440 of file SymmData.cc.

References core::conformation::symmetry::SymDof::allow_dof(), anchor_residue_, core::conformation::symmetry::CEN_DOCK_SCORE, core::conformation::symmetry::CONTACTS, dofs_, core::conformation::symmetry::FA_REP_SCORE, core::conformation::symmetry::VirtualCoordinate::get_origin(), core::conformation::symmetry::SymSlideInfo::get_slide_type(), core::conformation::symmetry::SymSlideInfo::get_SlideCriteriaType(), core::conformation::symmetry::SymSlideInfo::get_SlideCriteriaVal(), core::conformation::symmetry::VirtualCoordinate::get_x(), core::conformation::symmetry::VirtualCoordinate::get_y(), include_subunit_, interfaces_, core::conformation::symmetry::SymDof::jump_direction(), jump_string_to_virtual_pair_, core::conformation::symmetry::ORDERED_SEQUENTIAL, output_subunit_, core::conformation::symmetry::RANDOM, core::conformation::symmetry::SymDof::range1_lower(), core::conformation::symmetry::SymDof::range1_upper(), core::conformation::symmetry::SymDof::range2_lower(), core::conformation::symmetry::SymDof::range2_upper(), score_subunit_, core::conformation::symmetry::SEQUENTIAL, slide_info_, slide_order_string_, subunits_, symmetry_name_, core::conformation::symmetry::TR(), virt_num_to_virt_id_, and virtual_coordinates_.

Referenced by read_symmetry_data_from_stream().

vector1< Size > core::conformation::symmetry::SymmData::subunits_moved_by_jump ( std::string const &  jname) const

Definition at line 1634 of file SymmData.cc.

References leaves_of_jump(), and virt_id_to_subunit_num_.

Referenced by read_symmetry_data_from_stream(), and core::conformation::symmetry::setup_symmetric_conformation().

Friends And Related Function Documentation

bool operator!= ( SymmData const &  a,
SymmData const &  b 
)
friend
bool operator== ( SymmData const &  a,
SymmData const &  b 
)
friend

Definition at line 1645 of file SymmData.cc.

Member Data Documentation

std::vector< Size > core::conformation::symmetry::SymmData::allow_virtual_
private

Definition at line 96 of file SymmData.hh.

Referenced by core::conformation::symmetry::operator==().

std::string core::conformation::symmetry::SymmData::anchor_residue_
private

Definition at line 77 of file SymmData.hh.

Referenced by get_anchor_residue(), core::conformation::symmetry::operator==(), read_symmetry_data_from_stream(), set_anchor_residue(), and show().

core::Real core::conformation::symmetry::SymmData::cell_a_
private

Definition at line 101 of file SymmData.hh.

Referenced by get_cell_a(), core::conformation::symmetry::operator==(), read_symmetry_info_from_pdb(), and set_cell_a().

core::Real core::conformation::symmetry::SymmData::cell_alfa_
private

Definition at line 104 of file SymmData.hh.

Referenced by get_cell_alfa(), core::conformation::symmetry::operator==(), read_symmetry_info_from_pdb(), and set_cell_alfa().

core::Real core::conformation::symmetry::SymmData::cell_b_
private

Definition at line 102 of file SymmData.hh.

Referenced by get_cell_b(), core::conformation::symmetry::operator==(), read_symmetry_info_from_pdb(), and set_cell_b().

core::Real core::conformation::symmetry::SymmData::cell_beta_
private

Definition at line 105 of file SymmData.hh.

Referenced by get_cell_beta(), core::conformation::symmetry::operator==(), read_symmetry_info_from_pdb(), and set_cell_beta().

core::Real core::conformation::symmetry::SymmData::cell_c_
private

Definition at line 103 of file SymmData.hh.

Referenced by get_cell_c(), core::conformation::symmetry::operator==(), read_symmetry_info_from_pdb(), and set_cell_c().

core::Real core::conformation::symmetry::SymmData::cell_gamma_
private

Definition at line 106 of file SymmData.hh.

Referenced by get_cell_gamma(), core::conformation::symmetry::operator==(), and read_symmetry_info_from_pdb().

utility::vector1<char> core::conformation::symmetry::SymmData::components_
private

Definition at line 108 of file SymmData.hh.

Referenced by get_components(), core::conformation::symmetry::operator==(), and read_symmetry_data_from_stream().

std::map< Size, SymDof > core::conformation::symmetry::SymmData::dofs_
private

Definition at line 95 of file SymmData.hh.

Referenced by get_dofs(), core::conformation::symmetry::operator==(), read_symmetry_data_from_stream(), and show().

utility::vector1< Size > core::conformation::symmetry::SymmData::include_subunit_
private

Definition at line 98 of file SymmData.hh.

Referenced by get_include_subunit(), core::conformation::symmetry::operator==(), read_symmetry_data_from_stream(), and show().

core::Size core::conformation::symmetry::SymmData::interfaces_
private

Definition at line 75 of file SymmData.hh.

Referenced by get_interfaces(), core::conformation::symmetry::operator==(), read_symmetry_data_from_stream(), sanity_check(), set_interfaces(), and show().

std::map<std::string,utility::vector1<char> > core::conformation::symmetry::SymmData::jname2components_
private

Definition at line 110 of file SymmData.hh.

Referenced by get_jump_name_to_components(), core::conformation::symmetry::operator==(), and read_symmetry_data_from_stream().

std::map<std::string,utility::vector1<Size> > core::conformation::symmetry::SymmData::jname2subunits_
private

Definition at line 111 of file SymmData.hh.

Referenced by get_jump_name_to_subunits(), core::conformation::symmetry::operator==(), and read_symmetry_data_from_stream().

std::map< Size, WtedClones > core::conformation::symmetry::SymmData::jump_clones_
private

Definition at line 94 of file SymmData.hh.

Referenced by get_jump_clones(), core::conformation::symmetry::operator==(), and read_symmetry_data_from_stream().

std::map< std::string, Size > core::conformation::symmetry::SymmData::jump_string_to_jump_num_
private

Definition at line 87 of file SymmData.hh.

Referenced by get_jump_string_to_jump_num(), core::conformation::symmetry::operator==(), and read_symmetry_data_from_stream().

std::map< std::string, std::pair< std::string, std::string > > core::conformation::symmetry::SymmData::jump_string_to_virtual_pair_
private

Definition at line 86 of file SymmData.hh.

Referenced by get_parent_jump(), get_parent_virtual(), get_virtual_connects(), leaves_of_jump(), core::conformation::symmetry::operator==(), read_symmetry_data_from_stream(), sanity_check(), and show().

std::map<std::string,char> core::conformation::symmetry::SymmData::name2component_
private

Definition at line 109 of file SymmData.hh.

Referenced by get_subunit_name_to_component(), core::conformation::symmetry::operator==(), and read_symmetry_data_from_stream().

core::Size core::conformation::symmetry::SymmData::num_components_
private

Definition at line 74 of file SymmData.hh.

Referenced by get_num_components(), core::conformation::symmetry::operator==(), read_symmetry_data_from_stream(), and sanity_check().

utility::vector1< Size > core::conformation::symmetry::SymmData::output_subunit_
private

Definition at line 99 of file SymmData.hh.

Referenced by get_output_subunit(), core::conformation::symmetry::operator==(), read_symmetry_data_from_stream(), and show().

bool core::conformation::symmetry::SymmData::recenter_
private

Definition at line 78 of file SymmData.hh.

Referenced by get_recenter(), core::conformation::symmetry::operator==(), and read_symmetry_data_from_stream().

core::Size core::conformation::symmetry::SymmData::root_
private

Definition at line 79 of file SymmData.hh.

Referenced by get_root(), core::conformation::symmetry::operator==(), and read_symmetry_data_from_stream().

std::vector< numeric::xyzMatrix< core::Real> > core::conformation::symmetry::SymmData::rotation_matrices_
private

Definition at line 83 of file SymmData.hh.

Referenced by get_rotation_matrix(), core::conformation::symmetry::operator==(), and set_rotation_matrix().

utility::vector1< Size > core::conformation::symmetry::SymmData::score_multiply_subunit_
private

Definition at line 97 of file SymmData.hh.

Referenced by get_score_multiply_subunit(), core::conformation::symmetry::operator==(), sanity_check(), and set_score_multiply_subunit().

core::Size core::conformation::symmetry::SymmData::score_subunit_
private

Definition at line 76 of file SymmData.hh.

Referenced by get_score_subunit(), core::conformation::symmetry::operator==(), read_symmetry_data_from_stream(), and show().

SymSlideInfo core::conformation::symmetry::SymmData::slide_info_
private

Definition at line 80 of file SymmData.hh.

Referenced by get_slide_info(), core::conformation::symmetry::operator==(), read_symmetry_data_from_stream(), set_slide_info(), and show().

std::vector< std::string > core::conformation::symmetry::SymmData::slide_order_string_
private

Definition at line 81 of file SymmData.hh.

Referenced by core::conformation::symmetry::operator==(), read_symmetry_data_from_stream(), and show().

std::map< Size, std::string > core::conformation::symmetry::SymmData::subunit_num_to_virt_id_
private

Definition at line 93 of file SymmData.hh.

Referenced by get_subunit_num_to_virt_id(), core::conformation::symmetry::operator==(), and read_symmetry_data_from_stream().

core::Size core::conformation::symmetry::SymmData::subunits_
private

Definition at line 73 of file SymmData.hh.

Referenced by get_subunits(), core::conformation::symmetry::operator==(), read_symmetry_data_from_stream(), sanity_check(), set_subunits(), and show().

std::vector< std::vector< std::string > > core::conformation::symmetry::SymmData::symm_transforms_
private

Definition at line 82 of file SymmData.hh.

Referenced by core::conformation::symmetry::operator==(), and set_symm_transforms().

std::string core::conformation::symmetry::SymmData::symmetry_name_
private

Definition at line 71 of file SymmData.hh.

Referenced by get_symmetry_name(), core::conformation::symmetry::operator==(), read_symmetry_data_from_stream(), set_symmetry_name(), and show().

std::string core::conformation::symmetry::SymmData::symmetry_type_
private

Definition at line 72 of file SymmData.hh.

Referenced by get_symmetry_type(), core::conformation::symmetry::operator==(), and set_symmetry_type().

std::vector< numeric::xyzMatrix< core::Real> > core::conformation::symmetry::SymmData::translation_matrices_
private

Definition at line 84 of file SymmData.hh.

Referenced by get_translation_matrix(), core::conformation::symmetry::operator==(), and set_translation_matrix().

std::map< std::string, char > core::conformation::symmetry::SymmData::virt_id_to_subunit_chain_
private

Definition at line 90 of file SymmData.hh.

Referenced by components_moved_by_jump(), get_virt_id_to_subunit_chain(), core::conformation::symmetry::operator==(), read_symmetry_data_from_stream(), and sanity_check().

std::map< std::string, Size > core::conformation::symmetry::SymmData::virt_id_to_subunit_num_
private

Definition at line 89 of file SymmData.hh.

Referenced by get_virt_id_to_subunit_num(), leaves_of_jump(), core::conformation::symmetry::operator==(), read_symmetry_data_from_stream(), and subunits_moved_by_jump().

std::map< std::string, std::string > core::conformation::symmetry::SymmData::virt_id_to_subunit_residue_
private

Definition at line 91 of file SymmData.hh.

Referenced by get_virt_id_to_subunit_residue(), core::conformation::symmetry::operator==(), and read_symmetry_data_from_stream().

std::map< std::string, Size > core::conformation::symmetry::SymmData::virt_id_to_virt_num_
private

Definition at line 88 of file SymmData.hh.

Referenced by get_virtual_id_to_num(), core::conformation::symmetry::operator==(), and read_symmetry_data_from_stream().

std::map< Size, std::string > core::conformation::symmetry::SymmData::virt_num_to_virt_id_
private

Definition at line 92 of file SymmData.hh.

Referenced by get_virtual_num_to_id(), core::conformation::symmetry::operator==(), read_symmetry_data_from_stream(), and show().

std::map< std::string, VirtualCoordinate > core::conformation::symmetry::SymmData::virtual_coordinates_
private

Definition at line 85 of file SymmData.hh.

Referenced by get_num_virtual(), get_virtual_coordinates(), core::conformation::symmetry::operator==(), read_symmetry_data_from_stream(), sanity_check(), and show().

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