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

#include <SymmData.hh>

Inheritance diagram for core::conformation::symmetry::SymmData:
Inheritance graph
[legend]

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
 
 ~SymmData () override
 
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
 
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< Real > &score_multiply_vector)
 
void set_slide_info (SymSlideInfo const &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)
 
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< Sizesubunits_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, core::Sizejump_string_to_jump_num_
 
std::map< std::string, core::Sizevirt_id_to_virt_num_
 
std::map< std::string, core::Sizevirt_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< core::Size, std::string > virt_num_to_virt_id_
 
std::map< core::Size, std::string > subunit_num_to_virt_id_
 
std::map< core::Size, WtedClonesjump_clones_
 
std::map< core::Size, SymDofdofs_
 
std::vector< core::Sizeallow_virtual_
 
utility::vector1< core::Sizescore_multiply_subunit_
 
utility::vector1< core::Sizeinclude_subunit_
 
utility::vector1< core::Sizeoutput_subunit_
 
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)
 

Member Typedef Documentation

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

Constructor & Destructor Documentation

core::conformation::symmetry::SymmData::SymmData ( )
core::conformation::symmetry::SymmData::SymmData ( core::Size  nres,
core::Size  njump 
)
core::conformation::symmetry::SymmData::SymmData ( SymmData const &  src)
core::conformation::symmetry::SymmData::~SymmData ( )
overridedefault

Member Function Documentation

SymmDataOP core::conformation::symmetry::SymmData::clone ( ) const
vector1< char > core::conformation::symmetry::SymmData::components_moved_by_jump ( std::string const &  jname) const
string const & core::conformation::symmetry::SymmData::get_anchor_residue ( ) const
utility::vector1< char > const & core::conformation::symmetry::SymmData::get_components ( ) const
map< Size, SymDof > const & core::conformation::symmetry::SymmData::get_dofs ( ) const
vector1< Size > const & core::conformation::symmetry::SymmData::get_include_subunit ( ) const

References include_subunit_.

core::Size core::conformation::symmetry::SymmData::get_interfaces ( ) const
map< Size, WtedClones > const & core::conformation::symmetry::SymmData::get_jump_clones ( ) const
std::map< std::string, utility::vector1< char > > const & core::conformation::symmetry::SymmData::get_jump_name_to_components ( ) const
std::map< std::string, utility::vector1< Size > > const & core::conformation::symmetry::SymmData::get_jump_name_to_subunits ( ) const
map< string, Size > const & core::conformation::symmetry::SymmData::get_jump_string_to_jump_num ( ) const
std::string const & core::conformation::symmetry::SymmData::get_least_common_ancertor_jump ( std::string const &  jname1,
std::string const &  jname2 
) const
std::string const & core::conformation::symmetry::SymmData::get_least_common_ancertor_virtual ( std::string const &  vname1,
std::string const &  vname2 
) const
core::Size core::conformation::symmetry::SymmData::get_num_components ( ) const
core::Size core::conformation::symmetry::SymmData::get_num_virtual ( ) const
vector1< Size > const & core::conformation::symmetry::SymmData::get_output_subunit ( ) const

References output_subunit_.

std::string const & core::conformation::symmetry::SymmData::get_parent_jump ( std::string const &  jname) const
std::string const & core::conformation::symmetry::SymmData::get_parent_virtual ( std::string const &  vname) const
bool core::conformation::symmetry::SymmData::get_recenter ( ) const
core::Size core::conformation::symmetry::SymmData::get_root ( ) const
vector< numeric::xyzMatrix< core::Real > > const & core::conformation::symmetry::SymmData::get_rotation_matrix ( ) const

References rotation_matrices_.

vector1< Size > const & core::conformation::symmetry::SymmData::get_score_multiply_subunit ( ) const
core::Size core::conformation::symmetry::SymmData::get_score_subunit ( ) const
SymSlideInfo const & core::conformation::symmetry::SymmData::get_slide_info ( ) const
std::map< std::string, char > const & core::conformation::symmetry::SymmData::get_subunit_name_to_component ( ) const
map< Size, string > const & core::conformation::symmetry::SymmData::get_subunit_num_to_virt_id ( ) const
core::Size core::conformation::symmetry::SymmData::get_subunits ( ) const
string const & core::conformation::symmetry::SymmData::get_symmetry_name ( ) const

References symmetry_name_.

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

References symmetry_type_.

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

References translation_matrices_.

map< string, char > const & core::conformation::symmetry::SymmData::get_virt_id_to_subunit_chain ( ) const
map< string, Size > const & core::conformation::symmetry::SymmData::get_virt_id_to_subunit_num ( ) const
map< string, string > const & core::conformation::symmetry::SymmData::get_virt_id_to_subunit_residue ( ) const
map< string, pair< string, string > > const & core::conformation::symmetry::SymmData::get_virtual_connects ( ) const
map< string, VirtualCoordinate > const & core::conformation::symmetry::SymmData::get_virtual_coordinates ( ) const
map< string, Size > const & core::conformation::symmetry::SymmData::get_virtual_id_to_num ( ) const
map< Size, string > const & core::conformation::symmetry::SymmData::get_virtual_num_to_id ( ) const
bool core::conformation::symmetry::SymmData::is_ancestor_virtual ( std::string const &  ancestor,
std::string const &  child 
) const
vector1< string > core::conformation::symmetry::SymmData::leaves_of_jump ( std::string const &  jname) const
private
void core::conformation::symmetry::SymmData::read_symmetry_data_from_file ( std::string  filename)
void core::conformation::symmetry::SymmData::read_symmetry_data_from_stream ( std::istream &  infile)

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_mirror_z(), 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_, core::chemical::element::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, core::conformation::symmetry::VirtualCoordinate::set_mirror_z(), 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_, protocols::sparta::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::sanity_check ( )
void core::conformation::symmetry::SymmData::set_anchor_residue ( std::string  anchor)

References anchor_residue_.

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

References interfaces_.

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

References rotation_matrices_.

void core::conformation::symmetry::SymmData::set_score_multiply_subunit ( utility::vector1< Real > &  score_multiply_vector)
void core::conformation::symmetry::SymmData::set_slide_info ( SymSlideInfo const &  slide_info)

References slide_info_.

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

References subunits_.

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

References symm_transforms_.

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

References symmetry_name_.

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

References symmetry_type_.

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

References translation_matrices_.

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

Friends And Related Function Documentation

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

Member Data Documentation

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

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