Rosetta 3.4
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core::conformation::symmetry::SymmetryInfo Class Reference

#include <SymmetryInfo.hh>

Inheritance diagram for core::conformation::symmetry::SymmetryInfo:
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Collaboration diagram for core::conformation::symmetry::SymmetryInfo:
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List of all members.

Public Types

typedef utility::vector1< SizeClones
typedef utility::vector1
< std::pair< Size, Real > > 
WtedClones
typedef id::DOF_ID DOF_ID
typedef id::TorsionID TorsionID
typedef id::AtomID AtomID
typedef utility::vector1< DOF_IDDOF_IDs
 convenience: these could go somewhere else
typedef utility::vector1
< TorsionID
TorsionIDs
typedef utility::vector1< AtomIDAtomIDs

Public Member Functions

 SymmetryInfo ()
 ~SymmetryInfo ()
 SymmetryInfo (SymmData const &symmdata, Size const nres_subunit, Size const njump_subunit)
 SymmetryInfo (Size const nres_monomer, Size const njump_monomer, Size const N, std::map< Size, SymDof > dofs, Size const score_subunit, utility::vector1< Size > score_multiply, SymSlideInfo slide_info, Size const num_interfaces=1, std::string const &type="simple")
SymmetryInfoOP clone () const
void initialize (Size const nres_monomer, Size const njump_monomer, Size const N, Size const num_virtual, std::map< Size, SymDof > dofs, Size const score_subunit, utility::vector1< Size > score_multiply, SymSlideInfo slide_info, Size const num_interfaces=1, std::string const &type="simple")
void initialize (Size const nres_monomer, Size const njump_monomer, Size const N, Size const num_virtual, std::map< Size, WtedClones > jump_clones, std::map< Size, SymDof > dofs, Size const score_subunit, utility::vector1< Size > score_multiply, SymSlideInfo slide_info, Size const num_interfaces=1, std::string const &type="simple")
bool operator== (SymmetryInfo const &s)
bool operator!= (SymmetryInfo const &s)
Size bb_follows (Size const seqpos) const
Size chi_follows (Size const seqpos) const
Size jump_follows (Size const seqpos) const
std::vector< std::pair< Size,
Size > > 
map_symmetric_res_pairs (Size res1, Size res2)
bool bb_is_independent (Size const seqpos) const
bool chi_is_independent (Size const seqpos) const
bool fa_is_independent (Size const seqpos) const
bool jump_is_independent (Size const seqpos) const
bool is_virtual (Size const seqpos) const
void resize_asu (Size nres_new)
void update_nmonomer_jumps (Size nmonomer_new)
Size subunits () const
Size subunit_index (Size const seqpos) const
Size score_multiply_factor () const
utility::vector1< boolindependent_residues () const
Size num_bb_clones () const
Size num_chi_clones () const
Size num_jump_clones () const
Size num_independent_residues () const
Size num_total_residues () const
Size num_total_residues_with_pseudo () const
Size num_total_residues_without_pseudo () const
Size num_interfaces () const
Size num_virtuals () const
Size get_nres_subunit () const
Size get_njumps_subunit () const
bool dof_is_independent (DOF_ID const &id, Conformation const &conf) const
core::Real get_dof_derivative_weight (DOF_ID const &id, Conformation const &conf) const
bool torsion_is_independent (TorsionID const &id) const
bool atom_is_independent (AtomID const &id) const
DOF_IDs dependent_dofs (DOF_ID const &id, Conformation const &conf) const
 Returns a list of dofs that depend on id. Inefficient -- creates list anew each time.
TorsionIDs dependent_torsions (TorsionID const &id) const
 Returns a list of dofs that depend on id. Inefficient -- creates list anew each time.
AtomIDs dependent_atoms (AtomID const &id) const
Clones const & bb_clones (Size const seqpos) const
Clones const & chi_clones (Size const seqpos) const
Clones const & jump_clones (Size const base_jump) const
void add_bb_clone (Size const base_pos, Size const clone_pos)
void add_chi_clone (Size const base_pos, Size const clone_pos)
void add_jump_clone (Size const base_pos, Size const clone_jump, Real const wt)
std::map< Size, SymDofget_dofs () const
void set_dofs (std::map< Size, SymDof > dofs)
Size interface_number (Size const res1, Size const res2) const
Size score_multiply (Size const res1, Size const res2) const
void set_score_multiply_from_subunit_factors (utility::vector1< Size > const &score_multiply_vector_subunit, Size const nres_subunit, Size const n_subunits)
void set_score_multiply (Size const res, Size const factor)
bool get_use_symmetry () const
void set_use_symmetry (bool setting)
bool cp_weighting_during_minimization () const
void set_cp_weighting_during_minimization (bool setting)
SymSlideInfo get_slide_info () const
bool is_asymmetric_seqpos (Size const res) const
Size get_asymmetric_seqpos (Size const res) const
void update_score_multiply_factor ()
bool read_silent_struct (std::string const &filename)
bool write_silent_struct (std::string const &filename)

Friends

std::istream & operator>> (std::istream &s, SymmetryInfo &symminfo)
std::ostream & operator<< (std::ostream &s, const SymmetryInfo &symminfo)

Member Typedef Documentation

convenience: these could go somewhere else


Constructor & Destructor Documentation

core::conformation::symmetry::SymmetryInfo::SymmetryInfo ( )

Referenced by clone().

core::conformation::symmetry::SymmetryInfo::~SymmetryInfo ( )
core::conformation::symmetry::SymmetryInfo::SymmetryInfo ( SymmData const &  symmdata,
Size const  nres_subunit,
Size const  njump_subunit 
)
core::conformation::symmetry::SymmetryInfo::SymmetryInfo ( Size const  nres_monomer,
Size const  njump_monomer,
Size const  N,
std::map< Size, SymDof dofs,
Size const  score_subunit,
utility::vector1< Size score_multiply,
SymSlideInfo  slide_info,
Size const  num_interfaces = 1,
std::string const &  type = "simple" 
)

References initialize().


Member Function Documentation

void core::conformation::symmetry::SymmetryInfo::add_bb_clone ( Size const  base_pos,
Size const  clone_pos 
)

Referenced by initialize(), and resize_asu().

void core::conformation::symmetry::SymmetryInfo::add_chi_clone ( Size const  base_pos,
Size const  clone_pos 
)

Referenced by initialize(), and resize_asu().

void core::conformation::symmetry::SymmetryInfo::add_jump_clone ( Size const  base_pos,
Size const  clone_jump,
Real const  wt 
)
bool core::conformation::symmetry::SymmetryInfo::atom_is_independent ( AtomID const &  id) const

References fa_is_independent().

Referenced by dependent_atoms().

SymmetryInfo::Clones const & core::conformation::symmetry::SymmetryInfo::bb_clones ( Size const  seqpos) const
Size core::conformation::symmetry::SymmetryInfo::bb_follows ( Size const  seqpos) const
bool core::conformation::symmetry::SymmetryInfo::bb_is_independent ( Size const  seqpos) const
SymmetryInfo::Clones const & core::conformation::symmetry::SymmetryInfo::chi_clones ( Size const  seqpos) const
Size core::conformation::symmetry::SymmetryInfo::chi_follows ( Size const  seqpos) const

Referenced by chi_is_independent().

bool core::conformation::symmetry::SymmetryInfo::chi_is_independent ( Size const  seqpos) const
SymmetryInfoOP core::conformation::symmetry::SymmetryInfo::clone ( ) const

make a copy of this SymmetryInfo ( allocate actual memory for it )

References SymmetryInfo().

Referenced by map_symmetric_res_pairs().

bool core::conformation::symmetry::SymmetryInfo::cp_weighting_during_minimization ( ) const
SymmetryInfo::AtomIDs core::conformation::symmetry::SymmetryInfo::dependent_atoms ( AtomID const &  id) const

Returns set of AtomIDs that follow a given one. Inefficient: it creates a list each time

References atom_is_independent(), and bb_clones().

SymmetryInfo::DOF_IDs core::conformation::symmetry::SymmetryInfo::dependent_dofs ( DOF_ID const &  id,
Conformation const &  conf 
) const

Returns a list of dofs that depend on id. Inefficient -- creates list anew each time.

Returns set of DOF_IDs that follow a given one. Inefficient: it creates a list each time

References core::id::BB, bb_clones(), chi_clones(), dof_is_independent(), core::conformation::Conformation::fold_tree(), core::conformation::symmetry::guess_torsion_type_of_dof_id(), core::id::JUMP, and jump_clones().

SymmetryInfo::TorsionIDs core::conformation::symmetry::SymmetryInfo::dependent_torsions ( TorsionID const &  id) const

Returns a list of dofs that depend on id. Inefficient -- creates list anew each time.

Returns set of TorsionIDs that follow a given one. Inefficient: it creates a list each time

References core::id::BB, bb_clones(), chi_clones(), and torsion_is_independent().

bool core::conformation::symmetry::SymmetryInfo::dof_is_independent ( DOF_ID const &  id,
Conformation const &  conf 
) const
bool core::conformation::symmetry::SymmetryInfo::fa_is_independent ( Size const  seqpos) const
Size core::conformation::symmetry::SymmetryInfo::get_asymmetric_seqpos ( Size const  res) const
core::Real core::conformation::symmetry::SymmetryInfo::get_dof_derivative_weight ( DOF_ID const &  id,
Conformation const &  conf 
) const
std::map< Size, SymDof > core::conformation::symmetry::SymmetryInfo::get_dofs ( ) const
Size core::conformation::symmetry::SymmetryInfo::get_njumps_subunit ( ) const
Size core::conformation::symmetry::SymmetryInfo::get_nres_subunit ( ) const
SymSlideInfo core::conformation::symmetry::SymmetryInfo::get_slide_info ( ) const
bool core::conformation::symmetry::SymmetryInfo::get_use_symmetry ( ) const
utility::vector1< bool > core::conformation::symmetry::SymmetryInfo::independent_residues ( ) const
void core::conformation::symmetry::SymmetryInfo::initialize ( Size const  nres_monomer,
Size const  njump_monomer,
Size const  N,
Size const  num_virtual,
std::map< Size, SymDof dofs,
Size const  score_subunit,
utility::vector1< Size score_multiply,
SymSlideInfo  slide_info,
Size const  num_interfaces = 1,
std::string const &  type = "simple" 
)
void core::conformation::symmetry::SymmetryInfo::initialize ( Size const  nres_monomer,
Size const  njump_monomer,
Size const  N,
Size const  num_virtual,
std::map< Size, WtedClones jump_clones,
std::map< Size, SymDof dofs,
Size const  score_subunit,
utility::vector1< Size score_multiply,
SymSlideInfo  slide_info,
Size const  num_interfaces = 1,
std::string const &  type = "simple" 
)
Size core::conformation::symmetry::SymmetryInfo::interface_number ( Size const  res1,
Size const  res2 
) const
bool core::conformation::symmetry::SymmetryInfo::is_asymmetric_seqpos ( Size const  res) const
bool core::conformation::symmetry::SymmetryInfo::is_virtual ( Size const  seqpos) const
SymmetryInfo::Clones const & core::conformation::symmetry::SymmetryInfo::jump_clones ( Size const  base_jump) const

Referenced by dependent_dofs().

Size core::conformation::symmetry::SymmetryInfo::jump_follows ( Size const  seqpos) const

Referenced by jump_is_independent().

bool core::conformation::symmetry::SymmetryInfo::jump_is_independent ( Size const  seqpos) const
std::vector< std::pair< Size, Size > > core::conformation::symmetry::SymmetryInfo::map_symmetric_res_pairs ( Size  res1,
Size  res2 
)
Size core::conformation::symmetry::SymmetryInfo::num_bb_clones ( ) const
Size core::conformation::symmetry::SymmetryInfo::num_chi_clones ( ) const
Size core::conformation::symmetry::SymmetryInfo::num_independent_residues ( ) const
Size core::conformation::symmetry::SymmetryInfo::num_interfaces ( ) const
Size core::conformation::symmetry::SymmetryInfo::num_jump_clones ( ) const
Size core::conformation::symmetry::SymmetryInfo::num_total_residues ( ) const
Size core::conformation::symmetry::SymmetryInfo::num_total_residues_with_pseudo ( ) const
Size core::conformation::symmetry::SymmetryInfo::num_total_residues_without_pseudo ( ) const
Size core::conformation::symmetry::SymmetryInfo::num_virtuals ( ) const
bool core::conformation::symmetry::SymmetryInfo::operator!= ( SymmetryInfo const &  s)
bool core::conformation::symmetry::SymmetryInfo::operator== ( SymmetryInfo const &  s)
bool core::conformation::symmetry::SymmetryInfo::read_silent_struct ( std::string const &  filename)
void core::conformation::symmetry::SymmetryInfo::resize_asu ( Size  nres_new)
Size core::conformation::symmetry::SymmetryInfo::score_multiply ( Size const  res1,
Size const  res2 
) const
Size core::conformation::symmetry::SymmetryInfo::score_multiply_factor ( ) const
void core::conformation::symmetry::SymmetryInfo::set_cp_weighting_during_minimization ( bool  setting)
void core::conformation::symmetry::SymmetryInfo::set_dofs ( std::map< Size, SymDof dofs)

Referenced by update_nmonomer_jumps().

void core::conformation::symmetry::SymmetryInfo::set_score_multiply ( Size const  res,
Size const  factor 
)
void core::conformation::symmetry::SymmetryInfo::set_score_multiply_from_subunit_factors ( utility::vector1< Size > const &  score_multiply_vector_subunit,
Size const  nres_subunit,
Size const  n_subunits 
)

Referenced by initialize().

void core::conformation::symmetry::SymmetryInfo::set_use_symmetry ( bool  setting)
Size core::conformation::symmetry::SymmetryInfo::subunit_index ( Size const  seqpos) const
Size core::conformation::symmetry::SymmetryInfo::subunits ( ) const
bool core::conformation::symmetry::SymmetryInfo::torsion_is_independent ( TorsionID const &  id) const
void core::conformation::symmetry::SymmetryInfo::update_nmonomer_jumps ( Size  nmonomer_new)
void core::conformation::symmetry::SymmetryInfo::update_score_multiply_factor ( )
bool core::conformation::symmetry::SymmetryInfo::write_silent_struct ( std::string const &  filename)

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  s,
const SymmetryInfo symminfo 
) [friend]
std::istream& operator>> ( std::istream &  s,
SymmetryInfo symminfo 
) [friend]

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