#include <SymmetryInfo.hh>

Inheritance diagram for core::conformation::symmetry::SymmetryInfo:

Collaboration diagram for core::conformation::symmetry::SymmetryInfo:

Public Types
typedef utility::vector1< Size >	Clones

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_ID >	DOF_IDs
	convenience: these could go somewhere else More...

typedef utility::vector1 < TorsionID >	TorsionIDs

typedef utility::vector1< AtomID >	AtomIDs

Public Member Functions
	SymmetryInfo ()

virtual	~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< bool >	independent_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. More...

TorsionIDs	dependent_torsions (TorsionID const &id) const
	Returns a list of dofs that depend on id. Inefficient – creates list anew each time. More...

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, SymDof > const &	get_dofs () const

void	set_dofs (std::map< Size, SymDof > const &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)

std::string	get_jump_name (Size i) const

Size	get_jump_num (std::string i) const

void	set_jump_name (Size i, std::string)

Size	num_slidablejumps () const

void	set_multicomponent_info (utility::vector1< char > const &components, std::map< char, std::pair< Size, Size > > const &component_bounds, std::map< std::string, char > const &name2component, std::map< std::string, utility::vector1< char > > const &jname2component, std::map< std::string, utility::vector1< Size > > const &jname2subunits)

utility::vector1< char > const &	get_components () const

std::map< char, std::pair < Size, Size > > const &	get_component_bounds () 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::pair< Size, Size > const &	get_component_bounds (char c) const

Size	get_component_lower_bound (char c) const

Size	get_component_upper_bound (char c) const

char	get_component_of_residue (Size ir) const

char	get_subunit_name_to_component (std::string const &vname) const

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

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

Private Member Functions
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 Attributes
std::map< Size, Clones >	bb_clones_

std::map< Size, Clones >	chi_clones_

std::map< Size, Clones >	jump_clones_

std::map< Size, Real >	jump_clone_wts_

std::map< Size, Size >	bb_follows_

std::map< Size, Size >	chi_follows_

std::map< Size, Size >	jump_follows_

Clones	empty_list

Size	nres_monomer_

Size	scoring_subunit_

Size	npseudo_

Size	njump_monomer_

std::string	type_

Size	interfaces_

utility::vector1< Size >	score_multiply_

core::Size	score_multiply_factor_

std::map< Size, SymDof >	dofs_

bool	use_symmetry_

bool	cp_weighting_during_minimization_

SymSlideInfo	slide_info_

std::map< Size, std::string >	jnum2dofname_

std::map< std::string, Size >	dofname2jnum_

utility::vector1< char >	components_

std::map< char, std::pair < Size, Size > >	component_bounds_

std::map< std::string, char >	name2component_

std::map< std::string, utility::vector1< char > >	jname2components_

std::map< std::string, utility::vector1< Size > >	jname2subunits_

Friends
std::istream &	operator>> (std::istream &s, SymmetryInfo &symminfo)

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

Detailed Description

Definition at line 49 of file SymmetryInfo.hh.

Member Typedef Documentation

typedef id::AtomID core::conformation::symmetry::SymmetryInfo::AtomID

Definition at line 57 of file SymmetryInfo.hh.

typedef utility::vector1< AtomID > core::conformation::symmetry::SymmetryInfo::AtomIDs

Definition at line 62 of file SymmetryInfo.hh.

typedef utility::vector1< Size > core::conformation::symmetry::SymmetryInfo::Clones

Definition at line 52 of file SymmetryInfo.hh.

typedef id::DOF_ID core::conformation::symmetry::SymmetryInfo::DOF_ID

Definition at line 55 of file SymmetryInfo.hh.

typedef utility::vector1< DOF_ID > core::conformation::symmetry::SymmetryInfo::DOF_IDs

convenience: these could go somewhere else

Definition at line 60 of file SymmetryInfo.hh.

typedef id::TorsionID core::conformation::symmetry::SymmetryInfo::TorsionID

Definition at line 56 of file SymmetryInfo.hh.

typedef utility::vector1< TorsionID > core::conformation::symmetry::SymmetryInfo::TorsionIDs

Definition at line 61 of file SymmetryInfo.hh.

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

Definition at line 53 of file SymmetryInfo.hh.

Constructor & Destructor Documentation

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

Definition at line 54 of file SymmetryInfo.cc.

References score_multiply_factor_, and use_symmetry_.

Referenced by clone().

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

virtual

Definition at line 55 of file SymmetryInfo.cc.

core::conformation::symmetry::SymmetryInfo::SymmetryInfo	(	SymmData const &	symmdata,
		Size const	nres_subunit,
		Size const	njump_subunit
	)

Definition at line 71 of file SymmetryInfo.cc.

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"`
	)

Definition at line 96 of file SymmetryInfo.cc.

References initialize().

Member Function Documentation

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

Definition at line 1082 of file SymmetryInfo.cc.

References bb_clones_, and bb_follows_.

Referenced by initialize(), and resize_asu().

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

Definition at line 1102 of file SymmetryInfo.cc.

References chi_clones_, and chi_follows_.

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
	)

Definition at line 1122 of file SymmetryInfo.cc.

References bb_follows_, jump_clone_wts_, jump_clones_, and jump_follows_.

Referenced by initialize(), and update_nmonomer_jumps().

bool core::conformation::symmetry::SymmetryInfo::atom_is_independent ( AtomID const & id) const

Definition at line 1322 of file SymmetryInfo.cc.

References fa_is_independent().

Referenced by dependent_atoms().

SymmetryInfo::Clones const & core::conformation::symmetry::SymmetryInfo::bb_clones ( Size const seqpos) const

Definition at line 959 of file SymmetryInfo.cc.

References bb_clones_, and empty_list.

Referenced by dependent_atoms(), dependent_dofs(), dependent_torsions(), and map_symmetric_res_pairs().

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

Definition at line 798 of file SymmetryInfo.cc.

References bb_follows_.

Referenced by bb_is_independent().

bool core::conformation::symmetry::SymmetryInfo::bb_is_independent ( Size const seqpos) const

Definition at line 841 of file SymmetryInfo.cc.

References bb_follows().

Referenced by dof_is_independent(), fa_is_independent(), get_dof_derivative_weight(), independent_residues(), interface_number(), score_multiply(), and torsion_is_independent().

SymmetryInfo::Clones const & core::conformation::symmetry::SymmetryInfo::chi_clones ( Size const seqpos) const

Definition at line 969 of file SymmetryInfo.cc.

References chi_clones_, and empty_list.

Referenced by dependent_dofs(), and dependent_torsions().

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

Definition at line 805 of file SymmetryInfo.cc.

References chi_follows_.

Referenced by chi_is_independent().

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

Definition at line 847 of file SymmetryInfo.cc.

References chi_follows().

Referenced by dof_is_independent(), fa_is_independent(), get_dof_derivative_weight(), and torsion_is_independent().

SymmetryInfoOP core::conformation::symmetry::SymmetryInfo::clone ( ) const

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

Definition at line 114 of file SymmetryInfo.cc.

References SymmetryInfo().

Referenced by map_symmetric_res_pairs().

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

private

bool core::conformation::symmetry::SymmetryInfo::cp_weighting_during_minimization ( ) const

Definition at line 1222 of file SymmetryInfo.cc.

References cp_weighting_during_minimization_.

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

Definition at line 1349 of file SymmetryInfo.cc.

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

Definition at line 1247 of file SymmetryInfo.cc.

References core::id::BB, bb_clones(), chi_clones(), dof_is_independent(), core::kinematics::FoldTree::downstream_jump_residue(), core::conformation::Conformation::fold_tree(), core::kinematics::FoldTree::get_jump_that_builds_residue(), 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

Definition at line 1329 of file SymmetryInfo.cc.

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

Definition at line 1272 of file SymmetryInfo.cc.

References core::id::BB, bb_is_independent(), core::id::CHI, chi_is_independent(), core::conformation::Conformation::fold_tree(), core::kinematics::FoldTree::get_jump_that_builds_residue(), core::conformation::symmetry::guess_torsion_type_of_dof_id(), core::id::JUMP, and jump_is_independent().

Referenced by dependent_dofs().

bool core::conformation::symmetry::SymmetryInfo::fa_is_independent ( Size const seqpos) const

Definition at line 853 of file SymmetryInfo.cc.

References bb_is_independent(), and chi_is_independent().

Referenced by atom_is_independent().

Size core::conformation::symmetry::SymmetryInfo::get_asymmetric_seqpos ( Size const res) const

Definition at line 1372 of file SymmetryInfo.cc.

References get_use_symmetry(), num_independent_residues(), and subunits().

std::map< char, std::pair< Size, Size > > const & core::conformation::symmetry::SymmetryInfo::get_component_bounds ( ) const

Definition at line 1421 of file SymmetryInfo.cc.

References component_bounds_, and components_.

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

std::pair< Size, Size > const & core::conformation::symmetry::SymmetryInfo::get_component_bounds ( char c) const

Definition at line 1444 of file SymmetryInfo.cc.

References component_bounds_, and components_.

Size core::conformation::symmetry::SymmetryInfo::get_component_lower_bound ( char c) const

Definition at line 1452 of file SymmetryInfo.cc.

References component_bounds_, and components_.

char core::conformation::symmetry::SymmetryInfo::get_component_of_residue ( Size ir) const

Definition at line 1468 of file SymmetryInfo.cc.

References component_bounds_, components_, num_independent_residues(), and num_total_residues_without_pseudo().

Size core::conformation::symmetry::SymmetryInfo::get_component_upper_bound ( char c) const

Definition at line 1460 of file SymmetryInfo.cc.

References component_bounds_, and components_.

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

Definition at line 1415 of file SymmetryInfo.cc.

References components_.

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

core::Real core::conformation::symmetry::SymmetryInfo::get_dof_derivative_weight	(	DOF_ID const &	id,
		Conformation const &	conf
	)		const

Definition at line 1293 of file SymmetryInfo.cc.

References core::id::BB, bb_is_independent(), core::id::CHI, chi_is_independent(), core::conformation::Conformation::fold_tree(), core::kinematics::FoldTree::get_jump_that_builds_residue(), core::conformation::symmetry::guess_torsion_type_of_dof_id(), core::id::JUMP, and jump_clone_wts_.

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

Definition at line 1143 of file SymmetryInfo.cc.

References dofs_.

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

std::string core::conformation::symmetry::SymmetryInfo::get_jump_name ( Size i) const

Definition at line 1388 of file SymmetryInfo.cc.

References jnum2dofname_.

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

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

Definition at line 1433 of file SymmetryInfo.cc.

References components_, and jname2components_.

utility::vector1< char > const & core::conformation::symmetry::SymmetryInfo::get_jump_name_to_components ( std::string const & jname) const

Definition at line 1493 of file SymmetryInfo.cc.

References components_, and jname2components_.

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

Definition at line 1439 of file SymmetryInfo.cc.

References components_, and jname2subunits_.

utility::vector1< Size > const & core::conformation::symmetry::SymmetryInfo::get_jump_name_to_subunits ( std::string const & jname) const

Definition at line 1501 of file SymmetryInfo.cc.

References components_, and jname2subunits_.

Size core::conformation::symmetry::SymmetryInfo::get_jump_num ( std::string i) const

Definition at line 1394 of file SymmetryInfo.cc.

References dofname2jnum_.

Size core::conformation::symmetry::SymmetryInfo::get_njumps_subunit ( ) const

Definition at line 1209 of file SymmetryInfo.cc.

References njump_monomer_.

Size core::conformation::symmetry::SymmetryInfo::get_nres_subunit ( ) const

Definition at line 1203 of file SymmetryInfo.cc.

References nres_monomer_.

Referenced by core::pose::symmetry::get_symdof_subunits().

SymSlideInfo core::conformation::symmetry::SymmetryInfo::get_slide_info ( ) const

Definition at line 1234 of file SymmetryInfo.cc.

References slide_info_.

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

Definition at line 1427 of file SymmetryInfo.cc.

References components_, and name2component_.

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

char core::conformation::symmetry::SymmetryInfo::get_subunit_name_to_component ( std::string const & vname) const

Definition at line 1485 of file SymmetryInfo.cc.

References components_, and name2component_.

bool core::conformation::symmetry::SymmetryInfo::get_use_symmetry ( ) const

Definition at line 1216 of file SymmetryInfo.cc.

References use_symmetry_.

Referenced by get_asymmetric_seqpos(), is_asymmetric_seqpos(), and core::conformation::symmetry::is_symmetric().

utility::vector1< bool > core::conformation::symmetry::SymmetryInfo::independent_residues ( ) const

Definition at line 871 of file SymmetryInfo.cc.

References bb_is_independent(), and num_total_residues_with_pseudo().

Referenced by update_score_multiply_factor().

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"`
	)

Definition at line 121 of file SymmetryInfo.cc.

References add_bb_clone(), add_chi_clone(), add_jump_clone(), bb_clones_, chi_clones_, cp_weighting_during_minimization_, dofs_, interfaces_, jump_clones_, njump_monomer_, npseudo_, nres_monomer_, num_interfaces(), scoring_subunit_, set_score_multiply_from_subunit_factors(), slide_info_, type_, update_score_multiply_factor(), and use_symmetry_.

Referenced by SymmetryInfo().

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"`
	)

Definition at line 284 of file SymmetryInfo.cc.

References add_bb_clone(), add_chi_clone(), add_jump_clone(), bb_clones_, chi_clones_, cp_weighting_during_minimization_, dofs_, interfaces_, jump_clones_, njump_monomer_, npseudo_, nres_monomer_, num_interfaces(), scoring_subunit_, set_score_multiply_from_subunit_factors(), slide_info_, type_, update_score_multiply_factor(), and use_symmetry_.

Size core::conformation::symmetry::SymmetryInfo::interface_number	(	Size const	res1,
		Size const	res2
	)		const

Definition at line 1175 of file SymmetryInfo.cc.

References bb_is_independent(), and subunit_index().

bool core::conformation::symmetry::SymmetryInfo::is_asymmetric_seqpos ( Size const res) const

Definition at line 1365 of file SymmetryInfo.cc.

References get_use_symmetry(), num_independent_residues(), and subunits().

bool core::conformation::symmetry::SymmetryInfo::is_virtual ( Size const seqpos) const

Definition at line 793 of file SymmetryInfo.cc.

References num_total_residues_without_pseudo().

SymmetryInfo::Clones const & core::conformation::symmetry::SymmetryInfo::jump_clones ( Size const base_jump) const

Definition at line 979 of file SymmetryInfo.cc.

References empty_list, and jump_clones_.

Referenced by dependent_dofs().

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

Definition at line 812 of file SymmetryInfo.cc.

References jump_follows_.

Referenced by jump_is_independent().

bool core::conformation::symmetry::SymmetryInfo::jump_is_independent ( Size const seqpos) const

Definition at line 859 of file SymmetryInfo.cc.

References jump_follows().

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

std::vector< std::pair< Size, Size > > core::conformation::symmetry::SymmetryInfo::map_symmetric_res_pairs	(	Size	res1,
		Size	res2
	)

Definition at line 819 of file SymmetryInfo.cc.

References bb_clones(), clone(), core::sequence::end, num_independent_residues(), and num_total_residues().

Size core::conformation::symmetry::SymmetryInfo::num_bb_clones ( ) const

Definition at line 884 of file SymmetryInfo.cc.

References bb_clones_.

Referenced by num_total_residues(), num_total_residues_with_pseudo(), num_total_residues_without_pseudo(), and subunits().

Size core::conformation::symmetry::SymmetryInfo::num_chi_clones ( ) const

Definition at line 895 of file SymmetryInfo.cc.

References chi_clones_.

Size core::conformation::symmetry::SymmetryInfo::num_independent_residues ( ) const

Definition at line 910 of file SymmetryInfo.cc.

References bb_clones_.

Referenced by get_asymmetric_seqpos(), get_component_of_residue(), is_asymmetric_seqpos(), map_symmetric_res_pairs(), num_total_residues(), num_total_residues_with_pseudo(), num_total_residues_without_pseudo(), core::conformation::symmetry::replaced_symmetric_foldtree_with_new_monomer(), and subunit_index().

Size core::conformation::symmetry::SymmetryInfo::num_interfaces ( ) const

Definition at line 934 of file SymmetryInfo.cc.

References interfaces_.

Referenced by initialize(), and core::conformation::symmetry::operator<<().

Size core::conformation::symmetry::SymmetryInfo::num_jump_clones ( ) const

Definition at line 903 of file SymmetryInfo.cc.

References jump_clones_.

Size core::conformation::symmetry::SymmetryInfo::num_slidablejumps ( ) const

Definition at line 1406 of file SymmetryInfo.cc.

References dofs_.

Size core::conformation::symmetry::SymmetryInfo::num_total_residues ( ) const

Definition at line 916 of file SymmetryInfo.cc.

References num_bb_clones(), and num_independent_residues().

Referenced by map_symmetric_res_pairs().

Size core::conformation::symmetry::SymmetryInfo::num_total_residues_with_pseudo ( ) const

Definition at line 922 of file SymmetryInfo.cc.

References npseudo_, num_bb_clones(), and num_independent_residues().

Referenced by independent_residues().

Size core::conformation::symmetry::SymmetryInfo::num_total_residues_without_pseudo ( ) const

Definition at line 928 of file SymmetryInfo.cc.

References num_bb_clones(), and num_independent_residues().

Referenced by get_component_of_residue(), core::pose::symmetry::get_symdof_subunits(), is_virtual(), and score_multiply().

Size core::conformation::symmetry::SymmetryInfo::num_virtuals ( ) const

Definition at line 946 of file SymmetryInfo.cc.

References npseudo_.

bool core::conformation::symmetry::SymmetryInfo::operator!= ( SymmetryInfo const & s)

Definition at line 66 of file SymmetryInfo.cc.

bool core::conformation::symmetry::SymmetryInfo::operator== ( SymmetryInfo const & s)

Definition at line 58 of file SymmetryInfo.cc.

References bb_clones_, chi_clones_, jump_clones_, and npseudo_.

bool core::conformation::symmetry::SymmetryInfo::read_silent_struct ( std::string const & filename)

Definition at line 764 of file SymmetryInfo.cc.

void core::conformation::symmetry::SymmetryInfo::resize_asu ( Size nres_new)

Definition at line 991 of file SymmetryInfo.cc.

References add_bb_clone(), add_chi_clone(), bb_clones_, bb_follows_, chi_clones_, chi_follows_, protocols::forge::build::SegmentInsertConnectionScheme::N, nres_monomer_, scoring_subunit_, and subunits().

Size core::conformation::symmetry::SymmetryInfo::score_multiply	(	Size const	res1,
		Size const	res2
	)		const

Definition at line 1155 of file SymmetryInfo.cc.

References bb_is_independent(), num_total_residues_without_pseudo(), and score_multiply_.

Size core::conformation::symmetry::SymmetryInfo::score_multiply_factor ( ) const

Definition at line 940 of file SymmetryInfo.cc.

References score_multiply_factor_.

void core::conformation::symmetry::SymmetryInfo::set_cp_weighting_during_minimization ( bool setting)

Definition at line 1228 of file SymmetryInfo.cc.

References cp_weighting_during_minimization_.

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

void core::conformation::symmetry::SymmetryInfo::set_dofs ( std::map< Size, SymDof > const & dofs)

Definition at line 1149 of file SymmetryInfo.cc.

References dofs_.

Referenced by update_nmonomer_jumps().

void core::conformation::symmetry::SymmetryInfo::set_jump_name	(	Size	i,
		std::string	jname
	)

Definition at line 1400 of file SymmetryInfo.cc.

References dofname2jnum_, and jnum2dofname_.

void core::conformation::symmetry::SymmetryInfo::set_multicomponent_info	(	utility::vector1< char > const &	components,
		std::map< char, std::pair< Size, Size > > const &	component_bounds,
		std::map< std::string, char > const &	name2component,
		std::map< std::string, utility::vector1< char > > const &	jname2component,
		std::map< std::string, utility::vector1< Size > > const &	jname2subunits
	)

Definition at line 1511 of file SymmetryInfo.cc.

References component_bounds_, components_, jname2components_, jname2subunits_, and name2component_.

void core::conformation::symmetry::SymmetryInfo::set_score_multiply	(	Size const	res,
		Size const	factor
	)

Definition at line 1195 of file SymmetryInfo.cc.

References score_multiply_.

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
	)