core::conformation::symmetry::SymmetryInfo Class Reference

#include <SymmetryInfo.hh>

Inheritance 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 ()
	~SymmetryInfo () override
	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< Real > score_multiply, SymSlideInfo slide_info, Size const num_interfaces=1, std::string const &type="simple")
void	init_defaults ()
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< Real > 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< Real > score_multiply, SymSlideInfo slide_info, Size const num_interfaces=1, std::string const &type="simple")
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) const
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
bool	contiguous_monomers () const
bool	torsion_changes_move_other_monomers () const
void	torsion_changes_move_other_monomers (bool const setting)
Size	subunit_index (Size const seqpos) const
	What subunit does a particular residue come from? More...
Size	equivalent_residue_on_subunit (Size subunit_index, Size residue_id) const
	What is the equivalent residue on a particular subunit for the given residue? The logic here mimics the logic in subunit index in terms of subunit numbering. More...
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	last_independent_residue () const
void	num_virtuals (Size const setting)
Size	get_nres_subunit () const
void	set_nres_subunit (Size const setting)
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
Real	score_multiply (Size const res1, Size const res2) const
Real	deriv_multiply (Size const res1, Size const res2) const
void	set_score_multiply_from_subunit_factors (utility::vector1< Real > const &score_multiply_vector_subunit, Size const nres_subunit, Size const n_subunits)
void	set_score_multiply (Size const res, Size const factor)
void	set_flat_score_multiply (Size const nres, Size const factor)
bool	get_use_symmetry () const
bool	reset_score_multiply_to_reasonable_default ()
void	set_use_symmetry (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 (Size const &num_components, 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)
Size const &	get_num_components () const
utility::vector1< char > const &	get_components () const
char	get_component (Size i) 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
void	update_contiguous_monomers ()
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_
Size	last_indep_residue_
std::string	type_
Size	interfaces_
utility::vector1< Real >	score_multiply_
Real	reweight_symm_interactions_
Real	score_multiply_factor_
std::map< Size, SymDof >	dofs_
bool	use_symmetry_
SymSlideInfo	slide_info_
std::map< Size, std::string >	jnum2dofname_
std::map< std::string, Size >	dofname2jnum_
bool	contiguous_monomers_
bool	torsion_changes_move_other_monomers_
Size	num_components_
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)

Member Typedef Documentation

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

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

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

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

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

convenience: these could go somewhere else

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

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

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

Constructor & Destructor Documentation

core::conformation::symmetry::SymmetryInfo::SymmetryInfo

(

)

References init_defaults().

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

overridedefault

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

References dofname2jnum_, core::conformation::symmetry::SymmData::get_dofs(), core::conformation::symmetry::SymmData::get_interfaces(), core::conformation::symmetry::SymmData::get_jump_clones(), core::conformation::symmetry::SymmData::get_jump_string_to_jump_num(), core::conformation::symmetry::SymmData::get_num_virtual(), core::conformation::symmetry::SymmData::get_score_multiply_subunit(), core::conformation::symmetry::SymmData::get_score_subunit(), core::conformation::symmetry::SymmData::get_slide_info(), core::conformation::symmetry::SymmData::get_subunits(), init_defaults(), initialize(), jnum2dofname_, and core::conformation::symmetry::TR().

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< Real >	score_multiply,
		SymSlideInfo	slide_info,
		Size const	num_interfaces = 1,
		std::string const &	type = "simple"
	)

References contiguous_monomers_, initialize(), and torsion_changes_move_other_monomers_.

Member Function Documentation

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

References bb_clones_, bb_follows_, and update_contiguous_monomers().

Referenced by initialize(), resize_asu(), protocols::simple_moves::PeriodicBoxMover::setup_pose(), protocols::relax::RepeatProteinRelax::setup_repeat_symminfo(), protocols::cryst::MakeLayerMover::setup_xtal_symminfo(), and protocols::cryst::MakeLatticeMover::setup_xtal_symminfo().

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

References chi_clones_, and chi_follows_.

Referenced by initialize(), resize_asu(), protocols::relax::RepeatProteinRelax::setup_repeat_symminfo(), protocols::cryst::MakeLayerMover::setup_xtal_symminfo(), and protocols::cryst::MakeLatticeMover::setup_xtal_symminfo().

void core::conformation::symmetry::SymmetryInfo::add_jump_clone	(	Size const	base_pos,
		Size const	clone_jump,
		Real const	wt
	)

References bb_follows_, jump_clone_wts_, jump_clones_, and jump_follows_.

Referenced by initialize(), protocols::cryst::MakeLayerMover::setup_xtal_symminfo(), protocols::cryst::MakeLatticeMover::setup_xtal_symminfo(), and update_nmonomer_jumps().

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

References bb_clones_, and empty_list.

Referenced by dependent_atoms(), dependent_dofs(), dependent_torsions(), core::scoring::fiber_diffraction::find_pitch(), and map_symmetric_res_pairs().

Size core::conformation::symmetry::SymmetryInfo::bb_follows

(

Size const

seqpos

)

const

References bb_follows_.

Referenced by bb_is_independent().

bool core::conformation::symmetry::SymmetryInfo::bb_is_independent

(

Size const

seqpos

)

const

References bb_follows().

Referenced by deriv_multiply(), dof_is_independent(), fa_is_independent(), core::scoring::fiber_diffraction::find_max_r(), core::scoring::fiber_diffraction::find_min_xyz(), core::scoring::fiber_diffraction::find_pitch(), get_dof_derivative_weight(), independent_residues(), initialize(), interface_number(), core::conformation::symmetry::operator>>(), reset_score_multiply_to_reasonable_default(), resize_asu(), score_multiply(), core::scoring::fiber_diffraction::setup_cylindrical_coords(), protocols::cryst::MakeLayerMover::setup_xtal_symminfo(), protocols::cryst::MakeLatticeMover::setup_xtal_symminfo(), and torsion_is_independent().

SymmetryInfo::Clones const & core::conformation::symmetry::SymmetryInfo::chi_clones

(

Size const

seqpos

)

const

References chi_clones_, and empty_list.

Referenced by dependent_dofs(), and dependent_torsions().

Size core::conformation::symmetry::SymmetryInfo::chi_follows

(

Size const

seqpos

)

const

References chi_follows_.

Referenced by chi_is_independent().

bool core::conformation::symmetry::SymmetryInfo::chi_is_independent

(

Size const

seqpos

)

const

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

Referenced by dependent_dofs(), map_symmetric_res_pairs(), and core::conformation::symmetry::SymmetricConformation::SymmetricConformation().

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

private

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

inline

References contiguous_monomers_.

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(), clone(), 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

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

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

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

bool core::conformation::symmetry::SymmetryInfo::dof_is_independent	(	DOF_ID const &	id,
		Conformation const &	conf
	)		const

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().

Size core::conformation::symmetry::SymmetryInfo::equivalent_residue_on_subunit	(	Size	subunit_index,
		Size	residue_id
	)		const

What is the equivalent residue on a particular subunit for the given residue? The logic here mimics the logic in subunit index in terms of subunit numbering.

References bb_clones_, bb_follows_, contiguous_monomers_, nres_monomer_, and num_independent_residues().

Referenced by core::pack::interaction_graph::SymmOnTheFlyNode::set_rotamers().

bool core::conformation::symmetry::SymmetryInfo::fa_is_independent

(

Size const

seqpos

)

const

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

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

char core::conformation::symmetry::SymmetryInfo::get_component

(

Size

i

)

const

References components_.

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

(

)

const

References component_bounds_, and components_.

Referenced by core::pack::hbonds::HBondGraphInitializerIG::get_ind_res(), and core::conformation::symmetry::setup_symmetric_conformation().

std::pair< Size, Size > const & core::conformation::symmetry::SymmetryInfo::get_component_bounds

(

char

c

)

const

References component_bounds_, and components_.

Size core::conformation::symmetry::SymmetryInfo::get_component_lower_bound

(

char

c

)

const

References component_bounds_, and components_.

char core::conformation::symmetry::SymmetryInfo::get_component_of_residue

(

Size

ir

)

const

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

Referenced by core::pack::hbonds::HBondGraphInitializerIG::get_ind_res().

Size core::conformation::symmetry::SymmetryInfo::get_component_upper_bound

(

char

c

)

const

References component_bounds_, and components_.

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

(

)

const

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

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

References dofs_.

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

std::string core::conformation::symmetry::SymmetryInfo::get_jump_name

(

Size

i

)

const

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

References components_, and jname2components_.

utility::vector1< char > const & core::conformation::symmetry::SymmetryInfo::get_jump_name_to_components

(

std::string const &

jname

)

const

References components_, and jname2components_.

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

(

)

const

References components_, and jname2subunits_.

utility::vector1< Size > const & core::conformation::symmetry::SymmetryInfo::get_jump_name_to_subunits

(

std::string const &

jname

)

const

References components_, and jname2subunits_.

Size core::conformation::symmetry::SymmetryInfo::get_jump_num

(

std::string

i

)

const

References dofname2jnum_.

Size core::conformation::symmetry::SymmetryInfo::get_njumps_subunit

(

)

const

References njump_monomer_.

Size core::conformation::symmetry::SymmetryInfo::get_nres_subunit

(

)

const

References nres_monomer_.

Referenced by core::pose::symmetry::get_symdof_subunits(), and num_independent_residues().

Size const & core::conformation::symmetry::SymmetryInfo::get_num_components

(

)

const

References num_components_.

Referenced by core::pack::hbonds::HBondGraphInitializerIG::get_ind_res().

SymSlideInfo core::conformation::symmetry::SymmetryInfo::get_slide_info

(

)

const

References slide_info_.

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

(

)

const

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

References components_, and name2component_.

bool core::conformation::symmetry::SymmetryInfo::get_use_symmetry

(

)

const

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

References bb_is_independent(), and num_total_residues_with_pseudo().

Referenced by update_score_multiply_factor().

void core::conformation::symmetry::SymmetryInfo::init_defaults

(

)

References contiguous_monomers_, interfaces_, last_indep_residue_, njump_monomer_, npseudo_, nres_monomer_, num_components_, reweight_symm_interactions_, score_multiply_factor_, scoring_subunit_, torsion_changes_move_other_monomers_, and use_symmetry_.

Referenced by initialize(), and 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, SymDof >	dofs,
		Size const	score_subunit,
		utility::vector1< Real >	score_multiply,
		SymSlideInfo	slide_info,
		Size const	num_interfaces = 1,
		std::string const &	type = "simple"
	)

References add_bb_clone(), add_chi_clone(), add_jump_clone(), bb_clones_, bb_is_independent(), chi_clones_, dofs_, init_defaults(), interfaces_, jump_clones_, last_indep_residue_, njump_monomer_, npseudo_, nres_monomer_, num_interfaces(), num_total_residues_without_pseudo(), 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< Real >	score_multiply,
		SymSlideInfo	slide_info,
		Size const	num_interfaces = 1,
		std::string const &	type = "simple"
	)

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

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

References bb_is_independent(), and subunit_index().

bool core::conformation::symmetry::SymmetryInfo::is_asymmetric_seqpos

(

Size const

res

)

const

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

Referenced by core::pack::hbonds::HBondGraphInitializerIG::find_symmetric_hbonds().

bool core::conformation::symmetry::SymmetryInfo::is_virtual

(

Size const

seqpos

)

const

References num_total_residues_without_pseudo().

SymmetryInfo::Clones const & core::conformation::symmetry::SymmetryInfo::jump_clones

(

Size const

base_jump

)

const

References empty_list, and jump_clones_.

Referenced by dependent_dofs().

Size core::conformation::symmetry::SymmetryInfo::jump_follows

(

Size const

seqpos

)

const

References jump_follows_.

Referenced by jump_is_independent().

bool core::conformation::symmetry::SymmetryInfo::jump_is_independent

(

Size const

seqpos

)

const

References jump_follows().

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

Size core::conformation::symmetry::SymmetryInfo::last_independent_residue

(

)

const

References last_indep_residue_.

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

References bb_clones(), clone(), num_independent_residues(), and num_total_residues().

Size core::conformation::symmetry::SymmetryInfo::num_bb_clones

(

)

const

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

References chi_clones_.

Size core::conformation::symmetry::SymmetryInfo::num_independent_residues

(

)

const

References bb_clones_, and get_nres_subunit().

Referenced by equivalent_residue_on_subunit(), get_asymmetric_seqpos(), get_component_of_residue(), core::pack::hbonds::HBondGraphInitializerIG::get_ind_res(), 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

References interfaces_.

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

Size core::conformation::symmetry::SymmetryInfo::num_jump_clones

(

)

const

References jump_clones_.

Size core::conformation::symmetry::SymmetryInfo::num_slidablejumps

(

)

const

References dofs_.

Size core::conformation::symmetry::SymmetryInfo::num_total_residues

(

)

const

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

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

Referenced by independent_residues(), and resize_asu().

Size core::conformation::symmetry::SymmetryInfo::num_total_residues_without_pseudo

(

)

const

References num_bb_clones(), and num_independent_residues().

Referenced by core::conformation::symmetry::calculate_inverting_virtuals(), deriv_multiply(), get_component_of_residue(), core::pose::symmetry::get_symdof_subunits(), initialize(), is_virtual(), core::conformation::symmetry::operator>>(), reset_score_multiply_to_reasonable_default(), resize_asu(), and score_multiply().

Size core::conformation::symmetry::SymmetryInfo::num_virtuals

(

)

const

References npseudo_.

Referenced by protocols::relax::RepeatProteinRelax::setup_repeat_symminfo(), protocols::cryst::MakeLayerMover::setup_xtal_symminfo(), and protocols::cryst::MakeLatticeMover::setup_xtal_symminfo().

void core::conformation::symmetry::SymmetryInfo::num_virtuals

(

Size const

setting

)

References npseudo_.

bool core::conformation::symmetry::SymmetryInfo::read_silent_struct

(

std::string const &

filename

)

bool core::conformation::symmetry::SymmetryInfo::reset_score_multiply_to_reasonable_default

(

)

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

void core::conformation::symmetry::SymmetryInfo::resize_asu

(

Size

nres_new

)

References add_bb_clone(), add_chi_clone(), bb_clones_, bb_follows_, bb_is_independent(), chi_clones_, chi_follows_, last_indep_residue_, core::chemical::element::N, nres_monomer_, num_total_residues_with_pseudo(), num_total_residues_without_pseudo(), score_multiply_, scoring_subunit_, and subunits().

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

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

Size core::conformation::symmetry::SymmetryInfo::score_multiply_factor

(

)

const

References score_multiply_factor_.

Referenced by core::pack::hbonds::HBondGraphInitializerIG::find_symmetric_hbonds().

void core::conformation::symmetry::SymmetryInfo::set_dofs

(

std::map< Size, SymDof > const &

dofs

)

References dofs_.

Referenced by protocols::cryst::MakeLayerMover::setup_xtal_symminfo(), protocols::cryst::MakeLatticeMover::setup_xtal_symminfo(), and update_nmonomer_jumps().

void core::conformation::symmetry::SymmetryInfo::set_flat_score_multiply	(	Size const	nres,
		Size const	factor
	)

References score_multiply_.

Referenced by protocols::relax::RepeatProteinRelax::setup_repeat_symminfo(), protocols::cryst::MakeLayerMover::setup_xtal_symminfo(), and protocols::cryst::MakeLatticeMover::setup_xtal_symminfo().

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

References dofname2jnum_, and jnum2dofname_.

Referenced by protocols::cryst::MakeLayerMover::setup_xtal_symminfo(), and protocols::cryst::MakeLatticeMover::setup_xtal_symminfo().

void core::conformation::symmetry::SymmetryInfo::set_multicomponent_info	(	Size const &	num_components,
		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
	)

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

void core::conformation::symmetry::SymmetryInfo::set_nres_subunit

(

Size const

setting

)

References nres_monomer_.

Referenced by protocols::cryst::MakeLayerMover::setup_xtal_symminfo(), and protocols::cryst::MakeLatticeMover::setup_xtal_symminfo().

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

References score_multiply_.

Referenced by protocols::relax::RepeatProteinRelax::setup_repeat_symminfo(), protocols::cryst::MakeLayerMover::setup_xtal_symminfo(), and protocols::cryst::MakeLatticeMover::setup_xtal_symminfo().

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

References score_multiply_.

Referenced by initialize().

void core::conformation::symmetry::SymmetryInfo::set_use_symmetry

(

bool

setting

)

References use_symmetry_.

Referenced by core::conformation::symmetry::operator>>(), protocols::relax::RepeatProteinRelax::setup_repeat_symminfo(), protocols::cryst::MakeLayerMover::setup_xtal_symminfo(), and protocols::cryst::MakeLatticeMover::setup_xtal_symminfo().

Size core::conformation::symmetry::SymmetryInfo::subunit_index

(

Size const

seqpos

)

const

What subunit does a particular residue come from?

References bb_clones_, bb_follows_, contiguous_monomers_, and num_independent_residues().

Referenced by core::conformation::symmetry::calculate_inverting_virtuals(), core::pose::symmetry::get_symdof_subunits(), and interface_number().

Size core::conformation::symmetry::SymmetryInfo::subunits

(

)

const

References num_bb_clones().

Referenced by core::pack::interaction_graph::SymmOnTheFlyNode::compute_rotamer_pair_energy(), get_asymmetric_seqpos(), is_asymmetric_seqpos(), core::conformation::symmetry::operator<<(), core::conformation::symmetry::replaced_symmetric_foldtree_with_new_monomer(), resize_asu(), core::pack::interaction_graph::SymmOnTheFlyNode::set_rotamers(), and update_nmonomer_jumps().

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

private

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

inline

References torsion_changes_move_other_monomers_.

Referenced by protocols::relax::RepeatProteinRelax::setup_repeat_symminfo().

void core::conformation::symmetry::SymmetryInfo::torsion_changes_move_other_monomers ( bool const  setting )

inline

References torsion_changes_move_other_monomers_.

bool core::conformation::symmetry::SymmetryInfo::torsion_is_independent

(

TorsionID const &

id

)

const

References core::id::BB, bb_is_independent(), core::id::BRANCH, core::id::CHI, chi_is_independent(), core::id::JUMP, and jump_is_independent().

Referenced by dependent_torsions().

void core::conformation::symmetry::SymmetryInfo::update_contiguous_monomers ( )

private

this actually only tests to see if the independent residues are contiguous...

References bb_follows_, contiguous_monomers_, protocols::mean_field::max(), and protocols::mean_field::min().

Referenced by add_bb_clone().

void core::conformation::symmetry::SymmetryInfo::update_nmonomer_jumps

(

Size

nmonomer_new

)

References add_jump_clone(), dofname2jnum_, dofs_, jnum2dofname_, jump_clone_wts_, jump_clones_, jump_follows_, core::chemical::element::N, njump_monomer_, scoring_subunit_, set_dofs(), subunits(), and core::id::to_string().

void core::conformation::symmetry::SymmetryInfo::update_score_multiply_factor

(

)

References independent_residues(), score_multiply_, and score_multiply_factor_.

Referenced by initialize(), core::conformation::symmetry::operator>>(), protocols::relax::RepeatProteinRelax::setup_repeat_symminfo(), protocols::cryst::MakeLayerMover::setup_xtal_symminfo(), and protocols::cryst::MakeLatticeMover::setup_xtal_symminfo().

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

Member Data Documentation

std::map< Size, Clones > core::conformation::symmetry::SymmetryInfo::bb_clones_

private

Referenced by add_bb_clone(), bb_clones(), equivalent_residue_on_subunit(), initialize(), num_bb_clones(), num_independent_residues(), core::conformation::symmetry::operator<<(), core::conformation::symmetry::operator>>(), resize_asu(), and subunit_index().

std::map< Size, Size > core::conformation::symmetry::SymmetryInfo::bb_follows_

private

Referenced by add_bb_clone(), add_jump_clone(), bb_follows(), equivalent_residue_on_subunit(), core::conformation::symmetry::operator<<(), core::conformation::symmetry::operator>>(), resize_asu(), subunit_index(), and update_contiguous_monomers().

std::map< Size, Clones > core::conformation::symmetry::SymmetryInfo::chi_clones_

private

Referenced by add_chi_clone(), chi_clones(), initialize(), num_chi_clones(), core::conformation::symmetry::operator<<(), core::conformation::symmetry::operator>>(), and resize_asu().

std::map< Size, Size > core::conformation::symmetry::SymmetryInfo::chi_follows_

private

Referenced by add_chi_clone(), chi_follows(), core::conformation::symmetry::operator<<(), core::conformation::symmetry::operator>>(), and resize_asu().

std::map<char,std::pair<Size,Size> > core::conformation::symmetry::SymmetryInfo::component_bounds_

private

Referenced by get_component_bounds(), get_component_lower_bound(), get_component_of_residue(), get_component_upper_bound(), core::conformation::symmetry::operator<<(), core::conformation::symmetry::operator>>(), and set_multicomponent_info().

utility::vector1<char> core::conformation::symmetry::SymmetryInfo::components_

private

Referenced by get_component(), get_component_bounds(), get_component_lower_bound(), get_component_of_residue(), get_component_upper_bound(), get_components(), get_jump_name_to_components(), get_jump_name_to_subunits(), get_subunit_name_to_component(), core::conformation::symmetry::operator<<(), core::conformation::symmetry::operator>>(), and set_multicomponent_info().

bool core::conformation::symmetry::SymmetryInfo::contiguous_monomers_

private

Referenced by contiguous_monomers(), equivalent_residue_on_subunit(), init_defaults(), initialize(), subunit_index(), SymmetryInfo(), and update_contiguous_monomers().

std::map<std::string,Size> core::conformation::symmetry::SymmetryInfo::dofname2jnum_

private

Referenced by get_jump_num(), core::conformation::symmetry::operator<<(), core::conformation::symmetry::operator>>(), set_jump_name(), SymmetryInfo(), and update_nmonomer_jumps().

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

private

Referenced by get_dofs(), initialize(), num_slidablejumps(), core::conformation::symmetry::operator<<(), core::conformation::symmetry::operator>>(), set_dofs(), and update_nmonomer_jumps().

Clones core::conformation::symmetry::SymmetryInfo::empty_list

private

Referenced by bb_clones(), chi_clones(), and jump_clones().

Size core::conformation::symmetry::SymmetryInfo::interfaces_

private

Referenced by init_defaults(), initialize(), num_interfaces(), and core::conformation::symmetry::operator>>().

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

private

Referenced by get_jump_name_to_components(), core::conformation::symmetry::operator<<(), core::conformation::symmetry::operator>>(), and set_multicomponent_info().

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

private

Referenced by get_jump_name_to_subunits(), core::conformation::symmetry::operator<<(), core::conformation::symmetry::operator>>(), and set_multicomponent_info().

std::map<Size,std::string> core::conformation::symmetry::SymmetryInfo::jnum2dofname_

private

Referenced by get_jump_name(), core::conformation::symmetry::operator<<(), core::conformation::symmetry::operator>>(), set_jump_name(), SymmetryInfo(), and update_nmonomer_jumps().

std::map< Size, Real > core::conformation::symmetry::SymmetryInfo::jump_clone_wts_

private

Referenced by add_jump_clone(), get_dof_derivative_weight(), core::conformation::symmetry::operator<<(), core::conformation::symmetry::operator>>(), and update_nmonomer_jumps().

std::map< Size, Clones > core::conformation::symmetry::SymmetryInfo::jump_clones_

private

Referenced by add_jump_clone(), initialize(), jump_clones(), num_jump_clones(), core::conformation::symmetry::operator<<(), core::conformation::symmetry::operator>>(), and update_nmonomer_jumps().

std::map< Size, Size > core::conformation::symmetry::SymmetryInfo::jump_follows_

private

Referenced by add_jump_clone(), jump_follows(), core::conformation::symmetry::operator<<(), core::conformation::symmetry::operator>>(), and update_nmonomer_jumps().

Size core::conformation::symmetry::SymmetryInfo::last_indep_residue_

private

Referenced by init_defaults(), initialize(), last_independent_residue(), core::conformation::symmetry::operator>>(), and resize_asu().

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

private

Referenced by get_subunit_name_to_component(), core::conformation::symmetry::operator<<(), core::conformation::symmetry::operator>>(), and set_multicomponent_info().

Size core::conformation::symmetry::SymmetryInfo::njump_monomer_

private

Referenced by get_njumps_subunit(), init_defaults(), initialize(), core::conformation::symmetry::operator<<(), core::conformation::symmetry::operator>>(), and update_nmonomer_jumps().

Size core::conformation::symmetry::SymmetryInfo::npseudo_

private

Referenced by init_defaults(), initialize(), num_total_residues_with_pseudo(), num_virtuals(), core::conformation::symmetry::operator<<(), and core::conformation::symmetry::operator>>().

Size core::conformation::symmetry::SymmetryInfo::nres_monomer_

private

Referenced by equivalent_residue_on_subunit(), get_nres_subunit(), init_defaults(), initialize(), core::conformation::symmetry::operator<<(), core::conformation::symmetry::operator>>(), resize_asu(), and set_nres_subunit().

Size core::conformation::symmetry::SymmetryInfo::num_components_

private

Referenced by get_num_components(), init_defaults(), core::conformation::symmetry::operator<<(), core::conformation::symmetry::operator>>(), and set_multicomponent_info().

Real core::conformation::symmetry::SymmetryInfo::reweight_symm_interactions_

private

Referenced by deriv_multiply(), init_defaults(), and score_multiply().

utility::vector1< Real > core::conformation::symmetry::SymmetryInfo::score_multiply_

private

Referenced by core::conformation::symmetry::operator<<(), core::conformation::symmetry::operator>>(), reset_score_multiply_to_reasonable_default(), resize_asu(), score_multiply(), set_flat_score_multiply(), set_score_multiply(), set_score_multiply_from_subunit_factors(), and update_score_multiply_factor().

Real core::conformation::symmetry::SymmetryInfo::score_multiply_factor_

private

Referenced by init_defaults(), reset_score_multiply_to_reasonable_default(), score_multiply_factor(), and update_score_multiply_factor().

Size core::conformation::symmetry::SymmetryInfo::scoring_subunit_

private

Referenced by init_defaults(), initialize(), core::conformation::symmetry::operator<<(), core::conformation::symmetry::operator>>(), resize_asu(), and update_nmonomer_jumps().

SymSlideInfo core::conformation::symmetry::SymmetryInfo::slide_info_

private

Referenced by get_slide_info(), and initialize().

bool core::conformation::symmetry::SymmetryInfo::torsion_changes_move_other_monomers_

private

Referenced by init_defaults(), initialize(), SymmetryInfo(), and torsion_changes_move_other_monomers().

std::string core::conformation::symmetry::SymmetryInfo::type_

private

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

bool core::conformation::symmetry::SymmetryInfo::use_symmetry_

private

Referenced by get_use_symmetry(), init_defaults(), initialize(), and set_use_symmetry().

---

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

• src/core/conformation/symmetry/SymmetryInfo.hh
• src/core/conformation/symmetry/SymmetryInfo.cc