core::pose::symmetry Namespace Reference

Functions
static THREAD_LOCAL basic::Tracer	TR ("core.pose.symmetry.util")
bool	is_symmetric (scoring::Energies const &energies)
bool	is_symmetric (pose::Pose const &pose)
bool	is_mirror_symmetric (pose::Pose const &pose)
bool	is_symmetric (scoring::ScoreFunction const &scorefxn)
void	make_score_function_consistent_with_symmetric_state_of_pose (pose::Pose const &pose, scoring::ScoreFunctionOP &scorefxn)
conformation::symmetry::SymmetryInfoCOP	symmetry_info (pose::Pose const &pose)
bool	scorefxn_is_symmetric (conformation::Conformation const &conf)
bool	scorefxn_is_symmetric (pose::Pose const &pose)
void	make_symmetric_pose (pose::Pose &pose, conformation::symmetry::SymmetryInfo symmetry_info)
void	make_symmetric_pose (pose::Pose &pose, conformation::symmetry::SymmData &symmdata)
void	make_symmetric_pose (pose::Pose &pose, std::string symmdef_file)
void	make_asymmetric_pose (pose::Pose &pose)
void	extract_asymmetric_unit (core::pose::Pose const &pose_in, core::pose::Pose &pose_out, bool const with_virtual_atoms, bool const with_unknown_aa)
	extract the asu from a pose... unlike previous function symmetric clones are thrown out More...
core::pose::Pose	get_asymmetric_pose_copy_from_symmetric_pose (pose::Pose const &pose)
void	make_symmetric_pdb_info (pose::Pose const &pose, pose::PDBInfoOP pdb_info_src, pose::PDBInfoOP pdb_info_target)
void	extract_asymmetric_unit_pdb_info (pose::Pose const &pose, pose::PDBInfoCOP pdb_info_src, pose::PDBInfoOP pdb_info_target)
void	make_symmetric_movemap (pose::Pose const &pose, kinematics::MoveMap &movemap)
int	find_symmetric_basejump_anchor (pose::Pose &pose)
void	find_new_symmetric_jump_residues (core::pose::Pose &pose)
void	rotate_anchor_to_x_axis (core::pose::Pose &pose)
void	symmetrize_fold_tree (core::pose::Pose const &p, kinematics::FoldTree &f)
	Converts an asymmetric foldtree (f) with virtual root into a symmetric foldtree compatible with symmetric pose (p) More...
void	set_asymm_unit_fold_tree (core::pose::Pose &p, kinematics::FoldTree const &f)
void	partition_by_symm_jumps (utility::vector1< int > jump_numbers, core::kinematics::FoldTree const &ft, conformation::symmetry::SymmetryInfoCOP symm_info, ObjexxFCL::FArray1D_bool &partner1)
numeric::xyzVector< core::Real >	get_symm_axis (core::pose::Pose &pose)
core::pose::Pose	get_buildingblock_and_neighbor_subs (Pose const &pose_in, utility::vector1< Size > intra_subs)
core::pose::Pose	get_subpose (Pose const &pose, utility::vector1< std::string > subs)
utility::vector1< Size >	get_resis (Pose const &pose, utility::vector1< std::string > subs)
utility::vector1< std::string >	get_full_intracomponent_and_neighbor_subs (Pose const &pose, std::string sym_dof_name, Real contact_dist)
core::pose::Pose	get_full_intracomponent_and_neighbor_subpose (Pose const &pose, std::string sym_dof_name, Real contact_dist)
utility::vector1< Size >	get_full_intracomponent_and_neighbor_resis (Pose const &pose, std::string sym_dof_name, Real contact_dist)
core::pose::Pose	get_full_intracomponent_subpose (Pose const &pose, std::string sym_dof_name)
utility::vector1< Size >	get_full_intracomponent_resis (Pose const &pose, std::string sym_dof_name)
utility::vector1< std::string >	get_full_intracomponent_neighbor_subs (Pose const &pose, std::string sym_dof_name, Real contact_dist)
core::pose::Pose	get_full_intracomponent_neighbor_subpose (Pose const &pose, std::string sym_dof_name, Real contact_dist)
utility::vector1< Size >	get_full_intracomponent_neighbor_resis (Pose const &pose, std::string sym_dof_name, Real contact_dist)
bool	intracomponent_contact (Pose const &pose, std::string sym_dof_name, Real contact_dist)
utility::vector1< std::string >	get_intracomponent_and_neighbor_subs (Pose const &pose, std::string sym_dof_name, Real contact_dist)
core::pose::Pose	get_intracomponent_and_neighbor_subpose (Pose const &pose, std::string sym_dof_name, Real contact_dist)
utility::vector1< Size >	get_intracomponent_and_neighbor_resis (Pose const &pose, std::string sym_dof_name, Real contact_dist)
utility::vector1< std::string >	get_intracomponent_subs (Pose const &pose, std::string sym_dof_name, Real contact_dist)
core::pose::Pose	get_intracomponent_subpose (Pose const &pose, std::string sym_dof_name, Real contact_dist)
utility::vector1< Size >	get_intracomponent_resis (Pose const &pose, std::string sym_dof_name, Real contact_dist)
utility::vector1< std::string >	get_neighbor_subs (Pose const &pose, std::string sym_dof_name, Real contact_dist)
core::pose::Pose	get_neighbor_subpose (Pose const &pose, std::string sym_dof_name, Real contact_dist)
utility::vector1< Size >	get_neighbor_resis (Pose const &pose, std::string sym_dof_name, Real contact_dist)
utility::vector1< std::string >	get_intracomponent_and_intraneighbor_subs (Pose const &pose, std::string sym_dof_name, Real contact_dist)
core::pose::Pose	get_intracomponent_and_intraneighbor_subpose (Pose const &pose, std::string sym_dof_name, Real contact_dist)
utility::vector1< Size >	get_intracomponent_and_intraneighbor_resis (Pose const &pose, std::string sym_dof_name, Real contact_dist)
utility::vector1< std::string >	get_intracomponent_and_interneighbor_subs (Pose const &pose, std::string sym_dof_name, Real contact_dist)
core::pose::Pose	get_intracomponent_and_interneighbor_subpose (Pose const &pose, std::string sym_dof_name, Real contact_dist)
utility::vector1< Size >	get_intracomponent_and_interneighbor_resis (Pose const &pose, std::string sym_dof_name, Real contact_dist)
void	make_residue_mask_symmetric (core::pose::Pose const &p, utility::vector1< bool > &msk)
kinematics::FoldTree	sealed_symmetric_fold_tree (core::pose::Pose &pose)
int	get_sym_aware_jump_num (core::pose::Pose const &pose, core::Size jump_num)
utility::vector1< std::string >	sym_dof_names (core::pose::Pose const &pose)
int	sym_dof_jump_num (core::pose::Pose const &pose, std::string const &jname)
std::string	jump_num_sym_dof (core::pose::Pose const &pose, Size const &jnum)
utility::vector1< Size >	get_symdof_subunits (core::pose::Pose const &pose, std::string const &jname)
utility::vector1< char >	symmetric_components (core::pose::Pose const &pose)
bool	is_singlecomponent (core::pose::Pose const &pose)
bool	is_multicomponent (core::pose::Pose const &pose)
Size	get_component_lower_bound (core::pose::Pose const &pose, char c)
Size	get_component_upper_bound (core::pose::Pose const &pose, char c)
char	get_component_of_residue (core::pose::Pose const &pose, Size ir)
char	get_subunit_name_to_component (core::pose::Pose const &pose, std::string const &vname)
utility::vector1< char > const &	get_jump_name_to_components (core::pose::Pose const &pose, std::string const &jname)
utility::vector1< Size > const &	get_jump_name_to_subunits (core::pose::Pose const &pose, std::string const &jname)
std::string	get_resnum_to_subunit_component (core::pose::Pose const &pose, Size const &resnum)
utility::vector1< std::string >	get_full_intracomponent_subs (core::pose::Pose const &pose, std::string const &jname)

Function Documentation

void core::pose::symmetry::extract_asymmetric_unit	(	core::pose::Pose const &	pose_in,
		core::pose::Pose &	pose_out,
		bool const	with_virtual_atoms,
		bool const	with_unknown_aa
	)

extract the asu from a pose... unlike previous function symmetric clones are thrown out

Parameters

[in]	pose_in	Symmetric input pose containing the asymmetric subunit of interest
[out]	pose_out	Asymmetric subunit will be placed into this object
[in]	with_virtual_atoms	If true, virtual atoms related to symmetry will be kept with the asymmetric subunit. If false, virtual atoms will be removed (default=true)
[in]	with_unknown_aa	If false amino acids with type aa_unk will be ignored. If true, amino acids with type aa_unk will be extracted (default=false)
[in]	pose_in	Symmetric input pose containing the asymmetric subunit of interest
[out]	pose_out	Asymmetric subunit will be placed into this object
[in]	with_virtual_atoms	If true, virtual atoms related to symmetry will be kept with the asymmetric subunit. If false, virtual atoms will be removed (default=true)
[in]	with_unknown_aa	If false, amino acids with type aa_unk will be ignored. If true, amino acids with type aa_unk will be extracted (default=false)

References core::chemical::aa_h2o, core::chemical::aa_unk, core::chemical::aa_vrt, core::pose::addVirtualResAsRoot(), core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::pose::Pose::conformation(), core::conformation::Conformation::detect_disulfides(), extract_asymmetric_unit_pdb_info(), core::pose::Pose::fold_tree(), core::conformation::symmetry::get_asymm_unit_fold_tree(), core::pose::Pose::is_fullatom(), is_symmetric(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::Pose::secstruct(), core::pose::Pose::set_secstruct(), core::pose::Pose::size(), and core::conformation::symmetry::SymmetricConformation::Symmetry_Info().

Referenced by protocols::forge::remodel::RemodelGlobalFrame::align_segment(), protocols::hybridization::HybridizeProtocol::align_templates_by_domain(), protocols::loophash::LoopHashMoverWrapper::apply(), protocols::toolbox::task_operations::SelectBySASAOperation::apply(), protocols::rbsegment_relax::OptimizeThreadingMover::apply(), protocols::toolbox::task_operations::CrystalContactsOperation::apply(), protocols::toolbox::task_operations::RestrictNativeResiduesOperation::apply(), protocols::analysis::LoopAnalyzerMover::apply(), protocols::cryst::UpdateCrystInfo::apply(), protocols::simple_moves::PeriodicBoxMover::apply(), protocols::simple_moves::symmetry::ExtractAsymmetricUnitMover::apply(), protocols::toolbox::task_operations::DsspDesignOperation::apply(), protocols::flxbb::LayerDesignOperation::apply(), protocols::cryst::TagPoseWithRefinementStatsMover::apply(), protocols::forge::remodel::RemodelLoopMover::apply(), protocols::denovo_design::components::StructureData::check_pose_consistency(), protocols::simple_filters::GeometryFilter::compute(), protocols::simple_filters::MutationsFilter::compute(), protocols::protein_interface_design::filters::SequenceRecoveryFilter::compute(), core::scoring::cryst::PhenixInterface::fitBfactors(), protocols::cryst::DockLatticeMover::init(), core::scoring::cryst::PhenixInterface::initialize_target_evaluator(), protocols::forge::remodel::RemodelDesignMover::mode5_packertask(), protocols::simple_filters::RelativePoseFilter::parse_my_tag(), protocols::forge::remodel::RemodelLoopMover::repeat_propagation(), protocols::rbsegment_relax::setup_star_topology(), core::scoring::cryst::PhenixInterface::stealBfactorsFromFile(), and protocols::hybridization::HybridizeProtocol::validate_template().

void core::pose::symmetry::extract_asymmetric_unit_pdb_info	(	pose::Pose const &	pose,
		pose::PDBInfoCOP	pdb_info_src,
		pose::PDBInfoOP	pdb_info_target
	)

References core::pose::Pose::conformation(), is_symmetric(), and core::conformation::symmetry::SymmetricConformation::Symmetry_Info().

Referenced by extract_asymmetric_unit().

void core::pose::symmetry::find_new_symmetric_jump_residues

(

core::pose::Pose &

pose

)

References core::pose::Pose::conformation(), find_symmetric_basejump_anchor(), core::conformation::Conformation::fold_tree(), is_symmetric(), core::pose::Pose::residue(), core::scoring::rg, core::conformation::Conformation::size(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), and core::conformation::Residue::xyz().

Referenced by protocols::symmetric_docking::SymFoldandDockMoveRbJumpMover::apply().

int core::pose::symmetry::find_symmetric_basejump_anchor

(

pose::Pose &

pose

)

References core::pose::Pose::conformation(), core::kinematics::FoldTree::downstream_jump_residue(), core::conformation::Conformation::fold_tree(), core::kinematics::FoldTree::num_jump(), core::pose::Pose::residue(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by find_new_symmetric_jump_residues(), rotate_anchor_to_x_axis(), and protocols::simple_moves::symmetry::SymmetrySlider::very_far_away().

core::pose::Pose core::pose::symmetry::get_asymmetric_pose_copy_from_symmetric_pose

(

pose::Pose const &

pose

)

References core::chemical::aa_unk, core::chemical::aa_vrt, core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by protocols::fldsgn::CircularPermutation::apply().

core::pose::Pose core::pose::symmetry::get_buildingblock_and_neighbor_subs	(	Pose const &	pose_in,
		utility::vector1< Size >	intra_subs
	)

References core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::pose::Pose::energies(), core::scoring::fa_atr, is_multicomponent(), core::pose::Pose::residue(), core::scoring::Energies::residue_total_energies(), core::scoring::ScoreFunction::set_weight(), core::pose::Pose::size(), protocols::loops::start, and symmetry_info().

Referenced by protocols::matdes::InterfacePackingFilter::compute().

Size core::pose::symmetry::get_component_lower_bound	(	core::pose::Pose const &	pose,
		char	c
	)

References symmetry_info().

Referenced by protocols::matdes::get_intra_contacts(), and protocols::matdes::maximize_sub1_contact().

char core::pose::symmetry::get_component_of_residue	(	core::pose::Pose const &	pose,
		Size	ir
	)

References symmetry_info().

Referenced by protocols::matdes::ExtractSubposeMover::apply(), protocols::matdes::BuildingBlockInterfaceOperation::apply(), protocols::matdes::ClashCheckFilter::compute(), core::scoring::motif::MotifHash::get_matching_motifs(), and intracomponent_contact().

Size core::pose::symmetry::get_component_upper_bound	(	core::pose::Pose const &	pose,
		char	c
	)

References symmetry_info().

Referenced by protocols::matdes::get_intra_contacts(), and protocols::matdes::maximize_sub1_contact().

utility::vector1< Size > core::pose::symmetry::get_full_intracomponent_and_neighbor_resis	(	Pose const &	pose,
		std::string	sym_dof_name,
		Real	contact_dist
	)

References get_full_intracomponent_and_neighbor_subs(), and get_resis().

core::pose::Pose core::pose::symmetry::get_full_intracomponent_and_neighbor_subpose	(	Pose const &	pose,
		std::string	sym_dof_name,
		Real	contact_dist
	)

References get_full_intracomponent_and_neighbor_subs(), and get_subpose().

Referenced by protocols::simple_filters::InterfaceSasaFilter::compute().

utility::vector1< std::string > core::pose::symmetry::get_full_intracomponent_and_neighbor_subs	(	Pose const &	pose,
		std::string	sym_dof_name,
		Real	contact_dist
	)

References core::pose::Pose::fold_tree(), get_full_intracomponent_subs(), get_resnum_to_subunit_component(), is_singlecomponent(), core::conformation::Residue::name3(), core::kinematics::FoldTree::partition_by_jump(), core::pose::Pose::residue(), core::pose::Pose::size(), sym_dof_jump_num(), symmetry_info(), and core::conformation::Residue::xyz().

Referenced by get_full_intracomponent_and_neighbor_resis(), get_full_intracomponent_and_neighbor_subpose(), and get_full_intracomponent_neighbor_subs().

utility::vector1< Size > core::pose::symmetry::get_full_intracomponent_neighbor_resis	(	Pose const &	pose,
		std::string	sym_dof_name,
		Real	contact_dist
	)

References get_full_intracomponent_neighbor_subs(), and get_resis().

Referenced by protocols::simple_filters::ShapeComplementarityFilter::setup_multi_component_symm().

core::pose::Pose core::pose::symmetry::get_full_intracomponent_neighbor_subpose	(	Pose const &	pose,
		std::string	sym_dof_name,
		Real	contact_dist
	)

References get_full_intracomponent_neighbor_subs(), and get_subpose().

Referenced by protocols::simple_filters::InterfaceSasaFilter::compute().

utility::vector1< std::string > core::pose::symmetry::get_full_intracomponent_neighbor_subs	(	Pose const &	pose,
		std::string	sym_dof_name,
		Real	contact_dist
	)

References get_full_intracomponent_and_neighbor_subs(), get_full_intracomponent_subs(), and symmetry_info().

Referenced by get_full_intracomponent_neighbor_resis(), and get_full_intracomponent_neighbor_subpose().

utility::vector1< Size > core::pose::symmetry::get_full_intracomponent_resis	(	Pose const &	pose,
		std::string	sym_dof_name
	)

References get_full_intracomponent_subs(), and get_resis().

Referenced by protocols::simple_filters::ShapeComplementarityFilter::setup_multi_component_symm().

core::pose::Pose core::pose::symmetry::get_full_intracomponent_subpose	(	Pose const &	pose,
		std::string	sym_dof_name
	)

References get_full_intracomponent_subs(), and get_subpose().

Referenced by protocols::simple_filters::InterfaceSasaFilter::compute().

utility::vector1< std::string > core::pose::symmetry::get_full_intracomponent_subs	(	core::pose::Pose const &	pose,
		std::string const &	jname
	)

References core::pack::dunbrack::c, get_jump_name_to_components(), and get_jump_name_to_subunits().

Referenced by get_full_intracomponent_and_neighbor_subs(), get_full_intracomponent_neighbor_subs(), get_full_intracomponent_resis(), get_full_intracomponent_subpose(), get_intracomponent_and_interneighbor_subs(), get_intracomponent_subs(), get_neighbor_subs(), and intracomponent_contact().

utility::vector1< Size > core::pose::symmetry::get_intracomponent_and_interneighbor_resis	(	Pose const &	pose,
		std::string	sym_dof_name,
		Real	contact_dist
	)

References get_intracomponent_and_interneighbor_subs(), and get_resis().

core::pose::Pose core::pose::symmetry::get_intracomponent_and_interneighbor_subpose	(	Pose const &	pose,
		std::string	sym_dof_name,
		Real	contact_dist
	)

References get_intracomponent_and_interneighbor_subs(), and get_subpose().

utility::vector1< std::string > core::pose::symmetry::get_intracomponent_and_interneighbor_subs	(	Pose const &	pose,
		std::string	sym_dof_name,
		Real	contact_dist
	)

References get_full_intracomponent_subs(), get_intracomponent_and_neighbor_subs(), get_jump_name_to_components(), and symmetry_info().

Referenced by get_intracomponent_and_interneighbor_resis(), and get_intracomponent_and_interneighbor_subpose().

utility::vector1< Size > core::pose::symmetry::get_intracomponent_and_intraneighbor_resis	(	Pose const &	pose,
		std::string	sym_dof_name,
		Real	contact_dist
	)

References get_intracomponent_and_intraneighbor_subs(), and get_resis().

core::pose::Pose core::pose::symmetry::get_intracomponent_and_intraneighbor_subpose	(	Pose const &	pose,
		std::string	sym_dof_name,
		Real	contact_dist
	)

References get_intracomponent_and_intraneighbor_subs(), and get_subpose().

utility::vector1< std::string > core::pose::symmetry::get_intracomponent_and_intraneighbor_subs	(	Pose const &	pose,
		std::string	sym_dof_name,
		Real	contact_dist
	)

References get_intracomponent_and_neighbor_subs(), get_jump_name_to_components(), and symmetry_info().

Referenced by get_intracomponent_and_intraneighbor_resis(), and get_intracomponent_and_intraneighbor_subpose().

utility::vector1< Size > core::pose::symmetry::get_intracomponent_and_neighbor_resis	(	Pose const &	pose,
		std::string	sym_dof_name,
		Real	contact_dist
	)

References get_intracomponent_and_neighbor_subs(), and get_resis().

Referenced by protocols::matdes::ExtractSubposeMover::apply(), and protocols::matdes::InterfacePackingFilter::compute().

core::pose::Pose core::pose::symmetry::get_intracomponent_and_neighbor_subpose	(	Pose const &	pose,
		std::string	sym_dof_name,
		Real	contact_dist
	)

References get_intracomponent_and_neighbor_subs(), and get_subpose().

utility::vector1< std::string > core::pose::symmetry::get_intracomponent_and_neighbor_subs	(	Pose const &	pose,
		std::string	sym_dof_name,
		Real	contact_dist
	)

References core::pose::Pose::fold_tree(), get_resnum_to_subunit_component(), is_singlecomponent(), core::conformation::Residue::name3(), core::kinematics::FoldTree::partition_by_jump(), core::pose::Pose::residue(), core::pose::Pose::size(), protocols::loops::start, sym_dof_jump_num(), symmetry_info(), and core::conformation::Residue::xyz().

Referenced by get_intracomponent_and_interneighbor_subs(), get_intracomponent_and_intraneighbor_subs(), get_intracomponent_and_neighbor_resis(), get_intracomponent_and_neighbor_subpose(), get_intracomponent_subs(), and get_neighbor_subs().

utility::vector1< Size > core::pose::symmetry::get_intracomponent_resis	(	Pose const &	pose,
		std::string	sym_dof_name,
		Real	contact_dist
	)

References get_intracomponent_subs(), and get_resis().

core::pose::Pose core::pose::symmetry::get_intracomponent_subpose	(	Pose const &	pose,
		std::string	sym_dof_name,
		Real	contact_dist
	)

References get_intracomponent_subs(), and get_subpose().

utility::vector1< std::string > core::pose::symmetry::get_intracomponent_subs	(	Pose const &	pose,
		std::string	sym_dof_name,
		Real	contact_dist
	)

References get_full_intracomponent_subs(), get_intracomponent_and_neighbor_subs(), and symmetry_info().

Referenced by get_intracomponent_resis(), and get_intracomponent_subpose().

utility::vector1< char > const & core::pose::symmetry::get_jump_name_to_components	(	core::pose::Pose const &	pose,
		std::string const &	jname
	)

References symmetry_info().

Referenced by protocols::matdes::ExtractSubposeMover::apply(), get_full_intracomponent_subs(), get_intracomponent_and_interneighbor_subs(), and get_intracomponent_and_intraneighbor_subs().

utility::vector1< Size > const & core::pose::symmetry::get_jump_name_to_subunits	(	core::pose::Pose const &	pose,
		std::string const &	jname
	)

References symmetry_info().

Referenced by protocols::matdes::ExtractSubposeMover::apply(), protocols::matdes::BuildingBlockInterfaceOperation::apply(), protocols::simple_filters::InterfaceSasaFilter::compute(), protocols::matdes::ClashCheckFilter::compute(), get_full_intracomponent_subs(), core::scoring::motif::MotifHash::get_matching_motifs(), protocols::simple_filters::ShapeComplementarityFilter::setup_multi_component_symm(), and protocols::simple_filters::ShapeComplementarityFilter::write_area().

utility::vector1< Size > core::pose::symmetry::get_neighbor_resis	(	Pose const &	pose,
		std::string	sym_dof_name,
		Real	contact_dist
	)

References get_neighbor_subs(), and get_resis().

core::pose::Pose core::pose::symmetry::get_neighbor_subpose	(	Pose const &	pose,
		std::string	sym_dof_name,
		Real	contact_dist
	)

References get_neighbor_subs(), and get_subpose().

utility::vector1< std::string > core::pose::symmetry::get_neighbor_subs	(	Pose const &	pose,
		std::string	sym_dof_name,
		Real	contact_dist
	)

References get_full_intracomponent_subs(), get_intracomponent_and_neighbor_subs(), and symmetry_info().

Referenced by get_neighbor_resis(), and get_neighbor_subpose().

utility::vector1< Size > core::pose::symmetry::get_resis	(	Pose const &	pose,
		utility::vector1< std::string >	subs
	)

References get_resnum_to_subunit_component(), and symmetry_info().

Referenced by get_full_intracomponent_and_neighbor_resis(), get_full_intracomponent_neighbor_resis(), get_full_intracomponent_resis(), get_intracomponent_and_interneighbor_resis(), get_intracomponent_and_intraneighbor_resis(), get_intracomponent_and_neighbor_resis(), get_intracomponent_resis(), and get_neighbor_resis().

std::string core::pose::symmetry::get_resnum_to_subunit_component	(	core::pose::Pose const &	pose,
		Size const &	resnum
	)

References symmetry_info().

Referenced by get_full_intracomponent_and_neighbor_subs(), get_intracomponent_and_neighbor_subs(), get_resis(), get_subpose(), and intracomponent_contact().

core::pose::Pose core::pose::symmetry::get_subpose	(	Pose const &	pose,
		utility::vector1< std::string >	subs
	)

References get_resnum_to_subunit_component(), core::pose::Pose::residue(), protocols::loops::start, and symmetry_info().

Referenced by get_full_intracomponent_and_neighbor_subpose(), get_full_intracomponent_neighbor_subpose(), get_full_intracomponent_subpose(), get_intracomponent_and_interneighbor_subpose(), get_intracomponent_and_intraneighbor_subpose(), get_intracomponent_and_neighbor_subpose(), get_intracomponent_subpose(), and get_neighbor_subpose().

char core::pose::symmetry::get_subunit_name_to_component	(	core::pose::Pose const &	pose,
		std::string const &	vname
	)

References symmetry_info().

int core::pose::symmetry::get_sym_aware_jump_num	(	core::pose::Pose const &	pose,
		core::Size	jump_num
	)

References core::sequence::end, is_symmetric(), and symmetry_info().

Referenced by protocols::toolbox::task_operations::SelectBySASAOperation::apply(), protocols::simple_filters::InterfaceSasaFilter::compute(), protocols::matdes::InterfacePackingFilter::compute(), protocols::simple_filters::RotamerBoltzmannWeight::compute(), protocols::simple_filters::TaskAwareScoreTypeFilter::compute(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::matdes::SymUnsatHbondFilter::compute(), protocols::simple_filters::TaskAwareSASAFilter::compute(), protocols::matdes::OligomericAverageDegreeFilter::compute(), protocols::matdes::GetRBDOFValues::compute(), protocols::simple_filters::InterfaceSasaFilter::parse_my_tag(), protocols::simple_filters::ShapeComplementarityFilter::setup_single_component_symm(), and protocols::simple_filters::ShapeComplementarityFilter::write_area().

utility::vector1< Size > core::pose::symmetry::get_symdof_subunits	(	core::pose::Pose const &	pose,
		std::string const &	jname
	)

References core::pose::Pose::fold_tree(), core::conformation::symmetry::SymmetryInfo::get_nres_subunit(), is_symmetric(), core::conformation::symmetry::SymmetryInfo::num_total_residues_without_pseudo(), core::kinematics::FoldTree::partition_by_jump(), core::pose::Pose::size(), core::conformation::symmetry::SymmetryInfo::subunit_index(), sym_dof_jump_num(), and symmetry_info().

numeric::xyzVector< core::Real > core::pose::symmetry::get_symm_axis

(

core::pose::Pose &

pose

)

References core::pose::Pose::conformation(), is_symmetric(), core::pose::Pose::residue(), protocols::comparative_modeling::features::X, core::conformation::Residue::xyz(), and core::chemical::element::Y.

bool core::pose::symmetry::intracomponent_contact	(	Pose const &	pose,
		std::string	sym_dof_name,
		Real	contact_dist
	)

References core::pose::Pose::fold_tree(), get_component_of_residue(), get_full_intracomponent_subs(), get_resnum_to_subunit_component(), is_singlecomponent(), core::conformation::Residue::name3(), core::kinematics::FoldTree::partition_by_jump(), core::pose::Pose::residue(), core::pose::Pose::size(), protocols::loops::start, sym_dof_jump_num(), symmetry_info(), and core::conformation::Residue::xyz().

Referenced by protocols::simple_filters::ShapeComplementarityFilter::setup_multi_component_symm().

bool core::pose::symmetry::is_mirror_symmetric

(

pose::Pose const &

pose

)

Attempt to detect whether a pose is symmetric

References core::pose::Pose::conformation(), and core::conformation::symmetry::is_mirror_symmetric().

Referenced by core::io::silent::BinarySilentStruct::fill_pose().

bool core::pose::symmetry::is_multicomponent

(

core::pose::Pose const &

pose

)

References symmetry_info().

Referenced by protocols::simple_filters::InterfaceSasaFilter::compute(), get_buildingblock_and_neighbor_subs(), core::scoring::motif::MotifHash::get_matching_motifs(), and protocols::simple_filters::InterfaceSasaFilter::parse_my_tag().

bool core::pose::symmetry::is_singlecomponent

(

core::pose::Pose const &

pose

)

References symmetry_info().

Referenced by get_full_intracomponent_and_neighbor_subs(), get_intracomponent_and_neighbor_subs(), and intracomponent_contact().

bool core::pose::symmetry::is_symmetric

(

scoring::Energies const &

energies

)

Referenced by protocols::forge::remodel::RemodelLoopMover::abinitio_stage(), protocols::membrane::symmetry::SymmetricAddMembraneMover::add_membrane_virtual(), protocols::topology_broker::MembraneTopologyClaimer::add_mover(), protocols::simple_moves::StructProfileMover::add_MSAcst_to_pose(), protocols::hybridization::add_non_protein_cst(), protocols::fibril::SetupForFibrilMover::align(), protocols::hybridization::HybridizeProtocol::align_templates_by_domain(), protocols::matdes::MotifHitsRotamersOperation::alter_rotamer_set(), protocols::electron_density::ScaleMapIntensities::apply(), protocols::forge::remodel::RemodelRotamerLinks::apply(), protocols::electron_density::ReportFSC::apply(), protocols::loophash::LoopHashMoverWrapper::apply(), protocols::toolbox::task_operations::StoreTaskMover::apply(), protocols::protein_interface_design::movers::RandomMutation::apply(), protocols::toolbox::task_operations::StoreCombinedStoredTasksMover::apply(), protocols::matdes::SchemePlaceMotifsMover::apply(), protocols::protein_interface_design::movers::NucleotideMutation::apply(), protocols::symmetric_docking::SymFoldandDockSlideTrialMover::apply(), protocols::toolbox::task_operations::SelectBySASAOperation::apply(), protocols::pose_length_moves::FixAllLoopsMover::apply(), protocols::protein_interface_design::filters::FilterScanFilter::apply(), protocols::simple_moves::symmetry::SymmetricRMSMover::apply(), protocols::simple_moves::symmetry::SetupForSymmetryMover::apply(), protocols::toolbox::task_operations::StoreCompoundTaskMover::apply(), protocols::fibril::SetupForFibrilMover::apply(), protocols::rbsegment_relax::OptimizeThreadingMover::apply(), protocols::denovo_design::movers::SealFoldTreeMover::apply(), protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::apply(), protocols::normalmode::NormalModeMinimizer::apply(), protocols::matdes::SymDofMover::apply(), protocols::symmetric_docking::SymFoldandDockRbTrialMover::apply(), protocols::hybridization::CartesianSampler::apply(), protocols::md::CartesianMD::apply(), protocols::toolbox::task_operations::RestrictNativeResiduesOperation::apply(), protocols::simple_moves::ReturnSidechainMover::apply(), protocols::simple_moves::ConsensusDesignMover::apply(), core::pack::task::operation::NoRepackDisulfides::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::simple_moves::symmetry::SymDockingInitialPerturbation::apply(), protocols::toolbox::task_operations::JointSequenceOperation::apply(), protocols::denovo_design::movers::FoldTreeFromFoldGraphMover::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::denovo_design::residue_selectors::NamedSegmentSelector::apply(), protocols::toolbox::task_operations::SeqprofConsensusOperation::apply(), protocols::simple_moves::BackboneMover::apply(), protocols::rigid::WholeBodyTranslationMover::apply(), protocols::simple_moves::ReportEffectivePKA::apply(), protocols::relax::LocalRelax::apply(), protocols::relax::ClassicRelax::apply(), protocols::electron_density::BfactorFittingMover::apply(), protocols::simple_moves::symmetry::SymDockingSlideIntoContact::apply(), protocols::rigid::WholeBodyRotationMover::apply(), protocols::relax::CentroidRelax::apply(), protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::idealize::IdealizeMover::apply(), protocols::simple_moves::symmetry::ExtractAsymmetricUnitMover::apply(), protocols::toolbox::task_operations::DsspDesignOperation::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::simple_moves::symmetry::FaSymDockingSlideTogether::apply(), protocols::fldsgn::CircularPermutation::apply(), protocols::relax::FastRelax::apply(), protocols::hybridization::FoldTreeHybridize::apply(), protocols::toolbox::task_operations::RestrictToInterface::apply(), protocols::simple_moves::symmetry::ExtractAsymmetricPoseMover::apply(), protocols::flxbb::LayerDesignOperation::apply(), protocols::cryst::TagPoseWithRefinementStatsMover::apply(), protocols::denovo_design::movers::SetPoseSecstructFromStructureDataMover::apply(), protocols::hbnet::HBNet::apply(), protocols::forge::components::VarLengthBuild::apply(), protocols::hybridization::CartesianSampler::apply_constraints(), protocols::hybridization::CartesianHybridize::apply_frame(), protocols::hybridization::CartesianSampler::apply_frame(), protocols::idealize::basic_idealize(), protocols::relax::FastRelax::batch_apply(), protocols::electron_density::BfactorMultifunc::BfactorMultifunc(), protocols::forge::remodel::RemodelLoopMover::boost_closure_stage(), core::pack::rotamer_set::RotamerSets::build_rotamers(), core::scoring::CA_rmsd_symmetric(), protocols::hybridization::FragmentBiasAssigner::cal_perrsd_score(), protocols::simple_moves::StructProfileMover::calc_cenlist(), protocols::symmetric_docking::SymDockProtocol::calc_interaction_energy(), protocols::symmetric_docking::SymDockProtocol::calc_rms(), protocols::simple_moves::ddG::calculate(), core::scoring::fiber_diffraction::FiberDiffractionEnergyDens::calculate_rho_fast2(), protocols::fldsgn::BluePrintBDR::centroid_build(), protocols::hybridization::HybridizeProtocol::check_and_create_fragments(), protocols::denovo_design::components::StructureData::check_pose_consistency(), protocols::simple_moves::PeriodicBoxMover::check_virial_pressure(), protocols::jumping::close_chainbreaks(), protocols::relax::FastRelax::cmd_accept_to_best(), protocols::simple_filters::InterfaceSasaFilter::compute(), protocols::simple_filters::MutationsFilter::compute(), protocols::protein_interface_design::filters::SequenceRecoveryFilter::compute(), protocols::protein_interface_design::filters::BindingStrainFilter::compute(), protocols::protein_interface_design::filters::DesignableResiduesFilter::compute(), protocols::cryst::ReportGradientsMover::compute(), protocols::simple_filters::TaskAwareScoreTypeFilter::compute(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::simple_filters::LeastNativeLike9merFilter::compute(), protocols::simple_filters::ShapeComplementarityFilter::compute(), protocols::simple_filters::RotamerBoltzmannWeight::compute_Boltzmann_weight(), core::scoring::SmoothEnvPairPotential::compute_centroid_environment(), protocols::simple_filters::SymmetricMotifFilter::compute_d2(), core::scoring::SmoothEnvPairPotential::compute_dcentroid_environment(), core::scoring::MembranePotential::compute_membrane_embedding(), protocols::constraint_generator::compute_nres_in_asymmetric_unit(), core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::compute_one_body_energies(), core::pack::interaction_graph::SurfacePotential::compute_pose_surface_energy(), protocols::simple_moves::ConsensusDesignMover::create_consensus_design_task(), protocols::denovo_design::components::RemodelLoopMoverPoseFolder::create_false_movemap(), core::pack::interaction_graph::InteractionGraphFactory::create_interaction_graph(), protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator::create_rotamer_set(), protocols::cryst::crystRMS(), core::scoring::electron_density::ElectronDensity::dCCdBs(), protocols::simple_filters::DdGScan::ddG_for_single_residue(), protocols::hybridization::FragmentBiasAssigner::density(), protocols::hybridization::FragmentBiasAssigner::density_nbr(), protocols::electron_density::BfactorMultifunc::dfunc(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::disulfides_changed(), protocols::loop_modeling::refiners::MinimizationRefiner::do_apply(), protocols::hybridization::HybridizeProtocol::do_intrastage_docking(), protocols::relax::FastRelax::do_minimize(), protocols::electron_density::dockPoseIntoMap(), protocols::simple_moves::ClassicFragmentMover::end_bias_check(), protocols::rigid::MovePoseToMembraneCenterMover::estimate_membrane_center(), core::scoring::methods::ChainbreakEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensCenEnergy::eval_atom_derivative(), core::scoring::methods::RG_Energy_Fast::eval_atom_derivative(), core::scoring::electron_density::ElecDensEnergy::eval_atom_derivative(), core::scoring::electron_density::FastDensEnergy::eval_residue_pair_derivatives(), core::scoring::SmoothEnvPairPotential::evaluate_env_and_cbeta_deriv(), core::scoring::SmoothEnvPairPotential::evaluate_env_and_cbeta_scores(), extract_asymmetric_unit(), extract_asymmetric_unit_pdb_info(), core::io::silent::BinarySilentStruct::fill_pose(), core::io::silent::BinarySilentStruct::fill_struct(), protocols::rosetta_scripts::ParsedProtocol::final_score(), core::scoring::methods::ChainbreakEnergy::finalize_total_energy(), core::scoring::methods::CenPairMotifDegreeEnergy::finalize_total_energy(), core::scoring::methods::CenPairMotifEnergy::finalize_total_energy(), core::scoring::methods::D2H_SA_Energy::finalize_total_energy(), core::scoring::methods::MembraneLipo::finalize_total_energy(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::find_disulfides(), core::scoring::fiber_diffraction::find_max_r(), core::scoring::fiber_diffraction::find_min_xyz(), find_new_symmetric_jump_residues(), core::scoring::fiber_diffraction::find_num_scattering_atoms(), core::scoring::fiber_diffraction::find_pitch(), protocols::denovo_design::DisulfidizeMover::find_possible_disulfides(), protocols::hybridization::generate_centroid_constraints(), protocols::simple_moves::StructProfileMover::generate_counts(), protocols::simple_moves::StructProfileMover::generate_profile_score_wo_background(), protocols::simple_moves::StructProfileMover::get_closest_sequences(), protocols::simple_filters::SSElementBisectddGFilter::get_ddg_bisect_score(), protocols::cluster::GatherPosesMover::get_distance_measure(), core::indexed_structure_store::FragmentLookup::get_fragment_residue_spans(), core::scoring::motif::MotifHash::get_matching_motifs(), protocols::relax::LocalRelax::get_neighbor_graph(), protocols::cryst::get_nres_asu(), protocols::hybridization::get_num_residues_nonvirt(), protocols::hybridization::get_num_residues_prot(), protocols::fldsgn::potentials::SetSecStructEnergies::get_secstruct(), protocols::simple_filters::SSElementMotifContactFilter::get_ss_elements(), protocols::simple_filters::SSElementBisectddGFilter::get_ss_elements(), protocols::simple_filters::SSElementMotifContactFilter::get_SSelements_in_contact(), get_sym_aware_jump_num(), get_symdof_subunits(), get_symm_axis(), core::util::getMLweight(), core::util::getMLweight_cart(), protocols::hbnet::hbnet_symm_one_body_energies(), core::scoring::SecondaryStructurePotential::hspair(), protocols::forge::remodel::RemodelLoopMover::independent_stage(), protocols::hybridization::FragmentBiasAssigner::init(), core::scoring::motif::ResPairMotifQuery::init(), protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator::init_minmover(), protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator::init_task(), protocols::hybridization::HybridizeFoldtreeDynamic::initialize(), protocols::hybridization::HybridizeProtocol::initialize_and_sample_loops(), protocols::topology_broker::FoldandDockClaimer::initialize_dofs(), protocols::topology_broker::MembraneTopologyClaimer::initialize_dofs(), core::scoring::PolymerBondedEnergyContainer::initialize_peptide_bonded_pair_indices(), protocols::forge::remodel::RemodelLoopMover::insert_random_smallestmer_per_loop(), core::scoring::PolymerBondedEnergyContainer::is_valid(), protocols::forge::remodel::RemodelLoopMover::loophash_stage(), protocols::loops::loops_set_move_map(), make_asymmetric_pose(), protocols::topology_broker::FibrilModelingClaimer::make_fibril(), core::pack::make_new_symmetric_PackerTask_by_intersection(), core::pack::make_new_symmetric_PackerTask_by_requested_method(), core::pack::make_new_symmetric_PackerTask_by_truncation(), core::pack::make_new_symmetric_PackerTask_by_union(), make_residue_mask_symmetric(), make_score_function_consistent_with_symmetric_state_of_pose(), make_symmetric_movemap(), core::pack::make_symmetric_PackerTask_by_truncation(), make_symmetric_pdb_info(), make_symmetric_pose(), protocols::simple_moves::symmetry::SymRotamerTrialsMover::make_symmetric_task(), protocols::simple_moves::symmetry::SymEnergyCutRotamerTrialsMover::make_symmetric_task(), protocols::loops::loop_mover::refine::ShearMinCCDTrial::minimizer(), protocols::loops::loop_mover::refine::SmallMinCCDTrial::minimizer(), protocols::forge::remodel::RemodelDesignMover::mode5_packertask(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), protocols::cryst::ReportGradientsMover::normalization(), protocols::hybridization::FragmentBiasAssigner::old_rama(), protocols::electron_density::BfactorMultifunc::operator()(), core::scoring::symmetry::SymmetricScoreFunction::operator()(), core::scoring::ScoreFunction::operator()(), protocols::hybridization::MRMover::pack_missing_sidechains(), core::pack::pack_rotamers(), protocols::simple_filters::RelativePoseFilter::parse_my_tag(), protocols::simple_filters::InterfaceSasaFilter::parse_my_tag(), protocols::features::InterfaceDdGMover::parse_my_tag(), protocols::comparative_modeling::pick_loops_chainbreak(), protocols::comparative_modeling::GenericJobInputter::pose_from_job(), protocols::jd2::LargeNstructJobInputter::pose_from_job(), protocols::jd2::SilentFileJobInputter::pose_from_job(), protocols::topology_broker::MembraneTopologyClaimer::pre_process(), protocols::denovo_design::DisulfidizeMover::process_pose(), protocols::forge::remodel::RemodelLoopMover::randomize_stage(), core::util::rebuild_disulfide(), protocols::forge::remodel::RemodelLoopMover::repeat_propagation(), protocols::simple_filters::ConstraintScoreFilter::report_sm(), protocols::simple_filters::AlaScan::report_symmetry(), core::scoring::electron_density::ElectronDensity::rescale_fastscoring_temp_bins(), core::scoring::methods::MembraneCenPairEnergy::residue_pair_energy(), core::scoring::electron_density::FastDensEnergy::residue_pair_energy(), core::scoring::membrane::MPPairEnergy::residue_pair_energy(), core::scoring::electron_density::ElecDensEnergy::residue_pair_energy(), core::pack::rotamer_trials(), core::optimization::AtomTreeMinimizer::run(), protocols::simple_moves::StructProfileMover::save_MSAcst_file(), protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::score(), core::scoring::MembranePotential::score_normal_center(), sealed_symmetric_fold_tree(), protocols::symmetric_docking::SymDockingLowRes::set_default_protocol(), protocols::symmetric_docking::SymDockingHiRes::set_dock_mcm_protocol(), protocols::symmetric_docking::SymDockingHiRes::set_dock_ppk_protocol(), protocols::forge::remodel::RemodelLoopMover::set_segment_stage(), protocols::hbnet::HBNet::set_symmetry(), protocols::simple_moves::symmetry::SymmetrySlider::setup(), protocols::relax::CentroidRelax::setup_class_movemap_and_constraints(), core::scoring::fiber_diffraction::setup_cylindrical_coords(), protocols::hybridization::FoldTreeHybridize::setup_foldtree(), core::scoring::methods::SmoothEnvEnergy::setup_for_derivatives(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::setup_for_derivatives(), core::scoring::electron_density::ElecDensCenEnergy::setup_for_derivatives(), core::scoring::electron_density::ElecDensEnergy::setup_for_derivatives(), core::scoring::methods::EnvSmoothEnergy::setup_for_derivatives(), core::scoring::electron_density::FastDensEnergy::setup_for_derivatives(), core::scoring::methods::RG_Energy_Fast::setup_for_derivatives(), core::scoring::fiber_diffraction::FiberDiffractionEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::setup_for_scoring(), core::scoring::electron_density::FastDensEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensCenEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensEnergy::setup_for_scoring(), core::scoring::fiber_diffraction::FiberDiffractionEnergyDens::setup_for_scoring(), core::scoring::methods::CartesianBondedEnergy::setup_for_scoring(), protocols::idealize::IdealizeMover::setup_idealize_constraints(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::setup_movemap(), protocols::simple_moves::ddG::setup_task(), core::scoring::SecondaryStructurePotential::sheets_from_dimers(), protocols::protein_interface_design::filters::FilterScanFilter::single_substitution(), protocols::simple_moves::symmetry::SymmetrySlider::slide(), protocols::simple_moves::symmetry::SymmetrySlider::slide_away(), core::scoring::SecondaryStructurePotential::sspair(), core::util::switch_to_residue_type_set(), protocols::electron_density::symmetrizeBfactors(), symmetry_info(), protocols::protein_interface_design::SymMinimizeInterface(), core::scoring::MembranePotential::termini_penalty(), protocols::simple_filters::RelativePoseFilter::thread_seq(), protocols::features::InterfaceDdGMover::unbind(), protocols::simple_moves::ddG::unbind(), protocols::hybridization::HybridizeFoldtreeDynamic::update(), core::scoring::Energies::update_neighbor_links(), and protocols::simple_filters::ShapeComplementarityFilter::write_area().

bool core::pose::symmetry::is_symmetric

(

pose::Pose const &

pose

)

Attempt to detect whether a pose is symmetric

References core::pose::Pose::conformation(), and core::conformation::symmetry::is_symmetric().

bool core::pose::symmetry::is_symmetric

(

scoring::ScoreFunction const &

scorefxn

)

Referenced by protocols::forge::methods::fill_non_loop_cst_set(), and protocols::membrane::symmetry::symmetrize_spans().

std::string core::pose::symmetry::jump_num_sym_dof	(	core::pose::Pose const &	pose,
		Size const &	jnum
	)

References symmetry_info().

Referenced by protocols::simple_filters::InterfaceSasaFilter::parse_my_tag().

void core::pose::symmetry::make_asymmetric_pose

(

pose::Pose &

pose

)

References core::pose::Pose::conformation(), core::pose::Pose::energies(), is_symmetric(), core::pose::Pose::set_new_conformation(), and core::pose::Pose::set_new_energies_object().

Referenced by protocols::fldsgn::CircularPermutation::apply(), protocols::topology_broker::TopologyBroker::apply(), protocols::simple_moves::symmetry::ExtractAsymmetricPoseMover::apply(), protocols::sasa_scores::compute_avge_scores(), core::io::silent::BinarySilentStruct::fill_pose(), protocols::comparative_modeling::GenericJobInputter::pose_from_job(), protocols::jd2::LargeNstructJobInputter::pose_from_job(), protocols::jd2::SilentFileJobInputter::pose_from_job(), and protocols::features::DatabaseJobInputter::pose_from_job().

void core::pose::symmetry::make_residue_mask_symmetric	(	core::pose::Pose const &	p,
		utility::vector1< bool > &	msk
	)

References core::pose::Pose::conformation(), is_symmetric(), and core::conformation::symmetry::SymmetricConformation::Symmetry_Info().

Referenced by protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::toolbox::task_operations::RestrictToLoops::apply_helper(), protocols::loop_modeling::utilities::PrepareForFullatom::do_apply(), and protocols::hybridization::MRMover::pack_missing_sidechains().

void core::pose::symmetry::make_score_function_consistent_with_symmetric_state_of_pose	(	pose::Pose const &	pose,
		scoring::ScoreFunctionOP &	scorefxn
	)

References is_symmetric().

Referenced by protocols::denovo_design::components::RemodelLoopMoverPoseFolder::create_scorefxn(), protocols::features::get_current_model_score(), protocols::denovo_design::movers::get_score_function(), protocols::features::ResidueScoresFeatures::insert_residue_scores_rows(), protocols::features::TotalScoreFeatures::report_features(), protocols::features::StructureScoresFeatures::report_features(), protocols::features::RotamerRecoveryFeatures::report_features(), protocols::features::ResidueTotalScoresFeatures::report_features(), protocols::features::HBondFeatures::report_features(), and protocols::simple_filters::ConstraintScoreFilter::report_sm().

void core::pose::symmetry::make_symmetric_movemap	(	pose::Pose const &	pose,
		kinematics::MoveMap &	movemap
	)

References core::conformation::symmetry::SymDof::allow_dof(), core::pose::Pose::conformation(), core::id::D, core::conformation::Conformation::dof_id_from_torsion_id(), core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), core::kinematics::MoveMap::get(), core::pose::Pose::has_dof(), is_symmetric(), core::id::JUMP, core::conformation::Residue::natoms(), core::pose::Pose::num_jump(), core::pose::Pose::residue(), core::kinematics::MoveMap::set(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), core::kinematics::MoveMap::set_jump(), core::conformation::Conformation::size(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), core::id::THETA, core::kinematics::FoldTree::upstream_jump_residue(), core::conformation::symmetry::X_ANGLE_DOF, core::conformation::symmetry::X_DOF, core::conformation::symmetry::Y_ANGLE_DOF, core::conformation::symmetry::Y_DOF, core::conformation::symmetry::Z_ANGLE_DOF, and core::conformation::symmetry::Z_DOF.

Referenced by protocols::simple_moves::symmetry::TaskAwareSymMinMover::apply(), protocols::symmetric_docking::SymSidechainMinMover::apply(), protocols::hybridization::CartesianSampler::apply(), protocols::md::CartesianMD::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::simple_moves::symmetry::SymMinMover::apply(), protocols::simple_moves::BackboneMover::apply(), protocols::relax::LocalRelax::apply(), protocols::relax::ClassicRelax::apply(), protocols::symmetric_docking::SymInterfaceSidechainMinMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::relax::FastRelax::apply(), protocols::cryst::DockLatticeMover::apply(), protocols::hybridization::FoldTreeHybridize::apply(), protocols::idealize::basic_idealize(), protocols::relax::FastRelax::batch_apply(), protocols::simple_moves::PeriodicBoxMover::check_virial_pressure(), protocols::cryst::ReportGradientsMover::compute(), protocols::simple_filters::RotamerBoltzmannWeight::compute_Boltzmann_weight(), protocols::denovo_design::components::RemodelLoopMoverPoseFolder::create_false_movemap(), protocols::loop_modeling::utilities::PrepareForFullatom::do_apply(), protocols::hybridization::HybridizeProtocol::do_intrastage_docking(), protocols::electron_density::dockPoseIntoMap(), core::util::getMLweight(), core::util::getMLweight_cart(), protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator::init_minmover(), protocols::floppy_tail::FloppyTailMover::init_on_new_input(), protocols::topology_broker::FoldandDockClaimer::initialize_dofs(), protocols::topology_broker::FibrilModelingClaimer::initialize_dofs(), protocols::loops::loops_set_move_map(), protocols::cryst::DockLatticeMover::min_lattice(), protocols::simple_moves::symmetry::SymShakeStructureMover::minimize_with_constraints(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop(), protocols::hbnet::HBNet::place_rotamers_and_score(), core::util::rebuild_disulfide(), protocols::simple_moves::symmetry::SymShakeStructureMover::run_mc(), protocols::symmetric_docking::SymDockingHiRes::set_default(), protocols::symmetric_docking::SymDockingLowRes::set_default_move_map(), protocols::relax::CentroidRelax::setup_class_movemap_and_constraints(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::setup_movemap(), protocols::topology_broker::TopologyBroker::switch_to_fullatom(), and protocols::protein_interface_design::SymMinimizeInterface().

void core::pose::symmetry::make_symmetric_pdb_info	(	pose::Pose const &	pose,
		pose::PDBInfoOP	pdb_info_src,
		pose::PDBInfoOP	pdb_info_target
	)

References core::pose::Pose::conformation(), is_symmetric(), and core::pose::Pose::size().

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

void core::pose::symmetry::make_symmetric_pose	(	pose::Pose &	pose,
		conformation::symmetry::SymmetryInfo	symmetry_info
	)

constructs a symmetric pose with a symmetric conformation and energies object from a monomeric pose and symmetryinfo object. Unlike the version of make_symmetric_pose from symmdata, this does not expand the pose; it assumes the symmetric fold tree and residues are already present For example, this is used to reconstruct a symm pose from a silent file All data in the pose datacache will be cleared

References core::pose::Pose::conformation(), core::conformation::Conformation::detect_bonds(), core::pose::Pose::energies(), core::chemical::ResidueType::is_inverted_virtual_residue(), is_symmetric(), core::pose::Pose::pdb_info(), core::pose::Pose::residue_type(), core::pose::Pose::set_new_conformation(), core::pose::Pose::set_new_energies_object(), core::pose::Pose::size(), and symmetry_info().

Referenced by protocols::simple_moves::symmetry::DetectSymmetry::apply(), protocols::matdes::SymDofMover::apply(), protocols::cryst::MakeLayerMover::apply(), protocols::cryst::MakeLatticeMover::apply(), core::io::silent::BinarySilentStruct::fill_pose(), protocols::fibril::make_symmetric_fibril(), protocols::simple_moves::symmetry::SetupForSymmetryMover::make_symmetric_pose(), make_symmetric_pose(), protocols::simple_filters::RelativePoseFilter::parse_my_tag(), and protocols::simple_moves::PeriodicBoxMover::setup_pose().

void core::pose::symmetry::make_symmetric_pose	(	pose::Pose &	pose,
		conformation::symmetry::SymmData &	symmdata
	)

constructs a symmetric pose with a symmetric conformation and energies object from a monomeric pose and symmData object

References core::pose::conf2pdb_chain(), core::pose::Pose::conformation(), core::conformation::Conformation::detect_bonds(), core::conformation::Conformation::detect_disulfides(), core::pose::Pose::energies(), is_symmetric(), make_symmetric_pdb_info(), core::pose::Pose::pdb_info(), core::pose::Pose::set_new_conformation(), core::pose::Pose::set_new_energies_object(), and core::conformation::symmetry::setup_symmetric_conformation().

void core::pose::symmetry::make_symmetric_pose	(	pose::Pose &	pose,
		std::string	symmdef_file
	)

constructs a symmetric pose with a symmetric conformation and energies object from a monomeric pose and symmetry definition file on command line. Requires the presence of a symmetry_definition file

References make_symmetric_pose(), core::pose::Pose::num_jump(), and core::pose::Pose::size().

void core::pose::symmetry::partition_by_symm_jumps	(	utility::vector1< int >	jump_numbers,
		core::kinematics::FoldTree const &	ft,
		conformation::symmetry::SymmetryInfoCOP	symm_info,
		ObjexxFCL::FArray1D_bool &	partner1
	)

References core::kinematics::FoldTree::begin(), core::kinematics::FoldTree::end(), protocols::loops::start, and protocols::loops::stop.

Referenced by protocols::matdes::InterfacePackingFilter::compute(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::matdes::OligomericAverageDegreeFilter::compute(), protocols::simple_filters::ShapeComplementarityFilter::setup_single_component_symm(), and protocols::simple_filters::ShapeComplementarityFilter::write_area().

void core::pose::symmetry::rotate_anchor_to_x_axis

(

core::pose::Pose &

pose

)

References core::conformation::membrane::center, core::pose::Pose::conformation(), find_symmetric_basejump_anchor(), core::pose::Pose::fold_tree(), core::pose::Pose::jump(), core::conformation::Residue::name(), core::pose::Pose::residue(), core::pose::Pose::set_jump(), core::conformation::Conformation::upstream_jump_stub(), and core::conformation::Residue::xyz().

Referenced by protocols::symmetric_docking::SymFoldandDockSlideTrialMover::apply(), and protocols::symmetric_docking::SymFoldandDockRbTrialMover::apply().

bool core::pose::symmetry::scorefxn_is_symmetric

(

conformation::Conformation const &

conf

)

Attempt to detect whether a conformation is symmetric

bool core::pose::symmetry::scorefxn_is_symmetric

(

pose::Pose const &

pose

)

Attempt to detect whether a pose is symmetric

References core::pose::Pose::conformation(), and core::conformation::symmetry::is_symmetric().

core::kinematics::FoldTree core::pose::symmetry::sealed_symmetric_fold_tree

(

core::pose::Pose &

pose

)

References core::kinematics::FoldTree::clear(), core::pose::Pose::conformation(), core::kinematics::FoldTree::cutpoints(), core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), core::conformation::Residue::is_ligand(), is_symmetric(), core::conformation::Residue::is_terminus(), core::kinematics::FoldTree::num_jump(), core::conformation::Conformation::residue(), core::kinematics::FoldTree::root(), core::pose::Pose::size(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), core::kinematics::FoldTree::tree_from_jumps_and_cuts(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by protocols::forge::remodel::RemodelLoopMover::apply(), protocols::forge::components::VarLengthBuild::apply(), and protocols::forge::remodel::RemodelMover::design_refine_cart_relax().

void core::pose::symmetry::set_asymm_unit_fold_tree	(	core::pose::Pose &	p,
		kinematics::FoldTree const &	f
	)

References core::pose::Pose::conformation(), and core::conformation::symmetry::set_asymm_unit_fold_tree().

Referenced by protocols::rbsegment_relax::setup_disconnected(), protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops(), and protocols::hybridization::HybridizeFoldtreeDynamic::update().

int core::pose::symmetry::sym_dof_jump_num	(	core::pose::Pose const &	pose,
		std::string const &	jname
	)

References symmetry_info().

Referenced by protocols::toolbox::task_operations::SelectBySASAOperation::apply(), protocols::matdes::SymDofMover::apply(), protocols::simple_filters::InterfaceSasaFilter::compute(), protocols::matdes::InterfacePackingFilter::compute(), protocols::simple_filters::TaskAwareScoreTypeFilter::compute(), protocols::simple_filters::RotamerBoltzmannWeight::compute(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::matdes::SymUnsatHbondFilter::compute(), protocols::matdes::OligomericAverageDegreeFilter::compute(), protocols::matdes::GetRBDOFValues::compute(), get_full_intracomponent_and_neighbor_subs(), get_intracomponent_and_neighbor_subs(), get_symdof_subunits(), intracomponent_contact(), protocols::hbnet::HBNetStapleInterface::setup(), protocols::simple_filters::ShapeComplementarityFilter::setup_single_component_symm(), and protocols::simple_filters::ShapeComplementarityFilter::write_area().

utility::vector1< std::string > core::pose::symmetry::sym_dof_names

(

core::pose::Pose const &

pose

)

References core::sequence::end, and symmetry_info().

Referenced by protocols::matdes::ExtractSubposeMover::apply(), protocols::matdes::BuildingBlockInterfaceOperation::apply(), protocols::matdes::SymDofMover::apply(), protocols::matdes::GetRBDOFValues::compute(), protocols::matdes::SymDofMover::get_angles(), core::scoring::motif::MotifHash::get_matching_motifs(), protocols::matdes::SymDofMover::get_radial_disps(), protocols::matdes::SymDofMoverSampler::set_sym_dof_names(), protocols::hbnet::HBNet::set_symmetry(), and protocols::hbnet::HBNetStapleInterface::setup().

utility::vector1< char > core::pose::symmetry::symmetric_components

(

core::pose::Pose const &

pose

)

References symmetry_info().

Referenced by protocols::matdes::get_intra_contacts(), and protocols::matdes::maximize_sub1_contact().

void core::pose::symmetry::symmetrize_fold_tree	(	core::pose::Pose const &	p,
		kinematics::FoldTree &	f
	)

Converts an asymmetric foldtree (f) with virtual root into a symmetric foldtree compatible with symmetric pose (p)

Parameters

p	- A symmetric pose
f	- An asymmetric foldtree. This foldtree MUST have a virtual root

This function does not require the symm data

References core::pose::Pose::conformation(), and core::conformation::symmetry::symmetrize_fold_tree().

Referenced by protocols::loops::fold_tree_from_loops().

conformation::symmetry::SymmetryInfoCOP core::pose::symmetry::symmetry_info

(

pose::Pose const &

pose

)

Attempts to grab the symmetry info if the pose is symmetric

References core::pose::Pose::conformation(), is_symmetric(), and core::conformation::symmetry::SymmetricConformation::Symmetry_Info().

Referenced by protocols::forge::remodel::RemodelLoopMover::abinitio_stage(), protocols::simple_moves::StructProfileMover::add_MSAcst_to_pose(), protocols::matdes::MotifHitsRotamersOperation::alter_rotamer_set(), protocols::forge::remodel::RemodelRotamerLinks::apply(), protocols::toolbox::task_operations::StoreCombinedStoredTasksMover::apply(), protocols::toolbox::task_operations::SelectBySASAOperation::apply(), protocols::toolbox::task_operations::SelectByDeltaScoreOperation::apply(), protocols::matdes::ExtractSubposeMover::apply(), protocols::toolbox::task_operations::StoreCompoundTaskMover::apply(), core::select::residue_selector::SymmetricalResidueSelector::apply(), protocols::matdes::BuildingBlockInterfaceOperation::apply(), protocols::toolbox::task_operations::CrystalContactsOperation::apply(), protocols::simple_moves::symmetry::TaskAwareSymMinMover::apply(), core::pack::task::operation::NoRepackDisulfides::apply(), protocols::toolbox::task_operations::JointSequenceOperation::apply(), core::pack::rotamer_set::RotamerSets::build_rotamers(), protocols::simple_moves::StructProfileMover::calc_cenlist(), protocols::jumping::close_chainbreaks(), protocols::simple_filters::InterfaceSasaFilter::compute(), protocols::matdes::InterfacePackingFilter::compute(), protocols::protein_interface_design::filters::DesignableResiduesFilter::compute(), protocols::simple_filters::TaskAwareScoreTypeFilter::compute(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::matdes::SymUnsatHbondFilter::compute(), protocols::matdes::ClashCheckFilter::compute(), protocols::matdes::OligomericAverageDegreeFilter::compute(), protocols::forge::remodel::RemodelMover::design_refine_cart_relax(), protocols::forge::remodel::RemodelMover::design_refine_seq_relax(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::disulfides_changed(), protocols::simple_moves::ClassicFragmentMover::end_bias_check(), protocols::forge::methods::fill_non_loop_cst_set(), core::io::silent::BinarySilentStruct::fill_struct(), core::scoring::methods::CenPairMotifDegreeEnergy::finalize_total_energy(), core::scoring::methods::CenPairMotifEnergy::finalize_total_energy(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::find_disulfides(), core::scoring::fiber_diffraction::find_num_scattering_atoms(), protocols::simple_moves::StructProfileMover::generate_counts(), protocols::simple_moves::StructProfileMover::generate_profile_score_wo_background(), get_buildingblock_and_neighbor_subs(), protocols::simple_moves::StructProfileMover::get_closest_sequences(), get_component_lower_bound(), get_component_of_residue(), get_component_upper_bound(), protocols::simple_filters::SSElementBisectddGFilter::get_ddg_bisect_score(), core::indexed_structure_store::FragmentLookup::get_fragment_residue_spans(), get_full_intracomponent_and_neighbor_subs(), get_full_intracomponent_neighbor_subs(), get_intracomponent_and_interneighbor_subs(), get_intracomponent_and_intraneighbor_subs(), get_intracomponent_and_neighbor_subs(), get_intracomponent_subs(), get_jump_name_to_components(), get_jump_name_to_subunits(), core::scoring::motif::MotifHash::get_matching_motifs(), get_neighbor_subs(), get_resis(), get_resnum_to_subunit_component(), protocols::simple_filters::SSElementMotifContactFilter::get_ss_elements(), protocols::simple_filters::SSElementBisectddGFilter::get_ss_elements(), protocols::simple_filters::SSElementMotifContactFilter::get_SSelements_in_contact(), get_subpose(), get_subunit_name_to_component(), get_sym_aware_jump_num(), get_symdof_subunits(), core::scoring::motif::ResPairMotifQuery::init(), core::scoring::PolymerBondedEnergyContainer::initialize_peptide_bonded_pair_indices(), intracomponent_contact(), is_multicomponent(), is_singlecomponent(), core::scoring::PolymerBondedEnergyContainer::is_valid(), jump_num_sym_dof(), protocols::topology_broker::FibrilModelingClaimer::make_fibril(), make_symmetric_pose(), protocols::simple_filters::InterfaceSasaFilter::parse_my_tag(), protocols::simple_moves::StructProfileMover::save_MSAcst_file(), core::scoring::methods::CartesianBondedEnergy::setup_for_scoring(), protocols::simple_filters::ShapeComplementarityFilter::setup_single_component_symm(), sym_dof_jump_num(), sym_dof_names(), symmetric_components(), and protocols::simple_filters::ShapeComplementarityFilter::write_area().

static THREAD_LOCAL basic::Tracer core::pose::symmetry::TR ( "core.pose.symmetry.util"  )

static