core::pose::symmetry Namespace Reference

Functions
static 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)
core::Size	get_nres_asymmetric_unit (pose::Pose const &pose)
	Convenience function for the number of residues in a subunit. Will return the total size for a asymmetric pose. More...
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, bool keep_pdb_info_labels)
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)
	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, bool keep_pdb_info_labels)
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 const &sym_dof_name, Real contact_dist)
core::pose::Pose	get_full_intracomponent_and_neighbor_subpose (Pose const &pose, std::string const &sym_dof_name, Real contact_dist)
utility::vector1< Size >	get_full_intracomponent_and_neighbor_resis (Pose const &pose, std::string const &sym_dof_name, Real contact_dist)
core::pose::Pose	get_full_intracomponent_subpose (Pose const &pose, std::string const &sym_dof_name)
utility::vector1< Size >	get_full_intracomponent_resis (Pose const &pose, std::string const &sym_dof_name)
utility::vector1< std::string >	get_full_intracomponent_neighbor_subs (Pose const &pose, std::string const &sym_dof_name, Real contact_dist)
core::pose::Pose	get_full_intracomponent_neighbor_subpose (Pose const &pose, std::string const &sym_dof_name, Real contact_dist)
utility::vector1< Size >	get_full_intracomponent_neighbor_resis (Pose const &pose, std::string const &sym_dof_name, Real contact_dist)
bool	intracomponent_contact (Pose const &pose, std::string const &sym_dof_name, Real contact_dist)
utility::vector1< std::string >	get_intracomponent_and_neighbor_subs (Pose const &pose, std::string const &sym_dof_name, Real contact_dist)
core::pose::Pose	get_intracomponent_and_neighbor_subpose (Pose const &pose, std::string const &sym_dof_name, Real contact_dist)
utility::vector1< Size >	get_intracomponent_and_neighbor_resis (Pose const &pose, std::string const &sym_dof_name, Real contact_dist)
utility::vector1< std::string >	get_intracomponent_subs (Pose const &pose, std::string const &sym_dof_name, Real contact_dist)
core::pose::Pose	get_intracomponent_subpose (Pose const &pose, std::string const &sym_dof_name, Real contact_dist)
utility::vector1< Size >	get_intracomponent_resis (Pose const &pose, std::string const &sym_dof_name, Real contact_dist)
utility::vector1< std::string >	get_neighbor_subs (Pose const &pose, std::string const &sym_dof_name, Real contact_dist)
core::pose::Pose	get_neighbor_subpose (Pose const &pose, std::string const &sym_dof_name, Real contact_dist)
utility::vector1< Size >	get_neighbor_resis (Pose const &pose, std::string const &sym_dof_name, Real contact_dist)
utility::vector1< std::string >	get_intracomponent_and_intraneighbor_subs (Pose const &pose, std::string const &sym_dof_name, Real contact_dist)
core::pose::Pose	get_intracomponent_and_intraneighbor_subpose (Pose const &pose, std::string const &sym_dof_name, Real contact_dist)
utility::vector1< Size >	get_intracomponent_and_intraneighbor_resis (Pose const &pose, std::string const &sym_dof_name, Real contact_dist)
utility::vector1< std::string >	get_intracomponent_and_interneighbor_subs (Pose const &pose, std::string const &sym_dof_name, Real contact_dist)
core::pose::Pose	get_intracomponent_and_interneighbor_subpose (Pose const &pose, std::string const &sym_dof_name, Real contact_dist)
utility::vector1< Size >	get_intracomponent_and_interneighbor_resis (Pose const &pose, std::string const &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

extract_asymmetric_unit()

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

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)

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::conformation::Residue::chain(), core::conformation::Conformation::clear_glycan_trees(), core::pose::Pose::conformation(), core::conformation::Residue::connect_atom(), core::conformation::Residue::connected_residue_at_upper(), core::conformation::Conformation::contains_carbohydrate_residues(), core::conformation::Conformation::detect_disulfides(), extract_asymmetric_unit_pdb_info(), core::pose::Pose::fold_tree(), core::conformation::symmetry::get_asymm_unit_fold_tree(), core::conformation::Conformation::insert_chain_ending(), core::conformation::Residue::is_carbohydrate(), core::pose::Pose::is_fullatom(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_polymer_bonded(), is_symmetric(), core::conformation::Residue::is_upper_terminus(), core::conformation::Residue::n_possible_residue_connections(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::conformation::Residue::residue_connect_atom_index(), core::pose::Pose::secstruct(), core::pose::Pose::set_secstruct(), core::conformation::Conformation::setup_glycan_trees(), and core::pose::Pose::size().

Referenced by protocols::forge::remodel::RemodelGlobalFrame::align_segment(), protocols::hybridization::HybridizeProtocol::align_templates_by_domain(), protocols::analysis::LoopAnalyzerMover::apply(), protocols::cryst::TagPoseWithRefinementStatsMover::apply(), protocols::cryst::UpdateCrystInfo::apply(), protocols::loop_grower::FragmentExtension::apply(), protocols::loophash::LoopHashMoverWrapper::apply(), protocols::rbsegment_relax::OptimizeThreadingMover::apply(), protocols::symmetry::ExtractAsymmetricUnitMover::apply(), protocols::task_operations::CrystalContactsOperation::apply(), protocols::task_operations::SelectBySASAOperation::apply(), protocols::forge::remodel::RemodelLoopMover::apply(), protocols::simple_moves::PeriodicBoxMover::apply(), protocols::task_operations::DsspDesignOperation::apply(), protocols::flxbb::LayerDesignOperation::apply(), protocols::task_operations::RestrictNativeResiduesOperation::apply(), core::simple_metrics::metrics::RMSDMetric::calculate(), core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::calculate(), protocols::denovo_design::components::StructureData::check_pose_consistency(), core::scoring::dssp::Dssp::compute(), protocols::score_filters::GeometryFilter::compute(), protocols::protein_interface_design::filters::SequenceRecoveryFilter::compute(), protocols::simple_filters::MutationsFilter::compute(), protocols::loop_grower::LoopPartialSolutionStore::filter(), core::scoring::cryst::PhenixInterface::fitBfactors(), protocols::pose_creation::MergePDBMover::generate_overlaps(), core::io::pose_to_sfr::PoseToStructFileRepConverter::init_from_pose(), core::scoring::cryst::PhenixInterface::initialize_target_evaluator(), protocols::forge::remodel::RemodelDesignMover::mode5_packertask(), protocols::calc_taskop_filters::RelativePoseFilter::parse_my_tag(), core::select::residue_selector::SSElementSelector::parse_ss(), protocols::forge::remodel::RemodelLoopMover::repeat_propagation(), protocols::rbsegment_relax::setup_star_topology(), core::scoring::cryst::PhenixInterface::stealBfactorsFromFile(), and protocols::hybridization::HybridizeProtocol::validate_template().

extract_asymmetric_unit_pdb_info()

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 protocols::mean_field::min().

Referenced by extract_asymmetric_unit().

find_new_symmetric_jump_residues()

void core::pose::symmetry::find_new_symmetric_jump_residues

(

core::pose::Pose &

pose

)

References core::pose::Pose::conformation(), core::kinematics::FoldTree::cutpoints(), core::kinematics::FoldTree::downstream_jump_residue(), find_symmetric_basejump_anchor(), core::conformation::Conformation::fold_tree(), core::kinematics::FoldTree::get_jump_that_builds_residue(), is_symmetric(), core::kinematics::FoldTree::num_cutpoint(), core::kinematics::FoldTree::num_jump(), core::kinematics::FoldTree::reorder(), core::pose::Pose::residue(), core::scoring::rg, core::kinematics::FoldTree::root(), core::conformation::Conformation::size(), core::kinematics::FoldTree::tree_from_jumps_and_cuts(), core::kinematics::FoldTree::upstream_jump_residue(), and core::conformation::Residue::xyz().

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

find_symmetric_basejump_anchor()

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::conformation::Residue::name(), 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::symmetry::SymmetrySlider::very_far_away().

get_asymmetric_pose_copy_from_symmetric_pose()

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

(

pose::Pose const &

pose

)

References core::conformation::Residue::aa(), core::chemical::aa_unk, core::chemical::aa_vrt, core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::conformation::Conformation::clear_glycan_trees(), core::pose::Pose::conformation(), core::conformation::Conformation::contains_carbohydrate_residues(), core::chemical::ResidueType::is_lower_terminus(), core::conformation::Residue::is_lower_terminus(), core::chemical::ResidueType::is_upper_terminus(), core::pose::Pose::residue(), core::conformation::Conformation::setup_glycan_trees(), core::pose::Pose::size(), TR(), and core::conformation::Residue::type().

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

get_buildingblock_and_neighbor_subs()

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().

get_component_lower_bound()

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().

get_component_of_residue()

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().

get_component_upper_bound()

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().

get_full_intracomponent_and_neighbor_resis()

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

References get_full_intracomponent_and_neighbor_subs(), and get_resis().

get_full_intracomponent_and_neighbor_subpose()

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

References get_full_intracomponent_and_neighbor_subs(), and get_subpose().

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

get_full_intracomponent_and_neighbor_subs()

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

get_full_intracomponent_neighbor_resis()

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

get_full_intracomponent_neighbor_subpose()

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

References get_full_intracomponent_neighbor_subs(), and get_subpose().

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

get_full_intracomponent_neighbor_subs()

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

get_full_intracomponent_resis()

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

References get_full_intracomponent_subs(), and get_resis().

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

get_full_intracomponent_subpose()

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

References get_full_intracomponent_subs(), and get_subpose().

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

get_full_intracomponent_subs()

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

References 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().

get_intracomponent_and_interneighbor_resis()

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

References get_intracomponent_and_interneighbor_subs(), and get_resis().

get_intracomponent_and_interneighbor_subpose()

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

References get_intracomponent_and_interneighbor_subs(), and get_subpose().

get_intracomponent_and_interneighbor_subs()

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

get_intracomponent_and_intraneighbor_resis()

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

References get_intracomponent_and_intraneighbor_subs(), and get_resis().

get_intracomponent_and_intraneighbor_subpose()

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

References get_intracomponent_and_intraneighbor_subs(), and get_subpose().

get_intracomponent_and_intraneighbor_subs()

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

get_intracomponent_and_neighbor_resis()

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

get_intracomponent_and_neighbor_subpose()

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

References get_intracomponent_and_neighbor_subs(), and get_subpose().

get_intracomponent_and_neighbor_subs()

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

get_intracomponent_resis()

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

References get_intracomponent_subs(), and get_resis().

get_intracomponent_subpose()

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

References get_intracomponent_subs(), and get_subpose().

get_intracomponent_subs()

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

get_jump_name_to_components()

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().

get_jump_name_to_subunits()

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().

get_neighbor_resis()

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

References get_neighbor_subs(), and get_resis().

get_neighbor_subpose()

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

References get_neighbor_subs(), and get_subpose().

get_neighbor_subs()

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

get_nres_asymmetric_unit()

core::Size core::pose::symmetry::get_nres_asymmetric_unit

(

pose::Pose const &

pose

)

Convenience function for the number of residues in a subunit. Will return the total size for a asymmetric pose.

Convenience function for the number of residues in a subunit. Will return the total size for an asymmetric pose.

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

Referenced by protocols::pose_creation::MergePDBMover::determine_overlap(), and protocols::floppy_tail::FloppyTailMover::init_on_new_input().

get_resis()

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().

get_resnum_to_subunit_component()

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().

get_subpose()

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

References core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), get_resnum_to_subunit_component(), core::pose::Pose::residue(), core::pose::Pose::size(), 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().

get_subunit_name_to_component()

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

References symmetry_info().

get_sym_aware_jump_num()

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

References is_symmetric(), symmetry_info(), and TR().

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

get_symdof_subunits()

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().

get_symm_axis()

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.

intracomponent_contact()

bool core::pose::symmetry::intracomponent_contact	(	Pose const &	pose,
		std::string const &	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(), TR(), and core::conformation::Residue::xyz().

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

is_mirror_symmetric()

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().

is_multicomponent()

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(), and core::scoring::motif::MotifHash::get_matching_motifs().

is_singlecomponent()

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().

is_symmetric() [1/2]

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().

Referenced by core::scoring::nmr::apply_tensor_transformation(), core::scoring::nmr::apply_vector_rotation(), core::scoring::nmr::apply_vector_transformation(), protocols::forge::methods::fill_non_loop_cst_set(), and protocols::membrane::symmetry::symmetrize_spans().

is_symmetric() [2/2]

bool core::pose::symmetry::is_symmetric

(

scoring::Energies const &

energies

)

Referenced by protocols::forge::remodel::RemodelLoopMover::abinitio_stage(), core::optimization::activate_dof_deriv_terms_for_cart_min(), protocols::cyclic_peptide::crosslinker::Metal_HelperBase::add_linker_constraints_symmetric(), protocols::cyclic_peptide::crosslinker::Metal_HelperBase::add_linker_symmetric(), 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::ReportFSC::apply(), protocols::electron_density::ScaleMapIntensities::apply(), protocols::simple_moves::ReportEffectivePKA::apply(), protocols::carbohydrates::GlycanTreeMinMover::apply(), protocols::carbohydrates::GlycanTreeModeler::apply(), protocols::denovo_design::movers::SetPoseSecstructFromStructureDataMover::apply(), protocols::denovo_design::movers::FoldTreeFromFoldGraphMover::apply(), protocols::denovo_design::movers::SealFoldTreeMover::apply(), protocols::fibril::SetupForFibrilMover::apply(), protocols::hbnet::HBNet::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::hybridization::CartesianSampler::apply(), protocols::hybridization::FoldTreeHybridize::apply(), protocols::loop_grower::LoopGrower::apply(), protocols::loophash::LoopHashMoverWrapper::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::md::CartesianMD::apply(), protocols::minimization_packing::MinMover::apply(), protocols::minimization_packing::RotamerTrialsMover::apply(), protocols::minimization_packing::EnergyCutRotamerTrialsMover::apply(), protocols::normalmode::NormalModeMinimizer::apply(), protocols::pose_creation::MergePDBMover::apply(), protocols::protein_mpnn::ProteinMPNNMover::apply(), protocols::rbsegment_relax::OptimizeThreadingMover::apply(), protocols::relax::ClassicRelax::apply(), protocols::relax::FastRelax::apply(), protocols::relax::LocalRelax::apply(), protocols::relax::loop::LoopRelaxMover::apply(), protocols::rigid::WholeBodyTranslationMover::apply(), protocols::rigid::WholeBodyRotationMover::apply(), protocols::simple_moves::AddResidueLabelMover::apply(), protocols::simple_moves::ReturnSidechainMover::apply(), protocols::symmetric_docking::SymDockProtocol::apply(), protocols::symmetric_docking::SymFoldandDockRbTrialMover::apply(), protocols::symmetric_docking::SymFoldandDockSlideTrialMover::apply(), protocols::symmetry::SetupForSymmetryMover::apply(), protocols::symmetry::ExtractAsymmetricUnitMover::apply(), protocols::symmetry::ExtractAsymmetricPoseMover::apply(), protocols::symmetry::SymDockingInitialPerturbation::apply(), 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protocols::quantum_annealing::InteractionGraphSummaryMetric::calculate(), core::scoring::electron_density::calculate_density_nbr(), core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::calculate_penalty_once_from_scratch(), core::energy_methods::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::Worst9merFilter::compute(), protocols::cryst::ReportGradientsMover::compute(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), core::scoring::dssp::Dssp::compute(), protocols::protein_interface_design::filters::DesignableResiduesFilter::compute(), protocols::simple_filters::InterfaceSasaFilter::compute(), protocols::protein_interface_design::filters::SequenceRecoveryFilter::compute(), protocols::simple_filters::MutationsFilter::compute(), protocols::simple_filters::TaskAwareScoreTypeFilter::compute(), protocols::simple_filters::ShapeComplementarityFilter::compute(), core::select::util::SelectResiduesByLayer::compute(), protocols::calc_taskop_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(), core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::compute_scores(), core::scoring::create_and_store_atom_tree_minimization_graph(), protocols::calc_taskop_movers::ConsensusDesignMover::create_consensus_design_task(), protocols::denovo_design::components::RemodelLoopMoverPoseFolder::create_false_movemap(), core::pack::rotamer_set::RotamerSetFactory::create_rotamer_set(), protocols::pose_metric_calculators::RotamerBoltzCalculator::create_rotamer_set(), core::pack::rotamer_set::RotamerSetsFactory::create_rotamer_sets(), protocols::cryst::crystRMS(), core::scoring::electron_density::ElectronDensity::dCCdBs(), protocols::protein_interface_design::movers::SecretionOptimizationMover::DesignAroundApply(), protocols::electron_density::BfactorMultifunc::dfunc(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::disulfides_changed(), protocols::loop_modeling::refiners::MinimizationRefiner::do_apply(), 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protocols::loops::pick_loops_chainbreak(), protocols::jd2::SilentFileJobInputter::pose_from_job(), protocols::comparative_modeling::GenericJobInputter::pose_from_job(), protocols::jd2::LargeNstructJobInputter::pose_from_job(), protocols::topology_broker::MembraneTopologyClaimer::pre_process(), protocols::denovo_design::DisulfidizeMover::process_pose(), protocols::cryst::DockLatticeMover::randomize_chis(), protocols::forge::remodel::RemodelLoopMover::randomize_stage(), core::util::rebuild_disulfide(), protocols::loop_grower::LoopGrower::refine_cycle(), protocols::cryst::DockLatticeMover::regenerate_lattice(), protocols::forge::remodel::RemodelLoopMover::repeat_propagation(), protocols::simple_ddg::AlaScan::report_symmetry(), core::scoring::electron_density::ElectronDensity::rescale_fastscoring_temp_bins(), core::energy_methods::MembraneCenPairEnergy::residue_pair_energy(), core::energy_methods::MPPairEnergy::residue_pair_energy(), core::energy_methods::ElecDensEnergy::residue_pair_energy(), core::energy_methods::FastDensEnergy::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(), core::scoring::nmr::pcs::PCSSingleSet::set_atom_derivatives(), core::scoring::nmr::pre::PREMultiSet::set_atom_derivatives(), core::scoring::nmr::rdc::RDCMultiSet::set_atom_derivatives(), 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(), core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::set_up_residuearrayannealableenergy_for_packing(), core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyEnergy::set_up_residuearrayannealableenergy_for_packing(), protocols::symmetry::SymmetrySlider::setup(), protocols::minimization_packing::PackRotamersMover::setup(), core::optimization::CartesianMinimizerMap::setup(), protocols::relax::CentroidRelax::setup_class_movemap_and_constraints(), core::scoring::fiber_diffraction::setup_cylindrical_coords(), protocols::hybridization::FoldTreeHybridize::setup_foldtree(), core::scoring::ScoreFunction::setup_for_derivatives(), core::energy_methods::SmoothEnvEnergy::setup_for_derivatives(), core::energy_methods::ElecDensAllAtomCenEnergy::setup_for_derivatives(), core::energy_methods::ElecDensCenEnergy::setup_for_derivatives(), core::energy_methods::ElecDensEnergy::setup_for_derivatives(), core::energy_methods::EnvSmoothEnergy::setup_for_derivatives(), core::energy_methods::FastDensEnergy::setup_for_derivatives(), core::energy_methods::RG_Energy_Fast::setup_for_derivatives(), protocols::nmr::pcs::PCSEnergy::setup_for_minimizing(), protocols::nmr::pre::PREEnergy::setup_for_minimizing(), protocols::nmr::rdc::RDCEnergy::setup_for_minimizing(), core::scoring::ScoreFunction::setup_for_minimizing(), core::energy_methods::CartesianBondedEnergy::setup_for_scoring(), core::energy_methods::DNA_DihedralEnergy::setup_for_scoring(), core::energy_methods::ElecDensAllAtomCenEnergy::setup_for_scoring(), core::energy_methods::ElecDensCenEnergy::setup_for_scoring(), core::energy_methods::ElecDensEnergy::setup_for_scoring(), core::energy_methods::FastDensEnergy::setup_for_scoring(), core::energy_methods::FiberDiffractionEnergy::setup_for_scoring(), core::energy_methods::FiberDiffractionEnergyDens::setup_for_scoring(), core::energy_methods::GenericBondedEnergy::setup_for_scoring(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::setup_for_symmetry(), protocols::idealize::IdealizeMover::setup_idealize_constraints(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::setup_movemap(), protocols::carbohydrates::GlycanSampler::setup_movers(), protocols::simple_moves::ExplicitWaterMover::setup_pack(), core::energy_methods::MHCEpitopeEnergy::setup_symmetry(), protocols::simple_ddg::ddG::setup_task(), core::scoring::SecondaryStructurePotential::sheets_from_dimers(), protocols::nmr::rdc::RDCEnergy::show_additional_info(), protocols::protein_interface_design::filters::FilterScanFilter::single_substitution(), protocols::symmetry::SymmetrySlider::slide(), protocols::symmetry::SymmetrySlider::slide_away(), protocols::simple_filters::SpanTopologyMatchPoseFilter::span_file_topology(), 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::evolution::AlignmentCleanerTools::thread_sequence_on_pose(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::three_body_approximate_buried_unsat_calculation(), protocols::features::InterfaceDdGMover::unbind(), protocols::simple_ddg::ddG::unbind(), protocols::hybridization::HybridizeFoldtreeDynamic::update(), core::scoring::Energies::update_neighbor_links(), core::scoring::nmr::pcs::PCSSingleSet::update_spin_coordinates(), core::scoring::nmr::pre::PREMultiSet::update_spin_coordinates(), core::scoring::nmr::rdc::RDCMultiSet::update_spin_coordinates(), protocols::cyclic_peptide::crosslinker::TMA_Helper::update_tma_amide_bond_dependent_atoms_asymmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::update_tma_amide_bond_dependent_atoms_symmetric(), and protocols::simple_filters::ShapeComplementarityFilter::write_area().

jump_num_sym_dof()

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::compute().

make_asymmetric_pose()

void core::pose::symmetry::make_asymmetric_pose

(

pose::Pose &

pose

)

References core::conformation::Conformation::clear_glycan_trees(), core::pose::Pose::conformation(), core::conformation::Conformation::contains_carbohydrate_residues(), core::pose::Pose::energies(), is_symmetric(), core::pose::Pose::set_new_conformation(), core::pose::Pose::set_new_energies_object(), and core::conformation::Conformation::setup_glycan_trees().

Referenced by protocols::topology_broker::TopologyBroker::apply(), protocols::relax::RepeatProteinRelax::apply(), protocols::symmetry::ExtractAsymmetricPoseMover::apply(), protocols::fldsgn::CircularPermutation::apply(), protocols::sasa_scores::compute_avge_scores(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::fill_atom_neighbor_stuff(), core::io::silent::BinarySilentStruct::fill_pose(), core::pack::hbonds::hbond_graph_from_partial_rotsets(), protocols::jd2::SilentFileJobInputter::pose_from_job(), protocols::comparative_modeling::GenericJobInputter::pose_from_job(), protocols::features::DatabaseJobInputter::pose_from_job(), and protocols::jd2::LargeNstructJobInputter::pose_from_job().

make_residue_mask_symmetric()

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

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

Referenced by protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::relax::loop::LoopRelaxMover::apply(), protocols::simple_task_operations::RestrictToLoops::apply_helper(), and protocols::hybridization::MRMover::pack_missing_sidechains().

make_symmetric_movemap()

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::kinematics::MoveMap::get_atoms(), 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_atom(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_branches(), core::kinematics::MoveMap::set_chi(), core::kinematics::MoveMap::set_jump(), 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::carbohydrates::GlycanTreeMinMover::apply(), protocols::cryst::DockLatticeMover::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::hybridization::FoldTreeHybridize::apply(), protocols::md::CartesianMD::apply(), protocols::minimization_packing::MinMover::apply(), protocols::minimization_packing::symmetry::TaskAwareSymMinMover::apply(), protocols::relax::ClassicRelax::apply(), protocols::relax::FastRelax::apply(), protocols::relax::LocalRelax::apply(), protocols::relax::loop::LoopRelaxMover::apply(), protocols::symmetric_docking::SymSidechainMinMover::apply(), protocols::symmetric_docking::SymInterfaceSidechainMinMover::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::idealize::basic_idealize(), protocols::relax::FastRelax::batch_apply(), protocols::simple_moves::PeriodicBoxMover::check_virial_pressure(), protocols::cryst::ReportGradientsMover::compute(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::compute_Boltzmann_weight(), protocols::denovo_design::components::RemodelLoopMoverPoseFolder::create_false_movemap(), protocols::hybridization::HybridizeProtocol::do_intrastage_docking(), protocols::electron_density::dockPoseIntoMap(), core::select::movemap::MoveMapFactory::edit_movemap_given_pose(), core::util::getMLweight(), core::util::getMLweight_cart(), protocols::pose_metric_calculators::RotamerBoltzCalculator::init_minmover(), protocols::floppy_tail::FloppyTailMover::init_on_new_input(), protocols::topology_broker::FibrilModelingClaimer::initialize_dofs(), protocols::topology_broker::FoldandDockClaimer::initialize_dofs(), protocols::loops::loops_set_move_map(), protocols::hbnet::HBNet::minimize_network(), protocols::symmetry::SymShakeStructureMover::minimize_with_constraints(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), core::util::rebuild_disulfide(), protocols::loop_grower::LoopGrower::refine_cycle(), protocols::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::carbohydrates::GlycanSampler::setup_movers(), protocols::cryst::DockLatticeMover::slide_lattice(), protocols::topology_broker::TopologyBroker::switch_to_fullatom(), and protocols::protein_interface_design::SymMinimizeInterface().

make_symmetric_pdb_info()

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

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

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

make_symmetric_pose() [1/3]

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

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

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

make_symmetric_pose() [2/3]

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::cryst::MakeLatticeMover::apply(), protocols::cryst::MakeLayerMover::apply(), protocols::matdes::SymDofMover::apply(), protocols::symmetry::DetectSymmetry::apply(), core::io::silent::BinarySilentStruct::fill_pose(), protocols::pose_creation::MergePDBMover::generate_overlaps(), protocols::fibril::make_symmetric_fibril(), protocols::symmetry::SetupForSymmetryMover::make_symmetric_pose(), make_symmetric_pose(), protocols::calc_taskop_filters::RelativePoseFilter::parse_my_tag(), protocols::simple_moves::PeriodicBoxMover::setup_pose(), protocols::relax::RepeatProteinRelax::setup_repeat_pose(), and protocols::relax::RepeatProteinRelax::setup_repeat_pose_jumping().

make_symmetric_pose() [3/3]

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(), core::conformation::symmetry::SymmData::read_symmetry_data_from_file(), and core::pose::Pose::size().

partition_by_symm_jumps()

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::mean_field::max(), protocols::mean_field::min(), protocols::loops::start, and protocols::loops::stop.

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

rotate_anchor_to_x_axis()

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::kinematics::FoldTree::get_jump_that_builds_residue(), core::pose::Pose::jump(), core::conformation::Residue::name(), core::pose::Pose::residue(), core::kinematics::Jump::rotation_by_matrix(), core::pose::Pose::set_jump(), core::kinematics::FoldTree::upstream_jump_residue(), core::conformation::Conformation::upstream_jump_stub(), and core::conformation::Residue::xyz().

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

scorefxn_is_symmetric() [1/2]

bool core::pose::symmetry::scorefxn_is_symmetric

(

conformation::Conformation const &

conf

)

Attempt to detect whether a conformation is symmetric

scorefxn_is_symmetric() [2/2]

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().

sealed_symmetric_fold_tree()

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(), protocols::mean_field::max(), protocols::mean_field::min(), core::kinematics::FoldTree::num_jump(), core::conformation::Conformation::residue(), core::kinematics::FoldTree::root(), core::pose::Pose::size(), TR(), core::kinematics::FoldTree::tree_from_jumps_and_cuts(), and core::kinematics::FoldTree::upstream_jump_residue().

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

set_asymm_unit_fold_tree()

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().

sym_dof_jump_num()

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

References symmetry_info().

Referenced by protocols::task_operations::SelectBySASAOperation::apply(), protocols::matdes::SymDofMover::apply(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::compute(), protocols::matdes::InterfacePackingFilter::compute(), protocols::simple_filters::BuriedUnsatHbondFilter::compute(), protocols::simple_filters::InterfaceSasaFilter::compute(), protocols::matdes::SymUnsatHbondFilter::compute(), protocols::matdes::OligomericAverageDegreeFilter::compute(), protocols::simple_filters::TaskAwareScoreTypeFilter::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_packer_task_and_starting_residues(), protocols::simple_filters::ShapeComplementarityFilter::setup_single_component_symm(), and protocols::simple_filters::ShapeComplementarityFilter::write_area().

sym_dof_names()

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

(

core::pose::Pose const &

pose

)

References symmetry_info().

Referenced by protocols::matdes::ExtractSubposeMover::apply(), protocols::matdes::BuildingBlockInterfaceOperation::apply(), protocols::matdes::SymDofMover::apply(), protocols::simple_filters::BuriedUnsatHbondFilter::compute(), 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_packer_task_and_starting_residues().

symmetric_components()

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().

symmetrize_fold_tree()

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().

symmetry_info()

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(), and is_symmetric().

Referenced by protocols::forge::remodel::RemodelLoopMover::abinitio_stage(), protocols::simple_moves::StructProfileMover::add_MSAcst_to_pose(), protocols::matdes::MotifHitsRotamersOperation::alter_rotamer_set(), protocols::matdes::ExtractSubposeMover::apply(), protocols::minimization_packing::symmetry::TaskAwareSymMinMover::apply(), protocols::protein_mpnn::ProteinMPNNMover::apply(), protocols::simple_moves::AddResidueLabelMover::apply(), protocols::task_operations::StoreCombinedStoredTasksMover::apply(), protocols::task_operations::StoreCompoundTaskMover::apply(), protocols::matdes::BuildingBlockInterfaceOperation::apply(), protocols::task_operations::CrystalContactsOperation::apply(), protocols::task_operations::SelectByDeltaScoreOperation::apply(), protocols::task_operations::SelectBySASAOperation::apply(), core::select::residue_selector::ResidueIndexSelector::apply(), core::select::residue_selector::SymmetricalResidueSelector::apply(), protocols::forge::remodel::RemodelRotamerLinks::apply(), core::pack::task::operation::NoRepackDisulfides::apply(), protocols::task_operations::JointSequenceOperation::apply(), core::scoring::nmr::apply_tensor_transformation(), core::scoring::nmr::apply_vector_rotation(), core::scoring::nmr::apply_vector_transformation(), core::pack::rotamer_set::RotamerSets::build_rotamers(), protocols::simple_moves::StructProfileMover::calc_cenlist(), core::select::util::calc_sc_neighbors(), protocols::jumping::close_chainbreaks(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::matdes::InterfacePackingFilter::compute(), protocols::protein_interface_design::filters::DesignableResiduesFilter::compute(), protocols::simple_filters::InterfaceSasaFilter::compute(), protocols::matdes::ClashCheckFilter::compute(), protocols::matdes::SymUnsatHbondFilter::compute(), protocols::matdes::OligomericAverageDegreeFilter::compute(), protocols::simple_filters::TaskAwareScoreTypeFilter::compute(), core::select::util::SelectResiduesByLayer::compute(), protocols::forge::remodel::RemodelMover::design_refine_cart_relax(), protocols::forge::remodel::RemodelMover::design_refine_seq_relax(), protocols::protein_interface_design::movers::SecretionOptimizationMover::DesignAroundApply(), 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::energy_methods::CenPairMotifDegreeEnergy::finalize_total_energy(), core::energy_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_ddg::SSElementBisectddGFilter::get_ddg_bisect_score(), protocols::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_ddg::SSElementBisectddGFilter::get_ss_elements(), protocols::simple_filters::SSElementMotifContactFilter::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::nmr::pre::PRESingleSet::init_from_filedata(), core::scoring::nmr::pcs::PCSSingleSet::init_from_pcs_filedata(), core::scoring::nmr::pre::PREMultiSet::init_from_pre_singleset_vec(), core::scoring::nmr::rdc::RDCSingleSet::init_from_rdc_filedata(), core::scoring::nmr::rdc::RDCMultiSet::init_from_rdc_filedata(), 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(), core::select::residue_selector::SSElementSelector::parse_ss(), core::conformation::symmetry::replaced_symmetric_foldtree_with_new_monomer(), protocols::simple_moves::StructProfileMover::save_MSAcst_file(), core::scoring::nmr::pcs::PCSSingleSet::set_atom_derivatives(), core::scoring::nmr::pre::PREMultiSet::set_atom_derivatives(), core::scoring::nmr::rdc::RDCMultiSet::set_atom_derivatives(), protocols::nmr::pcs::PCSEnergy::setup_for_minimizing(), protocols::nmr::pre::PREEnergy::setup_for_minimizing(), protocols::nmr::rdc::RDCEnergy::setup_for_minimizing(), core::energy_methods::CartesianBondedEnergy::setup_for_scoring(), core::energy_methods::DNA_DihedralEnergy::setup_for_scoring(), core::energy_methods::GenericBondedEnergy::setup_for_scoring(), protocols::simple_filters::ShapeComplementarityFilter::setup_single_component_symm(), protocols::nmr::rdc::RDCEnergy::show_additional_info(), protocols::simple_filters::SpanTopologyMatchPoseFilter::span_file_topology(), sym_dof_jump_num(), sym_dof_names(), symmetric_components(), core::scoring::nmr::pcs::PCSSingleSet::update_spin_coordinates(), core::scoring::nmr::pre::PREMultiSet::update_spin_coordinates(), core::scoring::nmr::rdc::RDCMultiSet::update_spin_coordinates(), and protocols::simple_filters::ShapeComplementarityFilter::write_area().

TR()

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

static

Referenced by get_asymmetric_pose_copy_from_symmetric_pose(), get_sym_aware_jump_num(), intracomponent_contact(), and sealed_symmetric_fold_tree().