core::pose::symmetry Namespace Reference

Functions
static basic::Tracer	TR ("core.pose.symmetry.util")
static numeric::random::RandomGenerator	RG (408539)
bool	is_symmetric (scoring::Energies const &energies)
bool	is_symmetric (pose::Pose const &pose)
bool	is_symmetric (scoring::ScoreFunction const &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 with_virtual_atoms=true)
	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)
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)
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, int 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)
utility::vector1< Size >	get_symdof_subunits (core::pose::Pose const &pose, std::string const &jname)
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)

Function Documentation

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

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

Definition at line 207 of file util.cc.

References 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::chemical::LOWER_TERMINUS, core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), and core::chemical::UPPER_TERMINUS.

Referenced by protocols::loophash::LoopHashMoverWrapper::apply(), protocols::toolbox::task_operations::SelectBySASAOperation::apply(), protocols::toolbox::task_operations::RestrictNativeResiduesOperation::apply(), protocols::simple_moves::symmetry::ExtractAsymmetricUnitMover::apply(), protocols::flxbb::LayerDesignOperation::apply(), protocols::protein_interface_design::filters::SequenceRecoveryFilter::compute(), and protocols::simple_filters::RelativePoseFilter::parse_my_tag().

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

Definition at line 399 of file util.cc.

References core::pose::Pose::conformation(), is_symmetric(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), 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)

Definition at line 621 of file util.cc.

References core::io::serialization::clone(), core::pose::Pose::conformation(), find_symmetric_basejump_anchor(), core::conformation::Conformation::fold_tree(), is_symmetric(), core::pose::Pose::residue(), 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)

Definition at line 603 of file util.cc.

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)

Definition at line 279 of file util.cc.

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

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

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

Definition at line 1069 of file util.cc.

References symmetry_info().

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

Definition at line 1075 of file util.cc.

References symmetry_info().

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

Definition at line 1072 of file util.cc.

References symmetry_info().

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

Definition at line 1081 of file util.cc.

References symmetry_info().

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

Definition at line 1084 of file util.cc.

References symmetry_info().

Referenced by protocols::simple_filters::ShapeComplementarityFilter::compute(), and protocols::simple_filters::ShapeComplementarityFilter::report_sm().

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

Definition at line 1078 of file util.cc.

References symmetry_info().

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

Definition at line 998 of file util.cc.

References is_symmetric(), and symmetry_info().

Referenced by protocols::toolbox::task_operations::SelectBySASAOperation::apply(), protocols::simple_filters::InterfaceSasaFilter::compute(), protocols::simple_filters::RotamerBoltzmannWeight::compute(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::simple_filters::ShapeComplementarityFilter::compute(), and protocols::simple_filters::ShapeComplementarityFilter::report_sm().

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

Definition at line 1042 of file util.cc.

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::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)

Definition at line 867 of file util.cc.

References core::pose::Pose::conformation(), is_symmetric(), core::pose::Pose::residue(), core::scoring::rna::X, and core::conformation::Residue::xyz().

bool core::pose::symmetry::is_multicomponent

(

core::pose::Pose const &

pose)

Definition at line 1065 of file util.cc.

References symmetry_info().

bool core::pose::symmetry::is_singlecomponent

(

core::pose::Pose const &

pose)

Definition at line 1062 of file util.cc.

References symmetry_info().

bool core::pose::symmetry::is_symmetric

(

scoring::Energies const &

energies)

Definition at line 66 of file util.cc.

Referenced by protocols::topology_broker::MembraneTopologyClaimer::add_mover(), protocols::fibril::SetupForFibrilMover::align(), protocols::protein_interface_design::movers::RandomMutation::apply(), protocols::loophash::LoopHashMoverWrapper::apply(), protocols::simple_moves::symmetry::SetupForSymmetryMover::apply(), protocols::toolbox::task_operations::SelectBySASAOperation::apply(), protocols::simple_moves::symmetry::SymmetricRMSMover::apply(), protocols::symmetric_docking::SymFoldandDockSlideTrialMover::apply(), protocols::fibril::SetupForFibrilMover::apply(), protocols::simple_moves::ReturnSidechainMover::apply(), protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::apply(), protocols::symmetric_docking::SymFoldandDockRbTrialMover::apply(), protocols::hybridization::CartesianSampler::apply(), protocols::toolbox::task_operations::RestrictNativeResiduesOperation::apply(), protocols::simple_moves::ConsensusDesignMover::apply(), protocols::simple_moves::symmetry::SymDockingInitialPerturbation::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::toolbox::task_operations::SeqprofConsensusOperation::apply(), protocols::simple_moves::BackboneMover::apply(), protocols::toolbox::task_operations::JointSequenceOperation::apply(), protocols::simple_moves::symmetry::ExtractAsymmetricUnitMover::apply(), core::pack::task::operation::NoRepackDisulfides::apply(), protocols::rigid::WholeBodyTranslationMover::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::relax::ClassicRelax::apply(), protocols::rigid::WholeBodyRotationMover::apply(), protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::simple_moves::symmetry::SymDockingSlideIntoContact::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::simple_moves::symmetry::ExtractAsymmetricPoseMover::apply(), protocols::idealize::IdealizeMover::apply(), protocols::relax::CentroidRelax::apply(), protocols::simple_moves::symmetry::FaSymDockingSlideTogether::apply(), protocols::relax::FastRelax::apply(), protocols::fldsgn::CircularPermutation::apply(), protocols::flxbb::LayerDesignOperation::apply(), protocols::fldsgn::potentials::SetSecStructEnergies::apply(), protocols::forge::remodel::RemodelLoopMover::apply(), protocols::forge::components::VarLengthBuild::apply(), protocols::hybridization::CartesianSampler::apply_frame(), protocols::hybridization::CartesianHybridize::apply_frame(), protocols::idealize::basic_idealize(), protocols::relax::FastRelax::batch_apply(), protocols::forge::remodel::RemodelLoopMover::boost_closure_stage(), core::pack::rotamer_set::RotamerSets::build_rotamers(), core::scoring::CA_rmsd_symmetric(), protocols::symmetric_docking::SymDockProtocol::calc_interaction_energy(), protocols::symmetric_docking::SymDockProtocol::calc_rms(), protocols::simple_moves::ddG::calculate(), protocols::fldsgn::BluePrintBDR::centroid_build(), protocols::hybridization::HybridizeProtocol::check_and_create_fragments(), protocols::jumping::close_chainbreaks(), protocols::relax::FastRelax::cmd_accept_to_best(), protocols::simple_filters::InterfaceSasaFilter::compute(), protocols::protein_interface_design::filters::DesignableResiduesFilter::compute(), protocols::protein_interface_design::filters::SequenceRecoveryFilter::compute(), protocols::protein_interface_design::filters::BindingStrainFilter::compute(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::simple_filters::ShapeComplementarityFilter::compute(), protocols::simple_filters::RotamerBoltzmannWeight::compute_Boltzmann_weight(), protocols::simple_filters::SymmetricMotifFilter::compute_d2(), protocols::hybridization::CartesianSampler::compute_fragment_bias(), core::scoring::MembranePotential::compute_membrane_embedding(), 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(), core::pack::interaction_graph::InteractionGraphFactory::create_interaction_graph(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::disulfides_changed(), 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::PattersonCorrEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensCenEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensEnergy::eval_atom_derivative(), core::scoring::electron_density::FastDensEnergy::eval_atom_derivative(), core::scoring::methods::CartesianBondedEnergy::eval_residue_pair_derivatives(), extract_asymmetric_unit(), extract_asymmetric_unit_pdb_info(), core::io::silent::BinaryProteinSilentStruct::fill_pose(), core::io::silent::BinaryProteinSilentStruct::fill_struct(), protocols::rosetta_scripts::ParsedProtocol::final_score(), core::scoring::methods::MembraneLipo::finalize_total_energy(), core::scoring::methods::ChainbreakEnergy::finalize_total_energy(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::find_disulfides(), find_new_symmetric_jump_residues(), protocols::cluster::GatherPosesMover::get_distance_measure(), protocols::hybridization::get_num_residues_nonvirt(), get_sym_aware_jump_num(), get_symdof_subunits(), get_symm_axis(), core::scoring::SecondaryStructurePotential::hspair(), protocols::forge::remodel::RemodelLoopMover::independent_stage(), protocols::hybridization::HybridizeFoldtreeDynamic::initialize(), protocols::hybridization::HybridizeProtocol::initialize_and_sample_loops(), protocols::topology_broker::FoldandDockClaimer::initialize_dofs(), protocols::topology_broker::MembraneTopologyClaimer::initialize_dofs(), protocols::forge::remodel::RemodelLoopMover::insert_random_smallestmer_per_loop(), 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_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::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(), core::scoring::symmetry::SymmetricScoreFunction::operator()(), core::scoring::ScoreFunction::operator()(), core::pack::pack_rotamers(), protocols::simple_filters::RelativePoseFilter::parse_my_tag(), protocols::comparative_modeling::pick_loops_chainbreak(), protocols::comparative_modeling::GenericJobInputter::pose_from_job(), protocols::jd2::SilentFileJobInputter::pose_from_job(), protocols::forge::remodel::RemodelLoopMover::randomize_stage(), protocols::simple_filters::ShapeComplementarityFilter::report_sm(), protocols::simple_filters::AlaScan::report_symmetry(), core::scoring::methods::MembraneCenPairEnergy::residue_pair_energy(), core::scoring::electron_density::ElecDensEnergy::residue_pair_energy(), core::scoring::electron_density::FastDensEnergy::residue_pair_energy(), core::scoring::methods::CartesianBondedEnergy::residue_pair_energy_sorted(), core::pack::rotamer_trials(), core::optimization::AtomTreeMinimizer::run(), 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::simple_moves::symmetry::SymmetrySlider::setup(), protocols::relax::CentroidRelax::setup_class_movemap_and_constraints(), protocols::hybridization::FoldTreeHybridize::setup_foldtree(), core::scoring::electron_density::ElecDensEnergy::setup_for_derivatives(), core::scoring::electron_density::FastDensEnergy::setup_for_derivatives(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::setup_for_derivatives(), core::scoring::electron_density::ElecDensCenEnergy::setup_for_derivatives(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensCenEnergy::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(), core::scoring::SecondaryStructurePotential::sheets_from_dimers(), protocols::forge::remodel::RemodelLoopMover::simultaneous_stage(), 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(), protocols::simple_moves::ddG::symm_ddG(), symmetry_info(), SymMinimizeInterface(), core::scoring::MembranePotential::termini_penalty(), protocols::simple_filters::RelativePoseFilter::thread_seq(), protocols::hybridization::HybridizeFoldtreeDynamic::update(), and core::scoring::Energies::update_neighbor_links().

bool core::pose::symmetry::is_symmetric

(

pose::Pose const &

pose)

Attempt to detect whether a pose is symmetric

Definition at line 73 of file util.cc.

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

bool core::pose::symmetry::is_symmetric

(

scoring::ScoreFunction const &

scorefxn)

Definition at line 80 of file util.cc.

void core::pose::symmetry::make_asymmetric_pose

(

pose::Pose &

pose)

Definition at line 189 of file util.cc.

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::simple_moves::symmetry::ExtractAsymmetricPoseMover::apply(), protocols::fldsgn::CircularPermutation::apply(), protocols::topology_broker::TopologyBroker::apply(), protocols::sasa_scores::compute_avge_scores(), core::io::silent::BinaryProteinSilentStruct::fill_pose(), protocols::comparative_modeling::GenericJobInputter::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
	)

Definition at line 895 of file util.cc.

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

Referenced by protocols::toolbox::task_operations::RestrictToLoopsAndNeighbors::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), and protocols::comparative_modeling::LoopRelaxMover::apply().

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

Definition at line 444 of file util.cc.

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::symmetric_docking::SymSidechainMinMover::apply(), protocols::hybridization::CartesianSampler::apply(), protocols::simple_moves::symmetry::SymMinMover::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::simple_moves::BackboneMover::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::relax::ClassicRelax::apply(), protocols::symmetric_docking::SymInterfaceSidechainMinMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::relax::FastRelax::apply(), protocols::idealize::basic_idealize(), protocols::relax::FastRelax::batch_apply(), protocols::simple_filters::RotamerBoltzmannWeight::compute_Boltzmann_weight(), protocols::electron_density::dockPoseIntoMap(), protocols::topology_broker::FoldandDockClaimer::initialize_dofs(), protocols::topology_broker::FibrilModelingClaimer::initialize_dofs(), protocols::loops::loops_set_move_map(), 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::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 SymMinimizeInterface().

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

Definition at line 326 of file util.cc.

References core::pose::chr_chains(), core::io::serialization::clone(), core::pose::Pose::conformation(), is_symmetric(), and core::pose::Pose::total_residue().

Referenced by 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

Definition at line 115 of file util.cc.

References core::pose::Pose::conformation(), core::conformation::Conformation::detect_bonds(), core::pose::Pose::energies(), is_symmetric(), core::pose::Pose::pdb_info(), core::pose::Pose::set_new_conformation(), core::pose::Pose::set_new_energies_object(), symmetry_info(), and core::pose::Pose::total_residue().

Referenced by protocols::simple_moves::symmetry::DetectSymmetry::apply(), protocols::simple_moves::symmetry::SetupForSymmetryMover::apply(), core::io::silent::BinaryProteinSilentStruct::fill_pose(), protocols::fibril::make_symmetric_fibril(), make_symmetric_pose(), and protocols::simple_filters::RelativePoseFilter::parse_my_tag().

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

Definition at line 143 of file util.cc.

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

Definition at line 174 of file util.cc.

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

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
	)

Definition at line 803 of file util.cc.

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

Referenced by protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::simple_filters::ShapeComplementarityFilter::compute(), and protocols::simple_filters::ShapeComplementarityFilter::report_sm().

static numeric::random::RandomGenerator core::pose::symmetry::RG ( 408539  )

static

void core::pose::symmetry::rotate_anchor_to_x_axis

(

core::pose::Pose &

pose)

Definition at line 734 of file util.cc.

References 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

Definition at line 97 of file util.cc.

bool core::pose::symmetry::scorefxn_is_symmetric

(

pose::Pose const &

pose)

Attempt to detect whether a pose is symmetric

Definition at line 104 of file util.cc.

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)

Definition at line 918 of file util.cc.

References core::kinematics::FoldTree::clear(), core::pose::Pose::conformation(), core::kinematics::FoldTree::cutpoints(), core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), is_symmetric(), core::kinematics::FoldTree::num_jump(), core::kinematics::FoldTree::root(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), core::pose::Pose::total_residue(), core::kinematics::FoldTree::tree_from_jumps_and_cuts(), and core::kinematics::FoldTree::upstream_jump_residue().

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

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

Definition at line 796 of file util.cc.

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

Referenced by protocols::loops::set_single_loop_fold_tree(), and protocols::hybridization::HybridizeFoldtreeDynamic::update().

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

Definition at line 1037 of file util.cc.

References symmetry_info().

Referenced by protocols::toolbox::task_operations::SelectBySASAOperation::apply(), protocols::simple_filters::InterfaceSasaFilter::compute(), protocols::simple_filters::RotamerBoltzmannWeight::compute(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::simple_filters::ShapeComplementarityFilter::compute(), get_symdof_subunits(), and protocols::simple_filters::ShapeComplementarityFilter::report_sm().

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

(

core::pose::Pose const &

pose)

Definition at line 1025 of file util.cc.

References symmetry_info().

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

Definition at line 791 of file util.cc.

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

Definition at line 87 of file util.cc.

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

Referenced by protocols::toolbox::task_operations::SelectBySASAOperation::apply(), protocols::toolbox::task_operations::JointSequenceOperation::apply(), core::pack::task::operation::NoRepackDisulfides::apply(), protocols::jumping::close_chainbreaks(), protocols::simple_filters::InterfaceSasaFilter::compute(), protocols::protein_interface_design::filters::DesignableResiduesFilter::compute(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::simple_filters::ShapeComplementarityFilter::compute(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::disulfides_changed(), protocols::simple_moves::ClassicFragmentMover::end_bias_check(), core::scoring::methods::CartesianBondedEnergy::eval_residue_pair_derivatives(), core::io::silent::BinaryProteinSilentStruct::fill_struct(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::find_disulfides(), get_component_lower_bound(), get_component_of_residue(), get_component_upper_bound(), get_jump_name_to_components(), get_jump_name_to_subunits(), get_subunit_name_to_component(), get_sym_aware_jump_num(), get_symdof_subunits(), is_multicomponent(), is_singlecomponent(), protocols::topology_broker::FibrilModelingClaimer::make_fibril(), make_symmetric_pose(), protocols::simple_filters::ShapeComplementarityFilter::report_sm(), core::scoring::methods::CartesianBondedEnergy::residue_pair_energy_sorted(), core::scoring::methods::CartesianBondedEnergy::setup_for_scoring(), sym_dof_jump_num(), and sym_dof_names().

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

static