Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Functions
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::Realget_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< Sizeget_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< Sizeget_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< Sizeget_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< Sizeget_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< Sizeget_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< Sizeget_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< Sizeget_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< Sizeget_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< Sizeget_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< Sizeget_symdof_subunits (core::pose::Pose const &pose, std::string const &jname)
 
utility::vector1< char > symmetric_components (core::pose::Pose const &pose)
 
bool is_singlecomponent (core::pose::Pose const &pose)
 
bool is_multicomponent (core::pose::Pose const &pose)
 
Size get_component_lower_bound (core::pose::Pose const &pose, char c)
 
Size get_component_upper_bound (core::pose::Pose const &pose, char c)
 
char get_component_of_residue (core::pose::Pose const &pose, Size ir)
 
char get_subunit_name_to_component (core::pose::Pose const &pose, std::string const &vname)
 
utility::vector1< char > const & get_jump_name_to_components (core::pose::Pose const &pose, std::string const &jname)
 
utility::vector1< Size > const & get_jump_name_to_subunits (core::pose::Pose const &pose, std::string const &jname)
 
std::string get_resnum_to_subunit_component (core::pose::Pose const &pose, Size const &resnum)
 
utility::vector1< std::string > get_full_intracomponent_subs (core::pose::Pose const &pose, std::string const &jname)
 

Function Documentation

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

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

Parameters
[in]pose_inSymmetric input pose containing the asymmetric subunit of interest
[out]pose_outAsymmetric subunit will be placed into this object
[in]with_virtual_atomsIf 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::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::pose::Pose::is_fullatom(), is_symmetric(), 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::task_operations::SelectBySASAOperation::apply(), protocols::loophash::LoopHashMoverWrapper::apply(), protocols::rbsegment_relax::OptimizeThreadingMover::apply(), protocols::task_operations::CrystalContactsOperation::apply(), protocols::analysis::LoopAnalyzerMover::apply(), protocols::task_operations::RestrictNativeResiduesOperation::apply(), protocols::loop_grower::FragmentExtension::apply(), protocols::cryst::UpdateCrystInfo::apply(), protocols::simple_moves::PeriodicBoxMover::apply(), protocols::task_operations::DsspDesignOperation::apply(), protocols::symmetry::ExtractAsymmetricUnitMover::apply(), protocols::flxbb::LayerDesignOperation::apply(), protocols::cryst::TagPoseWithRefinementStatsMover::apply(), protocols::forge::remodel::RemodelLoopMover::apply(), core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::calculate(), core::simple_metrics::metrics::RMSDMetric::calculate(), protocols::denovo_design::components::StructureData::check_pose_consistency(), protocols::score_filters::GeometryFilter::compute(), protocols::simple_filters::MutationsFilter::compute(), protocols::protein_interface_design::filters::SequenceRecoveryFilter::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().

void core::pose::symmetry::extract_asymmetric_unit_pdb_info ( pose::Pose const &  pose,
pose::PDBInfoCOP  pdb_info_src,
pose::PDBInfoOP  pdb_info_target 
)
void core::pose::symmetry::find_new_symmetric_jump_residues ( core::pose::Pose pose)
int core::pose::symmetry::find_symmetric_basejump_anchor ( pose::Pose pose)
core::pose::Pose core::pose::symmetry::get_asymmetric_pose_copy_from_symmetric_pose ( pose::Pose const &  pose)
core::pose::Pose core::pose::symmetry::get_buildingblock_and_neighbor_subs ( Pose const &  pose_in,
utility::vector1< Size >  intra_subs 
)
Size core::pose::symmetry::get_component_lower_bound ( core::pose::Pose const &  pose,
char  c 
)
char core::pose::symmetry::get_component_of_residue ( core::pose::Pose const &  pose,
Size  ir 
)
Size core::pose::symmetry::get_component_upper_bound ( core::pose::Pose const &  pose,
char  c 
)
utility::vector1< Size > core::pose::symmetry::get_full_intracomponent_and_neighbor_resis ( Pose const &  pose,
std::string const &  sym_dof_name,
Real  contact_dist 
)
core::pose::Pose core::pose::symmetry::get_full_intracomponent_and_neighbor_subpose ( Pose const &  pose,
std::string const &  sym_dof_name,
Real  contact_dist 
)
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 
)
utility::vector1< Size > core::pose::symmetry::get_full_intracomponent_neighbor_resis ( Pose const &  pose,
std::string const &  sym_dof_name,
Real  contact_dist 
)
core::pose::Pose core::pose::symmetry::get_full_intracomponent_neighbor_subpose ( Pose const &  pose,
std::string const &  sym_dof_name,
Real  contact_dist 
)
utility::vector1< std::string > core::pose::symmetry::get_full_intracomponent_neighbor_subs ( Pose const &  pose,
std::string const &  sym_dof_name,
Real  contact_dist 
)
utility::vector1< Size > core::pose::symmetry::get_full_intracomponent_resis ( Pose const &  pose,
std::string const &  sym_dof_name 
)
core::pose::Pose core::pose::symmetry::get_full_intracomponent_subpose ( Pose const &  pose,
std::string const &  sym_dof_name 
)
utility::vector1< std::string > core::pose::symmetry::get_full_intracomponent_subs ( core::pose::Pose const &  pose,
std::string const &  jname 
)
utility::vector1< Size > core::pose::symmetry::get_intracomponent_and_interneighbor_resis ( Pose const &  pose,
std::string const &  sym_dof_name,
Real  contact_dist 
)
core::pose::Pose core::pose::symmetry::get_intracomponent_and_interneighbor_subpose ( Pose const &  pose,
std::string const &  sym_dof_name,
Real  contact_dist 
)
utility::vector1< std::string > core::pose::symmetry::get_intracomponent_and_interneighbor_subs ( Pose const &  pose,
std::string const &  sym_dof_name,
Real  contact_dist 
)
utility::vector1< Size > core::pose::symmetry::get_intracomponent_and_intraneighbor_resis ( Pose const &  pose,
std::string const &  sym_dof_name,
Real  contact_dist 
)
core::pose::Pose core::pose::symmetry::get_intracomponent_and_intraneighbor_subpose ( Pose const &  pose,
std::string const &  sym_dof_name,
Real  contact_dist 
)
utility::vector1< std::string > core::pose::symmetry::get_intracomponent_and_intraneighbor_subs ( Pose const &  pose,
std::string const &  sym_dof_name,
Real  contact_dist 
)
utility::vector1< Size > core::pose::symmetry::get_intracomponent_and_neighbor_resis ( Pose const &  pose,
std::string const &  sym_dof_name,
Real  contact_dist 
)
core::pose::Pose core::pose::symmetry::get_intracomponent_and_neighbor_subpose ( Pose const &  pose,
std::string const &  sym_dof_name,
Real  contact_dist 
)
utility::vector1< std::string > core::pose::symmetry::get_intracomponent_and_neighbor_subs ( Pose const &  pose,
std::string const &  sym_dof_name,
Real  contact_dist 
)
utility::vector1< Size > core::pose::symmetry::get_intracomponent_resis ( Pose const &  pose,
std::string const &  sym_dof_name,
Real  contact_dist 
)
core::pose::Pose core::pose::symmetry::get_intracomponent_subpose ( Pose const &  pose,
std::string const &  sym_dof_name,
Real  contact_dist 
)
utility::vector1< std::string > core::pose::symmetry::get_intracomponent_subs ( Pose const &  pose,
std::string const &  sym_dof_name,
Real  contact_dist 
)
utility::vector1< char > const & core::pose::symmetry::get_jump_name_to_components ( core::pose::Pose const &  pose,
std::string const &  jname 
)
utility::vector1< Size > const & core::pose::symmetry::get_jump_name_to_subunits ( core::pose::Pose const &  pose,
std::string const &  jname 
)
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().

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

utility::vector1< Size > core::pose::symmetry::get_resis ( Pose const &  pose,
utility::vector1< std::string >  subs 
)
std::string core::pose::symmetry::get_resnum_to_subunit_component ( core::pose::Pose const &  pose,
Size const &  resnum 
)
core::pose::Pose core::pose::symmetry::get_subpose ( Pose const &  pose,
utility::vector1< std::string >  subs 
)
char core::pose::symmetry::get_subunit_name_to_component ( core::pose::Pose const &  pose,
std::string const &  vname 
)

References symmetry_info().

int core::pose::symmetry::get_sym_aware_jump_num ( core::pose::Pose const &  pose,
core::Size  jump_num 
)
utility::vector1< Size > core::pose::symmetry::get_symdof_subunits ( core::pose::Pose const &  pose,
std::string const &  jname 
)
numeric::xyzVector< core::Real > core::pose::symmetry::get_symm_axis ( core::pose::Pose pose)
bool core::pose::symmetry::intracomponent_contact ( Pose const &  pose,
std::string const &  sym_dof_name,
Real  contact_dist 
)
bool core::pose::symmetry::is_mirror_symmetric ( pose::Pose const &  pose)
bool core::pose::symmetry::is_multicomponent ( core::pose::Pose const &  pose)
bool core::pose::symmetry::is_singlecomponent ( core::pose::Pose const &  pose)
bool core::pose::symmetry::is_symmetric ( scoring::Energies const &  energies)

Referenced by protocols::forge::remodel::RemodelLoopMover::abinitio_stage(), 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::simple_moves::AddResidueLabelMover::apply(), protocols::electron_density::ScaleMapIntensities::apply(), protocols::electron_density::ReportFSC::apply(), protocols::forge::remodel::RemodelRotamerLinks::apply(), protocols::task_operations::StoreTaskMover::apply(), protocols::task_operations::StoreCombinedStoredTasksMover::apply(), protocols::task_operations::SelectBySASAOperation::apply(), protocols::pose_length_moves::FixAllLoopsMover::apply(), protocols::symmetric_docking::SymFoldandDockSlideTrialMover::apply(), protocols::protein_interface_design::filters::FilterScanFilter::apply(), protocols::symmetry::SymmetricRMSMover::apply(), protocols::loophash::LoopHashMoverWrapper::apply(), protocols::task_operations::StoreCompoundTaskMover::apply(), protocols::rbsegment_relax::OptimizeThreadingMover::apply(), protocols::fibril::SetupForFibrilMover::apply(), core::select::residue_selector::SymmetricalResidueSelector::apply(), protocols::denovo_design::movers::SealFoldTreeMover::apply(), protocols::matdes::SymDofMover::apply(), protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::apply(), protocols::normalmode::NormalModeMinimizer::apply(), protocols::symmetry::SetupForSymmetryMover::apply(), protocols::symmetric_docking::SymFoldandDockRbTrialMover::apply(), protocols::task_operations::RestrictNativeResiduesOperation::apply(), protocols::md::CartesianMD::apply(), protocols::simple_moves::ReturnSidechainMover::apply(), protocols::hybridization::CartesianSampler::apply(), protocols::symmetry::SymDockingInitialPerturbation::apply(), core::pack::task::operation::NoRepackDisulfides::apply(), protocols::task_operations::JointSequenceOperation::apply(), protocols::hybridization::CartesianHybridize::apply(), core::select::residue_selector::ResidueIndexSelector::apply(), protocols::denovo_design::movers::FoldTreeFromFoldGraphMover::apply(), core::select::residue_selector::AsymmetricUnitSelector::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::denovo_design::residue_selectors::NamedSegmentSelector::apply(), protocols::task_operations::SeqprofConsensusOperation::apply(), protocols::carbohydrates::GlycanTreeMinMover::apply(), protocols::rigid::WholeBodyTranslationMover::apply(), protocols::simple_moves::ReportEffectivePKA::apply(), protocols::relax::LocalRelax::apply(), protocols::pose_creation::MergePDBMover::apply(), core::select::residue_selector::DensityFitResidueSelector::apply(), protocols::minimization_packing::RotamerTrialsMover::apply(), protocols::relax::ClassicRelax::apply(), protocols::symmetry::SymDockingSlideIntoContact::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::rigid::WholeBodyRotationMover::apply(), protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::idealize::IdealizeMover::apply(), protocols::carbohydrates::GlycanTreeModeler::apply(), protocols::task_operations::DsspDesignOperation::apply(), protocols::task_operations::PruneBuriedUnsatsOperation::apply(), protocols::symmetry::FaSymDockingSlideTogether::apply(), protocols::minimization_packing::MinMover::apply(), protocols::fldsgn::CircularPermutation::apply(), protocols::symmetry::ExtractAsymmetricUnitMover::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::hybridization::FoldTreeHybridize::apply(), protocols::relax::FastRelax::apply(), protocols::simple_task_operations::RestrictToInterface::apply(), protocols::symmetric_docking::SymDockProtocol::apply(), protocols::minimization_packing::EnergyCutRotamerTrialsMover::apply(), protocols::symmetry::ExtractAsymmetricPoseMover::apply(), protocols::flxbb::LayerDesignOperation::apply(), protocols::denovo_design::movers::SetPoseSecstructFromStructureDataMover::apply(), protocols::hbnet::HBNet::apply(), protocols::loop_grower::LoopGrower::apply(), protocols::forge::components::VarLengthBuild::apply(), protocols::hybridization::CartesianSampler::apply_constraints(), protocols::hybridization::CartesianHybridize::apply_frame(), protocols::idealize::basic_idealize(), protocols::relax::FastRelax::batch_apply(), protocols::electron_density::BfactorMultifunc::BfactorMultifunc(), protocols::forge::remodel::RemodelLoopMover::boost_closure_stage(), core::pack::rotamer_set::RotamerSets::build_rotamers(), core::scoring::CA_rmsd_symmetric(), protocols::simple_moves::StructProfileMover::calc_cenlist(), protocols::symmetric_docking::SymDockProtocol::calc_fnat(), protocols::symmetric_docking::SymDockProtocol::calc_interaction_energy(), protocols::symmetric_docking::SymDockProtocol::calc_Irms(), protocols::symmetric_docking::SymDockProtocol::calc_rms(), protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::calculate(), protocols::quantum_annealing::InteractionGraphSummaryMetric::calculate(), core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::calculate(), core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::calculate(), core::scoring::electron_density::calculate_density_nbr(), core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::calculate_penalty_once_from_scratch(), core::scoring::fiber_diffraction::FiberDiffractionEnergyDens::calculate_rho_fast2(), protocols::fldsgn::BluePrintBDR::centroid_build(), protocols::hybridization::HybridizeProtocol::check_and_create_fragments(), protocols::denovo_design::components::StructureData::check_pose_consistency(), protocols::simple_moves::PeriodicBoxMover::check_virial_pressure(), protocols::jumping::close_chainbreaks(), protocols::relax::FastRelax::cmd_accept_to_best(), protocols::simple_filters::InterfaceSasaFilter::compute(), protocols::simple_filters::MutationsFilter::compute(), protocols::cryst::ReportGradientsMover::compute(), protocols::protein_interface_design::filters::DesignableResiduesFilter::compute(), protocols::protein_interface_design::filters::SequenceRecoveryFilter::compute(), protocols::simple_filters::TaskAwareScoreTypeFilter::compute(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::simple_filters::LeastNativeLike9merFilter::compute(), protocols::simple_filters::ShapeComplementarityFilter::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(), 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::electron_density::BfactorMultifunc::dfunc(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::disulfides_changed(), protocols::loop_modeling::refiners::MinimizationRefiner::do_apply(), protocols::hybridization::HybridizeProtocol::do_intrastage_docking(), protocols::electron_density::dockPoseIntoMap(), core::select::movemap::MoveMapFactory::edit_movemap_given_pose(), protocols::simple_moves::ClassicFragmentMover::end_bias_check(), protocols::rigid::MovePoseToMembraneCenterMover::estimate_membrane_center(), core::scoring::methods::BranchEnergy::eval_atom_derivative(), core::scoring::methods::ChainbreakEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensCenEnergy::eval_atom_derivative(), core::scoring::methods::RG_Energy_Fast::eval_atom_derivative(), core::scoring::electron_density::ElecDensEnergy::eval_atom_derivative(), core::scoring::ScoreFunction::eval_long_range_twobody_energies(), core::scoring::ScoreFunction::eval_onebody_energies(), core::scoring::electron_density::FastDensEnergy::eval_residue_pair_derivatives(), core::scoring::ScoreFunction::eval_twobody_neighbor_energies(), core::scoring::SmoothEnvPairPotential::evaluate_env_and_cbeta_deriv(), core::scoring::SmoothEnvPairPotential::evaluate_env_and_cbeta_scores(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty::evaluate_rotamer_pair_energies(), extract_asymmetric_unit(), extract_asymmetric_unit_pdb_info(), core::io::silent::BinarySilentStruct::fill_pose(), core::io::silent::BinarySilentStruct::fill_struct(), protocols::loop_grower::LoopPartialSolutionStore::filter(), protocols::cyclic_peptide::crosslinker::Metal_HelperBase::filter_by_constraints_energy_symmetric(), protocols::cyclic_peptide::crosslinker::Metal_HelperBase::filter_by_sidechain_distance_symmetric(), protocols::nmr::filter_spinlabel_ensemble_by_packerenergy(), core::scoring::methods::BranchEnergy::finalize_total_energy(), core::scoring::methods::ChainbreakEnergy::finalize_total_energy(), core::scoring::methods::CenPairMotifEnergy::finalize_total_energy(), core::scoring::methods::CenPairMotifDegreeEnergy::finalize_total_energy(), core::scoring::methods::D2H_SA_Energy::finalize_total_energy(), core::scoring::methods::MembraneLipo::finalize_total_energy(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::find_disulfides(), core::scoring::fiber_diffraction::find_max_r(), core::scoring::fiber_diffraction::find_min_xyz(), find_new_symmetric_jump_residues(), core::scoring::fiber_diffraction::find_num_scattering_atoms(), core::scoring::fiber_diffraction::find_pitch(), protocols::hybridization::generate_centroid_constraints(), protocols::simple_moves::StructProfileMover::generate_counts(), protocols::simple_moves::StructProfileMover::generate_profile_score_wo_background(), protocols::simple_moves::StructProfileMover::get_closest_sequences(), protocols::simple_ddg::SSElementBisectddGFilter::get_ddg_bisect_score(), protocols::cluster::GatherPosesMover::get_distance_measure(), protocols::indexed_structure_store::FragmentLookup::get_fragment_residue_spans(), core::select::get_master_subunit_selection(), core::scoring::motif::MotifHash::get_matching_motifs(), protocols::matdes::get_matching_subunits(), protocols::relax::LocalRelax::get_neighbor_graph(), protocols::cryst::get_nres_asu(), get_nres_asymmetric_unit(), protocols::hybridization::get_num_residues_nonvirt(), protocols::hybridization::get_num_residues_prot(), core::select::residue_selector::get_residue_mapping_from_selectors(), core::scoring::get_score_function(), protocols::fldsgn::potentials::SetSecStructEnergies::get_secstruct(), protocols::simple_ddg::SSElementBisectddGFilter::get_ss_elements(), protocols::simple_filters::SSElementMotifContactFilter::get_ss_elements(), protocols::simple_filters::SSElementMotifContactFilter::get_SSelements_in_contact(), get_sym_aware_jump_num(), get_symdof_subunits(), get_symm_axis(), core::util::getMLweight(), core::util::getMLweight_cart(), protocols::hbnet::hbnet_symm_one_body_energies(), core::pack::hbonds::hbond_graph_from_partial_rotsets(), protocols::floppy_tail::FloppyTailMover::high_res(), core::scoring::SecondaryStructurePotential::hspair(), protocols::forge::remodel::RemodelLoopMover::independent_stage(), protocols::hybridization::FragmentBiasAssigner::init(), core::scoring::motif::ResPairMotifQuery::init(), core::scoring::nmr::pre::PRESingleSet::init_from_filedata(), core::scoring::nmr::pcs::PCSSingleSet::init_from_pcs_filedata(), core::io::pose_to_sfr::PoseToStructFileRepConverter::init_from_pose(), 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(), protocols::pose_metric_calculators::RotamerBoltzCalculator::init_minmover(), protocols::carbohydrates::GlycanSampler::init_objects(), protocols::floppy_tail::FloppyTailMover::init_on_new_input(), protocols::pose_metric_calculators::RotamerBoltzCalculator::init_task(), protocols::hybridization::HybridizeFoldtreeDynamic::initialize(), protocols::hybridization::HybridizeProtocol::initialize_and_sample_loops(), protocols::topology_broker::FoldandDockClaimer::initialize_dofs(), protocols::topology_broker::MembraneTopologyClaimer::initialize_dofs(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::initialize_graph_for_packing(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::initialize_graphs(), core::scoring::PolymerBondedEnergyContainer::initialize_peptide_bonded_pair_indices(), core::scoring::cryst::PhenixInterface::initialize_target_evaluator(), protocols::relax::FastRelax::inner_loop_accept_to_best_command(), protocols::minimization_packing::MinMover::inner_run_minimizer(), protocols::forge::remodel::RemodelLoopMover::insert_random_smallestmer_per_loop(), core::scoring::PolymerBondedEnergyContainer::is_valid(), protocols::forge::remodel::RemodelLoopMover::loophash_stage(), protocols::loops::loops_set_move_map(), make_asymmetric_pose(), protocols::topology_broker::FibrilModelingClaimer::make_fibril(), core::pack::interaction_graph::make_linmem_ig(), 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(), core::pack::make_symmetric_task(), protocols::loops::loop_mover::refine::ShearMinCCDTrial::minimizer(), protocols::loops::loop_mover::refine::SmallMinCCDTrial::minimizer(), protocols::forge::remodel::RemodelDesignMover::mode5_packertask(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), protocols::cryst::ReportGradientsMover::normalization(), protocols::electron_density::BfactorMultifunc::operator()(), core::scoring::ScoreFunction::operator()(), protocols::pose_creation::MergePDBMover::pack_and_minimize(), core::pack::pack_rotamers(), protocols::calc_taskop_filters::RelativePoseFilter::parse_my_tag(), core::select::residue_selector::SSElementSelector::parse_ss(), protocols::cryst::DockLatticeMover::perturb_chis(), protocols::comparative_modeling::pick_loops_chainbreak(), protocols::comparative_modeling::GenericJobInputter::pose_from_job(), protocols::jd2::LargeNstructJobInputter::pose_from_job(), protocols::jd2::SilentFileJobInputter::pose_from_job(), protocols::topology_broker::MembraneTopologyClaimer::pre_process(), protocols::denovo_design::DisulfidizeMover::process_pose(), protocols::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::scoring::methods::MembraneCenPairEnergy::residue_pair_energy(), core::scoring::membrane::MPPairEnergy::residue_pair_energy(), core::scoring::electron_density::FastDensEnergy::residue_pair_energy(), core::scoring::electron_density::ElecDensEnergy::residue_pair_energy(), core::pack::rotamer_trials(), core::optimization::AtomTreeMinimizer::run(), protocols::simple_moves::StructProfileMover::save_MSAcst_file(), protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::score(), core::scoring::MembranePotential::score_normal_center(), sealed_symmetric_fold_tree(), core::scoring::nmr::pcs::PCSSingleSet::set_atom_derivatives(), core::scoring::nmr::rdc::RDCMultiSet::set_atom_derivatives(), core::scoring::nmr::pre::PREMultiSet::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::voids_penalty_energy::VoidsPenaltyEnergy::set_up_residuearrayannealableenergy_for_packing(), core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::set_up_residuearrayannealableenergy_for_packing(), core::optimization::CartesianMinimizerMap::setup(), protocols::symmetry::SymmetrySlider::setup(), protocols::minimization_packing::PackRotamersMover::setup(), protocols::relax::CentroidRelax::setup_class_movemap_and_constraints(), core::scoring::fiber_diffraction::setup_cylindrical_coords(), protocols::hybridization::FoldTreeHybridize::setup_foldtree(), core::scoring::methods::SmoothEnvEnergy::setup_for_derivatives(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::setup_for_derivatives(), core::scoring::electron_density::ElecDensEnergy::setup_for_derivatives(), core::scoring::electron_density::ElecDensCenEnergy::setup_for_derivatives(), core::scoring::methods::EnvSmoothEnergy::setup_for_derivatives(), core::scoring::electron_density::FastDensEnergy::setup_for_derivatives(), core::scoring::methods::RG_Energy_Fast::setup_for_derivatives(), core::scoring::ScoreFunction::setup_for_derivatives(), protocols::nmr::rdc::RDCEnergy::setup_for_minimizing(), protocols::nmr::pcs::PCSEnergy::setup_for_minimizing(), protocols::nmr::pre::PREEnergy::setup_for_minimizing(), core::scoring::ScoreFunction::setup_for_minimizing(), core::scoring::methods::GenericBondedEnergy::setup_for_scoring(), core::scoring::fiber_diffraction::FiberDiffractionEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensEnergy::setup_for_scoring(), core::scoring::electron_density::FastDensEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensCenEnergy::setup_for_scoring(), core::scoring::fiber_diffraction::FiberDiffractionEnergyDens::setup_for_scoring(), core::scoring::methods::CartesianBondedEnergy::setup_for_scoring(), protocols::idealize::IdealizeMover::setup_idealize_constraints(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::setup_movemap(), protocols::carbohydrates::GlycanSampler::setup_movers(), protocols::simple_moves::ExplicitWaterMover::setup_pack(), core::scoring::mhc_epitope_energy::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::rdc::RDCMultiSet::update_spin_coordinates(), core::scoring::nmr::pre::PREMultiSet::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().

bool core::pose::symmetry::is_symmetric ( pose::Pose const &  pose)
std::string core::pose::symmetry::jump_num_sym_dof ( core::pose::Pose const &  pose,
Size const &  jnum 
)
void core::pose::symmetry::make_asymmetric_pose ( pose::Pose pose)
void core::pose::symmetry::make_residue_mask_symmetric ( core::pose::Pose const &  p,
utility::vector1< bool > &  msk 
)
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::conformation::Conformation::size(), 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::minimization_packing::symmetry::TaskAwareSymMinMover::apply(), protocols::symmetric_docking::SymSidechainMinMover::apply(), protocols::md::CartesianMD::apply(), protocols::hybridization::CartesianSampler::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::carbohydrates::GlycanTreeMinMover::apply(), protocols::relax::LocalRelax::apply(), protocols::relax::ClassicRelax::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::symmetric_docking::SymInterfaceSidechainMinMover::apply(), protocols::minimization_packing::MinMover::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::hybridization::FoldTreeHybridize::apply(), protocols::relax::FastRelax::apply(), protocols::cryst::DockLatticeMover::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::FoldandDockClaimer::initialize_dofs(), protocols::topology_broker::FibrilModelingClaimer::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_QuickCCD_Moves::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::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().

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 
)
void core::pose::symmetry::make_symmetric_pose ( pose::Pose pose,
conformation::symmetry::SymmetryInfo  symmetry_info 
)
void core::pose::symmetry::make_symmetric_pose ( pose::Pose pose,
conformation::symmetry::SymmData &  symmdata,
bool  keep_pdb_info_labels 
)
void core::pose::symmetry::make_symmetric_pose ( pose::Pose pose,
std::string  symmdef_file 
)

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

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

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

Attempt to detect whether a conformation is symmetric

bool core::pose::symmetry::scorefxn_is_symmetric ( pose::Pose const &  pose)

Attempt to detect whether a pose is symmetric

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

core::kinematics::FoldTree core::pose::symmetry::sealed_symmetric_fold_tree ( core::pose::Pose pose)
void core::pose::symmetry::set_asymm_unit_fold_tree ( core::pose::Pose p,
kinematics::FoldTree const &  f 
)
int core::pose::symmetry::sym_dof_jump_num ( core::pose::Pose const &  pose,
std::string const &  jname 
)
utility::vector1< std::string > core::pose::symmetry::sym_dof_names ( core::pose::Pose const &  pose)
utility::vector1< char > core::pose::symmetry::symmetric_components ( core::pose::Pose const &  pose)
void core::pose::symmetry::symmetrize_fold_tree ( core::pose::Pose const &  p,
kinematics::FoldTree &  f 
)

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

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

This function does not require the symm data

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

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

conformation::symmetry::SymmetryInfoCOP core::pose::symmetry::symmetry_info ( pose::Pose const &  pose)

Attempts to grab the symmetry info if the pose is symmetric

References core::pose::Pose::conformation(), 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::simple_moves::AddResidueLabelMover::apply(), protocols::forge::remodel::RemodelRotamerLinks::apply(), protocols::task_operations::StoreCombinedStoredTasksMover::apply(), protocols::task_operations::SelectBySASAOperation::apply(), protocols::matdes::ExtractSubposeMover::apply(), protocols::task_operations::SelectByDeltaScoreOperation::apply(), protocols::task_operations::StoreCompoundTaskMover::apply(), protocols::task_operations::CrystalContactsOperation::apply(), protocols::matdes::BuildingBlockInterfaceOperation::apply(), protocols::minimization_packing::symmetry::TaskAwareSymMinMover::apply(), core::select::residue_selector::SymmetricalResidueSelector::apply(), protocols::task_operations::JointSequenceOperation::apply(), core::pack::task::operation::NoRepackDisulfides::apply(), core::select::residue_selector::ResidueIndexSelector::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(), protocols::jumping::close_chainbreaks(), protocols::simple_filters::InterfaceSasaFilter::compute(), protocols::matdes::InterfacePackingFilter::compute(), protocols::protein_interface_design::filters::DesignableResiduesFilter::compute(), protocols::simple_filters::TaskAwareScoreTypeFilter::compute(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::matdes::SymUnsatHbondFilter::compute(), protocols::matdes::ClashCheckFilter::compute(), protocols::matdes::OligomericAverageDegreeFilter::compute(), protocols::forge::remodel::RemodelMover::design_refine_cart_relax(), protocols::forge::remodel::RemodelMover::design_refine_seq_relax(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::disulfides_changed(), protocols::simple_moves::ClassicFragmentMover::end_bias_check(), protocols::forge::methods::fill_non_loop_cst_set(), core::io::silent::BinarySilentStruct::fill_struct(), core::scoring::methods::CenPairMotifDegreeEnergy::finalize_total_energy(), core::scoring::methods::CenPairMotifEnergy::finalize_total_energy(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::find_disulfides(), core::scoring::fiber_diffraction::find_num_scattering_atoms(), protocols::simple_moves::StructProfileMover::generate_counts(), protocols::simple_moves::StructProfileMover::generate_profile_score_wo_background(), get_buildingblock_and_neighbor_subs(), protocols::simple_moves::StructProfileMover::get_closest_sequences(), get_component_lower_bound(), get_component_of_residue(), get_component_upper_bound(), protocols::simple_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(), protocols::simple_moves::StructProfileMover::save_MSAcst_file(), core::scoring::nmr::pcs::PCSSingleSet::set_atom_derivatives(), core::scoring::nmr::rdc::RDCMultiSet::set_atom_derivatives(), core::scoring::nmr::pre::PREMultiSet::set_atom_derivatives(), protocols::nmr::rdc::RDCEnergy::setup_for_minimizing(), protocols::nmr::pcs::PCSEnergy::setup_for_minimizing(), protocols::nmr::pre::PREEnergy::setup_for_minimizing(), core::scoring::methods::GenericBondedEnergy::setup_for_scoring(), core::scoring::methods::CartesianBondedEnergy::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::rdc::RDCMultiSet::update_spin_coordinates(), core::scoring::nmr::pre::PREMultiSet::update_spin_coordinates(), and protocols::simple_filters::ShapeComplementarityFilter::write_area().

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