Rosetta 3.4
Functions
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)
 extract the asu from a pose... unlike previous function symmetric clones are thrown out
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)
numeric::xyzVector< core::Realget_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)

Function Documentation

void core::pose::symmetry::extract_asymmetric_unit ( core::pose::Pose const &  pose_in,
core::pose::Pose pose_out 
)
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)
numeric::xyzVector< core::Real > core::pose::symmetry::get_symm_axis ( core::pose::Pose pose)
bool core::pose::symmetry::is_symmetric ( pose::Pose const &  pose)

Attempt to detect whether a pose is symmetric

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

bool core::pose::symmetry::is_symmetric ( scoring::ScoreFunction const &  scorefxn)
bool core::pose::symmetry::is_symmetric ( scoring::Energies const &  energies)

Referenced by protocols::topology_broker::MembraneTopologyClaimer::add_mover(), protocols::fibril::SetupForFibrilMover::align(), protocols::toolbox::task_operations::JointSequenceOperation::apply(), protocols::symmetric_docking::SymFoldandDockSlideTrialMover::apply(), protocols::symmetric_docking::SymFoldandDockRbTrialMover::apply(), protocols::simple_moves::symmetry::SymmetricRMSMover::apply(), protocols::simple_moves::symmetry::FaSymDockingSlideTogether::apply(), protocols::simple_moves::symmetry::SymDockingSlideIntoContact::apply(), protocols::simple_moves::symmetry::SymDockingInitialPerturbation::apply(), protocols::simple_moves::symmetry::ExtractAsymmetricPoseMover::apply(), protocols::simple_moves::symmetry::ExtractAsymmetricUnitMover::apply(), protocols::simple_moves::symmetry::SetupForSymmetryMover::apply(), protocols::simple_moves::GreedyOptMutationMover::apply(), protocols::rigid::WholeBodyRotationMover::apply(), protocols::rigid::WholeBodyTranslationMover::apply(), protocols::relax::FastRelax::apply(), protocols::relax::ClassicRelax::apply(), protocols::protein_interface_design::movers::RandomMutation::apply(), protocols::protein_interface_design::filters::FilterScanFilter::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply(), protocols::loophash::LoopHashMoverWrapper::apply(), protocols::idealize::IdealizeMover::apply(), protocols::forge::remodel::RemodelLoopMover::apply(), protocols::forge::components::VarLengthBuild::apply(), protocols::fibril::SetupForFibrilMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::comparative_modeling::hybridize::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::jumping::close_chainbreaks(), protocols::relax::FastRelax::cmd_accept_to_best(), protocols::protein_interface_design::filters::BindingStrainFilter::compute(), protocols::simple_filters::RotamerBoltzmannWeight::compute_Boltzmann_weight(), 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::relax::FastRelax::do_minimize(), protocols::electron_density::dockPoseIntoMap(), protocols::simple_moves::ClassicFragmentMover::end_bias_check(), protocols::rigid::MovePoseToMembraneCenterMover::estimate_membrane_center(), core::scoring::electron_density::PattersonCorrEnergy::eval_atom_derivative(), core::scoring::electron_density::FastDensEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensCenEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::eval_atom_derivative(), extract_asymmetric_unit(), extract_asymmetric_unit_pdb_info(), core::io::silent::BinaryProteinSilentStruct::fill_pose(), core::io::silent::BinaryProteinSilentStruct::fill_struct(), core::scoring::methods::MembraneLipo::finalize_total_energy(), find_new_symmetric_jump_residues(), protocols::cluster::GatherPosesMover::get_distance_measure(), get_symm_axis(), protocols::jd2::JobDistributor::go_main(), protocols::forge::remodel::RemodelLoopMover::independent_stage(), protocols::comparative_modeling::hybridize::HybridizeFoldtreeDynamic::initialize(), protocols::comparative_modeling::hybridize::HybridizeProtocol::initialize_and_sample_loops(), protocols::topology_broker::MembraneTopologyClaimer::initialize_dofs(), protocols::topology_broker::FoldandDockClaimer::initialize_dofs(), protocols::forge::remodel::RemodelLoopMover::insert_random_smallestmer_per_loop(), is_symmetric(), protocols::loops::loops_set_move_map(), make_asymmetric_pose(), protocols::topology_broker::FibrilModelingClaimer::make_fibril(), make_residue_mask_symmetric(), make_symmetric_movemap(), make_symmetric_pdb_info(), make_symmetric_pose(), protocols::simple_moves::symmetry::SymRotamerTrialsMover::make_symmetric_task(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), core::scoring::symmetry::SymmetricScoreFunction::operator()(), core::scoring::ScoreFunction::operator()(), core::pack::pack_rotamers(), protocols::comparative_modeling::pick_loops_chainbreak(), protocols::jd2::SilentFileJobInputter::pose_from_job(), protocols::comparative_modeling::GenericJobInputter::pose_from_job(), protocols::forge::remodel::RemodelLoopMover::randomize_stage(), protocols::simple_filters::AlaScan::report_symmetry(), protocols::protein_interface_design::AlaScan::report_symmetry(), core::scoring::methods::MembraneCenPairEnergy::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(), scorefxn_is_symmetric(), 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::comparative_modeling::hybridize::FoldTreeHybridize::setup_foldtree(), core::scoring::electron_density::FastDensEnergy::setup_for_derivatives(), core::scoring::electron_density::ElecDensEnergy::setup_for_derivatives(), core::scoring::electron_density::ElecDensCenEnergy::setup_for_derivatives(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::setup_for_derivatives(), core::scoring::electron_density::ElecDensCenEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::setup_for_scoring(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::setup_movemap(), protocols::forge::remodel::RemodelLoopMover::simultaneous_stage(), protocols::simple_moves::symmetry::SymmetrySlider::slide(), protocols::simple_moves::symmetry::SymmetrySlider::slide_away(), protocols::simple_moves::ddG::symm_ddG(), symmetry_info(), SymMinimizeInterface(), core::scoring::MembranePotential::termini_penalty(), and protocols::protein_interface_design::filters::RelativePoseFilter::thread_seq().

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::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::SymInterfaceSidechainMinMover::apply(), protocols::symmetric_docking::SymSidechainMinMover::apply(), protocols::simple_moves::symmetry::SymMinMover::apply(), protocols::relax::FastRelax::apply(), protocols::relax::ClassicRelax::apply(), protocols::comparative_modeling::LoopRelaxMover::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_QuickCCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::simple_moves::symmetry::SymShakeStructureMover::run_mc(), protocols::symmetric_docking::SymDockingHiRes::set_default(), protocols::symmetric_docking::SymDockingLowRes::set_default_move_map(), 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 
)
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

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::SetupForSymmetryMover::apply(), core::io::silent::BinaryProteinSilentStruct::fill_pose(), protocols::fibril::make_symmetric_fibril(), and make_symmetric_pose().

void core::pose::symmetry::make_symmetric_pose ( pose::Pose pose,
conformation::symmetry::SymmData &  symmdata 
)
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::n_residue(), and core::pose::Pose::num_jump().

static numeric::random::RandomGenerator core::pose::symmetry::RG ( 408539  ) [static]
void core::pose::symmetry::rotate_anchor_to_x_axis ( core::pose::Pose pose)
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 is_symmetric().

bool core::pose::symmetry::scorefxn_is_symmetric ( conformation::Conformation const &  conf)

Attempt to detect whether a conformation 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 
)
void core::pose::symmetry::symmetrize_fold_tree ( core::pose::Pose const &  p,
kinematics::FoldTree &  f 
)
conformation::symmetry::SymmetryInfoCOP core::pose::symmetry::symmetry_info ( pose::Pose const &  pose)
static basic::Tracer core::pose::symmetry::TR ( "core.pose.symmetry.util"  ) [static]
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