![]() |
Rosetta Core
2014.35
|
Variables | |
static basic::Tracer | TR ("core.pose.symmetry.util") |
static numeric::random::RandomGenerator | RG (408539) |
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
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(), basic::options::option, core::pose::Pose::pdb_info(), residue, core::pose::Pose::residue(), runtime_assert, and core::conformation::symmetry::SymmetricConformation::Symmetry_Info().
Referenced by core::scoring::cryst::PhenixInterface::fitBfactors(), core::scoring::cryst::PhenixInterface::initialize_target_evaluator(), and core::scoring::cryst::PhenixInterface::stealBfactorsFromFile().
void core::pose::symmetry::extract_asymmetric_unit_pdb_info | ( | pose::Pose const & | pose, |
pose::PDBInfoCOP | pdb_info_src, | ||
pose::PDBInfoOP | pdb_info_target | ||
) |
References core::pose::Pose::conformation(), is_symmetric(), nres, and core::conformation::symmetry::SymmetricConformation::Symmetry_Info().
Referenced by extract_asymmetric_unit().
void core::pose::symmetry::find_new_symmetric_jump_residues | ( | core::pose::Pose & | pose | ) |
References anchor, core::pose::Pose::conformation(), numeric::xyzVector< class >::distance(), find_symmetric_basejump_anchor(), core::conformation::Conformation::fold_tree(), is_symmetric(), jumps, basic::options::option, core::pose::Pose::residue(), runtime_assert, basic::options::OptionKeys::fold_and_dock::set_anchor_at_closest_point, core::conformation::Conformation::size(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), numeric::random::RandomGenerator::uniform(), and core::conformation::Residue::xyz().
int core::pose::symmetry::find_symmetric_basejump_anchor | ( | pose::Pose & | pose | ) |
References core::pose::Pose::conformation(), core::kinematics::FoldTree::downstream_jump_residue(), core::conformation::Conformation::fold_tree(), core::kinematics::FoldTree::num_jump(), core::pose::Pose::residue(), core::kinematics::FoldTree::upstream_jump_residue(), and utility_exit_with_message.
Referenced by find_new_symmetric_jump_residues(), and rotate_anchor_to_x_axis().
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 | ||
) |
References core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::pose::Pose::energies(), core::scoring::fa_atr, is_multicomponent(), core::pose::Pose::n_residue(), core::pose::Pose::residue(), core::scoring::Energies::residue_total_energies(), core::scoring::ScoreFunction::set_weight(), start, symmetry_info(), and utility_exit_with_message.
Size core::pose::symmetry::get_component_lower_bound | ( | core::pose::Pose const & | pose, |
char | c | ||
) |
References symmetry_info().
char core::pose::symmetry::get_component_of_residue | ( | core::pose::Pose const & | pose, |
Size | ir | ||
) |
References symmetry_info().
Referenced by intracomponent_contact().
Size core::pose::symmetry::get_component_upper_bound | ( | core::pose::Pose const & | pose, |
char | c | ||
) |
References symmetry_info().
utility::vector1< Size > core::pose::symmetry::get_full_intracomponent_and_neighbor_resis | ( | Pose const & | pose, |
std::string | sym_dof_name, | ||
Real | contact_dist | ||
) |
References get_full_intracomponent_and_neighbor_subs(), and get_resis().
core::pose::Pose core::pose::symmetry::get_full_intracomponent_and_neighbor_subpose | ( | Pose const & | pose, |
std::string | sym_dof_name, | ||
Real | contact_dist | ||
) |
References get_full_intracomponent_and_neighbor_subs(), and get_subpose().
utility::vector1< std::string > core::pose::symmetry::get_full_intracomponent_and_neighbor_subs | ( | Pose const & | pose, |
std::string | sym_dof_name, | ||
Real | contact_dist | ||
) |
References numeric::xyzVector< class >::distance_squared(), core::pose::Pose::fold_tree(), get_full_intracomponent_subs(), get_resnum_to_subunit_component(), is_singlecomponent(), core::conformation::Residue::name3(), core::kinematics::FoldTree::partition_by_jump(), core::pose::Pose::residue(), sym_dof_jump_num(), symmetry_info(), core::pose::Pose::total_residue(), utility_exit_with_message, and core::conformation::Residue::xyz().
Referenced by get_full_intracomponent_and_neighbor_resis(), get_full_intracomponent_and_neighbor_subpose(), and get_full_intracomponent_neighbor_subs().
utility::vector1< Size > core::pose::symmetry::get_full_intracomponent_neighbor_resis | ( | Pose const & | pose, |
std::string | sym_dof_name, | ||
Real | contact_dist | ||
) |
References get_full_intracomponent_neighbor_subs(), and get_resis().
core::pose::Pose core::pose::symmetry::get_full_intracomponent_neighbor_subpose | ( | Pose const & | pose, |
std::string | sym_dof_name, | ||
Real | contact_dist | ||
) |
References get_full_intracomponent_neighbor_subs(), and get_subpose().
utility::vector1< std::string > core::pose::symmetry::get_full_intracomponent_neighbor_subs | ( | Pose const & | pose, |
std::string | sym_dof_name, | ||
Real | contact_dist | ||
) |
utility::vector1< Size > core::pose::symmetry::get_full_intracomponent_resis | ( | Pose const & | pose, |
std::string | sym_dof_name | ||
) |
References get_full_intracomponent_subs(), and get_resis().
core::pose::Pose core::pose::symmetry::get_full_intracomponent_subpose | ( | Pose const & | pose, |
std::string | sym_dof_name | ||
) |
References get_full_intracomponent_subs(), and get_subpose().
utility::vector1< std::string > core::pose::symmetry::get_full_intracomponent_subs | ( | core::pose::Pose const & | pose, |
std::string const & | jname | ||
) |
References core::pack::dunbrack::c, get_jump_name_to_components(), get_jump_name_to_subunits(), and s.
Referenced by get_full_intracomponent_and_neighbor_subs(), get_full_intracomponent_neighbor_subs(), get_full_intracomponent_resis(), get_full_intracomponent_subpose(), get_intracomponent_and_interneighbor_subs(), get_intracomponent_subs(), get_neighbor_subs(), and intracomponent_contact().
utility::vector1< Size > core::pose::symmetry::get_intracomponent_and_interneighbor_resis | ( | Pose const & | pose, |
std::string | sym_dof_name, | ||
Real | contact_dist | ||
) |
References get_intracomponent_and_interneighbor_subs(), and get_resis().
core::pose::Pose core::pose::symmetry::get_intracomponent_and_interneighbor_subpose | ( | Pose const & | pose, |
std::string | sym_dof_name, | ||
Real | contact_dist | ||
) |
References get_intracomponent_and_interneighbor_subs(), and get_subpose().
utility::vector1< std::string > core::pose::symmetry::get_intracomponent_and_interneighbor_subs | ( | Pose const & | pose, |
std::string | sym_dof_name, | ||
Real | contact_dist | ||
) |
utility::vector1< Size > core::pose::symmetry::get_intracomponent_and_intraneighbor_resis | ( | Pose const & | pose, |
std::string | sym_dof_name, | ||
Real | contact_dist | ||
) |
References get_intracomponent_and_intraneighbor_subs(), and get_resis().
core::pose::Pose core::pose::symmetry::get_intracomponent_and_intraneighbor_subpose | ( | Pose const & | pose, |
std::string | sym_dof_name, | ||
Real | contact_dist | ||
) |
References get_intracomponent_and_intraneighbor_subs(), and get_subpose().
utility::vector1< std::string > core::pose::symmetry::get_intracomponent_and_intraneighbor_subs | ( | Pose const & | pose, |
std::string | sym_dof_name, | ||
Real | contact_dist | ||
) |
utility::vector1< Size > core::pose::symmetry::get_intracomponent_and_neighbor_resis | ( | Pose const & | pose, |
std::string | sym_dof_name, | ||
Real | contact_dist | ||
) |
References get_intracomponent_and_neighbor_subs(), and get_resis().
core::pose::Pose core::pose::symmetry::get_intracomponent_and_neighbor_subpose | ( | Pose const & | pose, |
std::string | sym_dof_name, | ||
Real | contact_dist | ||
) |
References get_intracomponent_and_neighbor_subs(), and get_subpose().
utility::vector1< std::string > core::pose::symmetry::get_intracomponent_and_neighbor_subs | ( | Pose const & | pose, |
std::string | sym_dof_name, | ||
Real | contact_dist | ||
) |
References numeric::xyzVector< class >::distance_squared(), core::pose::Pose::fold_tree(), get_resnum_to_subunit_component(), is_singlecomponent(), core::conformation::Residue::name3(), core::kinematics::FoldTree::partition_by_jump(), core::pose::Pose::residue(), start, sym_dof_jump_num(), symmetry_info(), core::pose::Pose::total_residue(), utility_exit_with_message, and core::conformation::Residue::xyz().
Referenced by get_intracomponent_and_interneighbor_subs(), get_intracomponent_and_intraneighbor_subs(), get_intracomponent_and_neighbor_resis(), get_intracomponent_and_neighbor_subpose(), get_intracomponent_subs(), and get_neighbor_subs().
utility::vector1< Size > core::pose::symmetry::get_intracomponent_resis | ( | Pose const & | pose, |
std::string | sym_dof_name, | ||
Real | contact_dist | ||
) |
References get_intracomponent_subs(), and get_resis().
core::pose::Pose core::pose::symmetry::get_intracomponent_subpose | ( | Pose const & | pose, |
std::string | sym_dof_name, | ||
Real | contact_dist | ||
) |
References get_intracomponent_subs(), and get_subpose().
utility::vector1< std::string > core::pose::symmetry::get_intracomponent_subs | ( | Pose const & | pose, |
std::string | sym_dof_name, | ||
Real | contact_dist | ||
) |
References get_full_intracomponent_subs(), get_intracomponent_and_neighbor_subs(), and symmetry_info().
Referenced by get_intracomponent_resis(), and get_intracomponent_subpose().
utility::vector1< char > const & core::pose::symmetry::get_jump_name_to_components | ( | core::pose::Pose const & | pose, |
std::string const & | jname | ||
) |
References symmetry_info().
Referenced by get_full_intracomponent_subs(), get_intracomponent_and_interneighbor_subs(), and get_intracomponent_and_intraneighbor_subs().
utility::vector1< Size > const & core::pose::symmetry::get_jump_name_to_subunits | ( | core::pose::Pose const & | pose, |
std::string const & | jname | ||
) |
References symmetry_info().
Referenced by get_full_intracomponent_subs().
utility::vector1< Size > core::pose::symmetry::get_neighbor_resis | ( | Pose const & | pose, |
std::string | sym_dof_name, | ||
Real | contact_dist | ||
) |
References get_neighbor_subs(), and get_resis().
core::pose::Pose core::pose::symmetry::get_neighbor_subpose | ( | Pose const & | pose, |
std::string | sym_dof_name, | ||
Real | contact_dist | ||
) |
References get_neighbor_subs(), and get_subpose().
utility::vector1< std::string > core::pose::symmetry::get_neighbor_subs | ( | Pose const & | pose, |
std::string | sym_dof_name, | ||
Real | contact_dist | ||
) |
References get_full_intracomponent_subs(), get_intracomponent_and_neighbor_subs(), and symmetry_info().
Referenced by get_neighbor_resis(), and get_neighbor_subpose().
utility::vector1< Size > core::pose::symmetry::get_resis | ( | Pose const & | pose, |
utility::vector1< std::string > | subs | ||
) |
References get_resnum_to_subunit_component(), and symmetry_info().
Referenced by get_full_intracomponent_and_neighbor_resis(), get_full_intracomponent_neighbor_resis(), get_full_intracomponent_resis(), get_intracomponent_and_interneighbor_resis(), get_intracomponent_and_intraneighbor_resis(), get_intracomponent_and_neighbor_resis(), get_intracomponent_resis(), and get_neighbor_resis().
std::string core::pose::symmetry::get_resnum_to_subunit_component | ( | core::pose::Pose const & | pose, |
Size const & | resnum | ||
) |
References symmetry_info().
Referenced by get_full_intracomponent_and_neighbor_subs(), get_intracomponent_and_neighbor_subs(), get_resis(), get_subpose(), and intracomponent_contact().
core::pose::Pose core::pose::symmetry::get_subpose | ( | Pose const & | pose, |
utility::vector1< std::string > | subs | ||
) |
References get_resnum_to_subunit_component(), core::pose::Pose::residue(), start, and symmetry_info().
Referenced by get_full_intracomponent_and_neighbor_subpose(), get_full_intracomponent_neighbor_subpose(), get_full_intracomponent_subpose(), get_intracomponent_and_interneighbor_subpose(), get_intracomponent_and_intraneighbor_subpose(), get_intracomponent_and_neighbor_subpose(), get_intracomponent_subpose(), and get_neighbor_subpose().
char core::pose::symmetry::get_subunit_name_to_component | ( | core::pose::Pose const & | pose, |
std::string const & | vname | ||
) |
References symmetry_info().
int core::pose::symmetry::get_sym_aware_jump_num | ( | core::pose::Pose const & | pose, |
core::Size | jump_num | ||
) |
References is_symmetric(), symmetry_info(), and utility_exit_with_message.
utility::vector1< Size > core::pose::symmetry::get_symdof_subunits | ( | core::pose::Pose const & | pose, |
std::string const & | jname | ||
) |
References core::pose::Pose::fold_tree(), core::conformation::symmetry::SymmetryInfo::get_nres_subunit(), is_symmetric(), core::conformation::symmetry::SymmetryInfo::num_total_residues_without_pseudo(), core::kinematics::FoldTree::partition_by_jump(), core::conformation::symmetry::SymmetryInfo::subunit_index(), sym_dof_jump_num(), symmetry_info(), core::pose::Pose::total_residue(), and utility_exit_with_message.
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 | sym_dof_name, | ||
Real | contact_dist | ||
) |
References numeric::xyzVector< class >::distance_squared(), core::pose::Pose::fold_tree(), get_component_of_residue(), get_full_intracomponent_subs(), get_resnum_to_subunit_component(), is_singlecomponent(), core::conformation::Residue::name3(), core::kinematics::FoldTree::partition_by_jump(), core::pose::Pose::residue(), start, sym_dof_jump_num(), symmetry_info(), core::pose::Pose::total_residue(), utility_exit_with_message, and core::conformation::Residue::xyz().
bool core::pose::symmetry::is_multicomponent | ( | core::pose::Pose const & | pose | ) |
References symmetry_info().
Referenced by get_buildingblock_and_neighbor_subs().
bool core::pose::symmetry::is_singlecomponent | ( | core::pose::Pose const & | pose | ) |
References symmetry_info().
Referenced by get_full_intracomponent_and_neighbor_subs(), get_intracomponent_and_neighbor_subs(), and intracomponent_contact().
bool core::pose::symmetry::is_symmetric | ( | scoring::Energies const & | energies | ) |
Referenced by core::pack::task::operation::NoRepackDisulfides::apply(), core::pack::rotamer_set::RotamerSets::build_rotamers(), core::scoring::CA_rmsd_symmetric(), 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(), core::pack::interaction_graph::InteractionGraphFactory::create_interaction_graph(), core::scoring::electron_density::ElectronDensity::dCCdBs(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::disulfides_changed(), core::scoring::methods::ChainbreakEnergy::eval_atom_derivative(), core::scoring::methods::RG_Energy_Fast::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::BinarySilentStruct::fill_pose(), core::io::silent::BinarySilentStruct::fill_struct(), core::scoring::methods::ChainbreakEnergy::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(), find_new_symmetric_jump_residues(), core::indexed_structure_store::FragmentLookup::get_fragment_residue_spans(), get_sym_aware_jump_num(), get_symdof_subunits(), get_symm_axis(), core::util::getMLweight(), core::util::getMLweight_cart(), core::scoring::SecondaryStructurePotential::hspair(), make_asymmetric_pose(), core::pack::make_new_symmetric_PackerTask_by_intersection(), core::pack::make_new_symmetric_PackerTask_by_requested_method(), core::pack::make_new_symmetric_PackerTask_by_truncation(), core::pack::make_new_symmetric_PackerTask_by_union(), make_residue_mask_symmetric(), make_score_function_consistent_with_symmetric_state_of_pose(), make_symmetric_movemap(), core::pack::make_symmetric_PackerTask_by_truncation(), make_symmetric_pdb_info(), make_symmetric_pose(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), core::scoring::symmetry::SymmetricScoreFunction::operator()(), core::scoring::ScoreFunction::operator()(), core::pack::pack_rotamers(), 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::scoring::methods::CartesianBondedEnergy::residue_pair_energy_sorted(), core::pack::rotamer_trials(), core::optimization::AtomTreeMinimizer::run(), core::scoring::MembranePotential::score_normal_center(), sealed_symmetric_fold_tree(), core::scoring::methods::EnvSmoothEnergy::setup_for_derivatives(), 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::methods::RG_Energy_Fast::setup_for_derivatives(), core::scoring::rna::RNA_SuiteEnergy::setup_for_scoring(), core::scoring::methods::Rama2BOffsetEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensCenEnergy::setup_for_scoring(), core::scoring::methods::CartesianBondedEnergy::setup_for_scoring(), core::scoring::SecondaryStructurePotential::sheets_from_dimers(), core::scoring::SecondaryStructurePotential::sspair(), core::util::switch_to_residue_type_set(), symmetry_info(), core::scoring::MembranePotential::termini_penalty(), 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
References core::pose::Pose::conformation(), and core::conformation::symmetry::is_symmetric().
bool core::pose::symmetry::is_symmetric | ( | scoring::ScoreFunction const & | scorefxn | ) |
std::string core::pose::symmetry::jump_num_sym_dof | ( | core::pose::Pose const & | pose, |
Size const & | jnum | ||
) |
References symmetry_info().
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_score_function_consistent_with_symmetric_state_of_pose | ( | pose::Pose const & | pose, |
scoring::ScoreFunctionOP & | scorefxn | ||
) |
References is_symmetric().
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(), utility::pointer::owning_ptr< T >::get(), core::kinematics::MoveMap::get(), core::pose::Pose::has_dof(), is_symmetric(), core::id::JUMP, jump_move, core::conformation::Residue::natoms(), core::pose::Pose::num_jump(), core::pose::Pose::residue(), runtime_assert, 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 core::util::getMLweight(), and core::util::getMLweight_cart().
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(), basic::options::OptionKeys::symmetry::detect_bonds, core::conformation::Conformation::detect_bonds(), core::pose::Pose::energies(), is_symmetric(), basic::options::option, 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 core::io::silent::BinarySilentStruct::fill_pose(), and make_symmetric_pose().
void core::pose::symmetry::make_symmetric_pose | ( | pose::Pose & | pose, |
conformation::symmetry::SymmData & | symmdata | ||
) |
constructs a symmetric pose with a symmetric conformation and energies object from a monomeric pose and symmData object
References core::pose::conf2pdb_chain(), core::pose::Pose::conformation(), core::conformation::Conformation::detect_bonds(), core::conformation::Conformation::detect_disulfides(), core::pose::Pose::energies(), is_symmetric(), make_symmetric_pdb_info(), option, core::pose::Pose::pdb_info(), core::pose::Pose::set_new_conformation(), core::pose::Pose::set_new_energies_object(), and core::conformation::symmetry::setup_symmetric_conformation().
void core::pose::symmetry::make_symmetric_pose | ( | pose::Pose & | pose, |
std::string | symmdef_file | ||
) |
constructs a symmetric pose with a symmetric conformation and energies object from a monomeric pose and symmetry definition file on command line. Requires the presence of a symmetry_definition file
References make_symmetric_pose(), core::pose::Pose::n_residue(), core::pose::Pose::num_jump(), and option.
void core::pose::symmetry::partition_by_symm_jumps | ( | utility::vector1< int > | jump_numbers, |
core::kinematics::FoldTree const & | ft, | ||
conformation::symmetry::SymmetryInfoCOP | symm_info, | ||
ObjexxFCL::FArray1D_bool & | partner1 | ||
) |
References core::kinematics::FoldTree::begin(), core::kinematics::FoldTree::end(), njumps, and start.
void core::pose::symmetry::rotate_anchor_to_x_axis | ( | core::pose::Pose & | pose | ) |
References anchor, core::conformation::membrane::center, core::pose::Pose::conformation(), numeric::xyzVector< class >::cross(), numeric::xyzMatrix< class >::det(), find_symmetric_basejump_anchor(), core::pose::Pose::fold_tree(), core::pose::Pose::jump(), core::conformation::Residue::name(), numeric::xyzVector< class >::normalize(), core::pose::Pose::residue(), runtime_assert, core::pose::Pose::set_jump(), numeric::conversions::to_degrees(), numeric::xyzMatrix< class >::transpose(), core::conformation::Conformation::upstream_jump_stub(), core::conformation::Residue::xyz(), and numeric::z_rotation_matrix_degrees().
bool core::pose::symmetry::scorefxn_is_symmetric | ( | conformation::Conformation const & | conf | ) |
Attempt to detect whether a conformation is symmetric
bool core::pose::symmetry::scorefxn_is_symmetric | ( | pose::Pose const & | pose | ) |
Attempt to detect whether a pose is symmetric
References core::pose::Pose::conformation(), and core::conformation::symmetry::is_symmetric().
core::kinematics::FoldTree core::pose::symmetry::sealed_symmetric_fold_tree | ( | core::pose::Pose & | pose | ) |
References core::kinematics::FoldTree::clear(), core::pose::Pose::conformation(), core::kinematics::FoldTree::cutpoints(), core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), is_symmetric(), jumps, 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().
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 | ||
) |
References symmetry_info().
Referenced by get_full_intracomponent_and_neighbor_subs(), get_intracomponent_and_neighbor_subs(), get_symdof_subunits(), and intracomponent_contact().
utility::vector1< std::string > core::pose::symmetry::sym_dof_names | ( | core::pose::Pose const & | pose | ) |
References symmetry_info().
utility::vector1< char > core::pose::symmetry::symmetric_components | ( | core::pose::Pose const & | pose | ) |
References symmetry_info().
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 | ) |
Attempts to grab the symmetry info if the pose is symmetric
References core::pose::Pose::conformation(), is_symmetric(), runtime_assert, and core::conformation::symmetry::SymmetricConformation::Symmetry_Info().
Referenced by core::pack::task::operation::NoRepackDisulfides::apply(), core::pack::rotamer_set::RotamerSets::build_rotamers(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::disulfides_changed(), core::scoring::methods::CartesianBondedEnergy::eval_residue_pair_derivatives(), core::io::silent::BinarySilentStruct::fill_struct(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::find_disulfides(), get_buildingblock_and_neighbor_subs(), get_component_lower_bound(), get_component_of_residue(), get_component_upper_bound(), core::indexed_structure_store::FragmentLookup::get_fragment_residue_spans(), get_full_intracomponent_and_neighbor_subs(), get_full_intracomponent_neighbor_subs(), get_intracomponent_and_interneighbor_subs(), get_intracomponent_and_intraneighbor_subs(), get_intracomponent_and_neighbor_subs(), get_intracomponent_subs(), get_jump_name_to_components(), get_jump_name_to_subunits(), get_neighbor_subs(), get_resis(), get_resnum_to_subunit_component(), get_subpose(), get_subunit_name_to_component(), get_sym_aware_jump_num(), get_symdof_subunits(), intracomponent_contact(), is_multicomponent(), is_singlecomponent(), jump_num_sym_dof(), make_symmetric_pose(), core::scoring::methods::CartesianBondedEnergy::residue_pair_energy_sorted(), core::scoring::rna::RNA_SuiteEnergy::setup_for_scoring(), core::scoring::methods::Rama2BOffsetEnergy::setup_for_scoring(), core::scoring::methods::CartesianBondedEnergy::setup_for_scoring(), sym_dof_jump_num(), sym_dof_names(), and symmetric_components().
|
static |
|
static |