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Rosetta
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a collection of functions making a single residue More...
#include <ResidueFactory.hh>
Static Public Member Functions | |
| static ResidueOP | create_residue (chemical::ResidueType const &rsd_type) |
| creates residue of desired type, coords are ideal values in some default spatial orientation More... | |
| static ResidueOP | create_residue (chemical::ResidueType const &rsd_type, Residue const ¤t_rsd, Conformation const &conformation, bool preserve_c_beta=false, bool allow_alternate_backbone_matching=false) |
| rotamer-style creation, uses backbone of existing residue (current_rsd) More... | |
a collection of functions making a single residue
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static |
creates residue of desired type, coords are ideal values in some default spatial orientation
Referenced by protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::add_aa_virt_rsd_as_root(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::add_aa_virt_rsd_as_root(), protocols::toolbox::sample_around::add_another_virtual_res(), protocols::environment::EnvClaimBroker::add_chainbreak_variants(), protocols::relax::add_coordinate_constraints_to_pose(), protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::add_flanking_virtual_residues(), protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper::add_linker_asymmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_asymmetric(), protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper::add_linker_symmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_symmetric(), protocols::membrane::AddMembraneMover::add_membrane_virtual(), protocols::membrane::symmetry::SymmetricAddMembraneMover::add_membrane_virtual(), core::scoring::rna::data::RNA_DMS_Potential::add_probe_to_pose(), protocols::loop_grower::LoopPartialSolution::add_sheets(), protocols::denovo_design::components::add_to_pose(), protocols::environment::add_variant(), core::pose::add_variant_type_to_residue(), core::io::pose_from_sfr::PoseFromSFRBuilder::add_variant_type_to_residue(), protocols::toolbox::sample_around::add_virtual_res(), protocols::rna::movers::ErraserMinimizerMover::add_virtual_res(), protocols::relax::add_virtual_residue_to_cterm(), protocols::environment::EnvClaimBroker::add_virtual_residues(), core::pose::addVirtualResAsRoot(), protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), core::pose::append_pose_with_glycan_residues(), protocols::seeded_abinitio::GrowPeptides::append_residues_cterminally(), protocols::seeded_abinitio::GrowPeptides::append_residues_nterminally(), protocols::hydrate::append_single_far_away_water(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::append_virtual_anchor(), protocols::loop_grower::SheetSampler::apply(), protocols::ncbb::oop::OopCreatorMover::apply(), protocols::relax::loop::LoopRelaxMover::apply(), protocols::rna::movers::RNAThreadAndMinimizeMover::apply(), protocols::fldsgn::CircularPermutation::apply(), protocols::forge::components::VarLengthBuild::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::idealize::IdealizeMover::apply(), protocols::protein_interface_design::movers::LoopLengthChange::apply(), protocols::simple_moves::ExplicitWaterMover::apply(), protocols::indexed_structure_store::apply_residue_entries_to_pose(), protocols::simple_moves::ExplicitWaterMover::attach_rotamer_clouds_to_pose_and_rotset(), protocols::fold_from_loops::utils::attach_unfolded_pose_to_pose_c_term(), protocols::fold_from_loops::utils::attach_unfolded_pose_to_pose_n_term(), core::pack::rotamer_set::build_anchorless_water_rotamers(), core::pack::rotamers::SingleLigandRotamerLibrary::build_base_rotamers(), core::pack::rotamer_set::build_fixed_O_water_rotamers_independent(), protocols::splice::SpliceOut::build_ideal_segment(), protocols::splice::SpliceIn::build_ideal_segment(), protocols::splice::SpliceInTail::build_ideal_segment(), protocols::splice::SpliceOutTail::build_ideal_segment(), core::pack::rotamer_set::build_lib_dna_rotamers(), core::pack::rotamer_set::build_moving_O_water_rotamers_dependent(), core::pack::rotamer_set::build_moving_O_water_rotamers_independent(), core::pack::rotamer_set::RotamerSet_::build_optimize_H_rotamers(), core::scoring::GenBornPotential::build_placeholders(), core::pack::rotamer_set::build_random_dna_rotamers(), core::pack::rotamer_set::build_rna_chi_rotamers(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), core::pack::rotamer_set::build_rotated_water_rotamers(), core::pack::rotamer_set::build_single_anchor_water_rotamers_independet(), core::scoring::fiber_diffraction::centroid_scatter(), core::conformation::change_cys_state(), protocols::simple_filters::SidechainRmsdFilter::compute(), protocols::denovo_design::construct_dummy_pose(), protocols::flexpep_docking::FlexPepDockingAbInitio::convertPSERtoASP(), protocols::flexpep_docking::FlexPepDockingAbInitio::convertPSERtoGLU(), protocols::relax::coordinate_constrain_selection(), protocols::protein_interface_design::movers::copy_hotspot_to_pose(), protocols::membrane::visualize::VisualizeEmbeddingMover::create_embedding_virtual(), protocols::hotspot_hashing::HotspotStubSet::create_hotspot_after_pose(), protocols::membrane::visualize::VisualizeMembraneMover::create_membrane_virtual(), core::pack::rotamer_set::create_oriented_water_rotamer(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::create_rotamers_from_chisets(), core::chemical::carbohydrates::CarbohydrateInfo::determine_anomeric_pseudotorsion(), core::import_pose::atom_tree_diffs::dump_atom_tree_diff(), protocols::sic_dock::dump_loophash_linkers(), protocols::simple_ddg::ddG::duplicate_waters_across_jump(), core::pack::rotamers::SingleResidueRotamerLibrary::emergency_rotamer(), protocols::metal_interface::MatchGrafter::ensure_proper_his_tautomers(), protocols::pose_length_moves::NearNativeLoopCloser::extendRegion(), protocols::pose_length_moves::PossibleLoop::extendRegion(), protocols::pose_length_moves::InsertResMover::extendRegion(), protocols::loop_grower::LoopComparator::fill_pose(), core::scoring::motif::ResPairMotif::fill_pose_with_motif(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::fill_rotamer_vector(), core::pack::rotamers::SingleBasicRotamerLibrary::fill_rotamer_vector(), core::conformation::form_disulfide_helper(), protocols::kinmatch::FunGroupTK::FunGroupTK(), protocols::residue_optimization::MetapatchEnumeration::generate_derived_types(), protocols::legacy_sewing::Assembly::generate_native_rotamers_map(), protocols::toolbox::match_enzdes_util::TheozymeInvrotTree::generate_targets_and_inverse_rotamers(), protocols::magnesium::get_mg_rsd(), protocols::hydrate::get_ready_for_sew_packing(), core::import_pose::RNA_HelixAssembler::get_residue(), core::conformation::get_residue_from_name(), core::conformation::get_residue_from_name1(), protocols::simple_moves::AddCavitiesMover::get_suck_res(), protocols::magnesium::get_useful_HOH_coords(), protocols::hotspot_hashing::StubGenerator::getStubByName(), protocols::forge::methods::grow_left_rtype(), protocols::forge::methods::grow_right_rtype(), protocols::hydrate::hydrate_cavities(), protocols::hydrate::hydrate_hyfile(), core::conformation::idealize_position(), protocols::simple_moves::sidechain_moves::SidechainMoverBase::idealize_sidechains(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), protocols::motifs::MotifSearch::incorporate_motifs(), protocols::chemically_conjugated_docking::UBQ_GTPaseMover::initialize(), protocols::scoring::methods::TargetClashEnergy::initiate_voxel(), core::scoring::motif::Xfrag::insert(), core::conformation::insert_ideal_bonds_at_polymer_junction(), core::conformation::insert_ideal_mainchain_bonds(), core::conformation::is_ideal_position(), core::energy_methods::IdealParametersDatabase::lookup_angle_legacy(), core::energy_methods::IdealParametersDatabase::lookup_bondangle_buildideal(), core::energy_methods::IdealParametersDatabase::lookup_bondlength_buildideal(), core::energy_methods::IdealParametersDatabase::lookup_length_legacy(), core::energy_methods::IdealParametersDatabase::lookup_torsion_legacy(), protocols::protein_interface_design::movers::PlaceOnLoop::loop_length(), protocols::motifs::make_base_pair_mutation(), protocols::simple_moves::sidechain_moves::SidechainMover::make_move(), core::pose::make_pose_from_sequence(), core::fragment::make_pose_from_sequence_(), protocols::cryst::MakeLayerMover::make_vrt(), protocols::simple_moves::PeriodicBoxMover::make_vrt(), protocols::cryst::MakeLatticeMover::make_vrt(), protocols::rotamer_recovery::RRComparerAutomorphicRMSD::measure_rotamer_recovery(), protocols::forge::build::BuildManager::modify(), core::scoring::nmr::NMRDummySpinlabelConformer::NMRDummySpinlabelConformer(), protocols::topology_broker::TMHTopologySamplerClaimer::output_membrane_vector(), protocols::cyclic_peptide::PeptideStubMover::perform_single_iteration(), protocols::hydrate::place_de_novo_wat_at_anchor(), core::scoring::motif::Xfres::place_sidechain_in_pose(), protocols::cyclic_peptide::crosslinker::TMA_Helper::place_tma_asymmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::place_tma_symmetric(), protocols::antibody::snugdock::SnugDockProtocol::place_VRT_at_residue_COM(), protocols::flexpep_docking::FlexPepDockingProtocol::polyAla(), core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff(), core::pose::rna::position_cutpoint_phosphate_torsions(), protocols::stepwise::modeler::rna::phosphate::position_five_prime_phosphate_SLOW(), protocols::cyclic_peptide::PeptideStubMover::preserve_old_mainchain_torsions(), protocols::match::MatcherMover::process_pose(), protocols::motifs::LigandMotifSearch::protein_dna_motif(), protocols::motifs::MotifSearch::protein_dna_motif(), protocols::anchored_design::AnchoredDesignMover::randomize_input_sequence(), protocols::legacy_sewing::read_native_residue_file(), core::conformation::symmetry::SymmetricConformation::recalculate_transforms(), core::scoring::constraints::BackboneStubConstraint::remapped_clone(), core::scoring::constraints::BackboneStubLinearConstraint::remapped_clone(), protocols::stepwise::monte_carlo::mover::DeleteMover::remove_singletons_and_update_pose_focus(), core::pose::remove_variant_type_from_residue(), core::conformation::replace_conformation_residue_copying_existing_coordinates(), core::pose::replace_pose_residue_copying_existing_coordinates(), protocols::flexpep_docking::FlexPepDockingAbInitio::restorePSER(), protocols::environment::rm_variant(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::ROT2res(), protocols::denovo_design::components::rsd_op(), protocols::hydrate::set_dew_waters_not_to_be_included(), protocols::antibody::snugdock::SnugDockProtocol::setup_ab_ag_foldtree(), protocols::relax::RepeatProteinRelax::setup_repeat_pose(), protocols::relax::RepeatProteinRelax::setup_repeat_pose_jumping(), core::conformation::symmetry::setup_symmetric_conformation(), core::scoring::lkball::setup_water_builders_for_residue_type(), protocols::loop_grower::LoopGrower::single_grow(), protocols::motifs::single_residue_from_stream(), protocols::dna::substitute_residue(), core::util::switch_to_centroid_rot_set(), core::util::switch_to_residue_type_set(), protocols::topology_broker::SymmetryClaimer::symmetry_duplicate(), core::pose::carbohydrates::tautomerize_anomer(), protocols::legacy_sewing::Assembly::to_multichain_pose(), protocols::legacy_sewing::Assembly::to_pose(), protocols::sewing::data_storage::SmartAssembly::to_pose(), and protocols::loop_grower::LoopGrower::update_to_stored().
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rotamer-style creation, uses backbone of existing residue (current_rsd)
1.9.1