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core::conformation::ResidueFactory Class Reference

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 &current_rsd, Conformation const &conformation, bool preserve_c_beta=false)
 rotamer-style creation, uses backbone of existing residue (current_rsd) More...
 

Detailed Description

a collection of functions making a single residue

Member Function Documentation

ResidueOP core::conformation::ResidueFactory::create_residue ( chemical::ResidueType const &  rsd_type)
static

creates residue of desired type, coords are ideal values in some default spatial orientation

Referenced by protocols::swa::rna::StepWiseRNA_PoseSetup::add_aa_virt_rsd_as_root(), protocols::relax::add_coordinate_constraints_to_pose(), core::pose::add_variant_type_to_residue(), protocols::relax::add_virtual_residue_to_cterm(), core::pose::addVirtualResAsRoot(), protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), protocols::seeded_abinitio::GrowPeptides::append_residues_cterminally(), protocols::seeded_abinitio::GrowPeptides::append_residues_nterminally(), protocols::rna::RNA_StructureParameters::append_virtual_anchor(), protocols::protein_interface_design::movers::LoopLengthChange::apply(), protocols::simple_moves::O2M_MutateMover::apply(), protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::apply(), protocols::match::MatcherMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::idealize::IdealizeMover::apply(), protocols::fldsgn::CircularPermutation::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::forge::components::VarLengthBuild::apply(), core::pack::rotamer_set::build_fixed_O_water_rotamers_independent(), 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(), protocols::rna::RNA_HelixAssembler::build_on_base_pair(), core::pack::rotamer_set::RotamerSet_::build_optimize_H_rotamers(), core::scoring::GenBornPotential::build_placeholders(), core::scoring::FACTSPotential::build_placeholders(), core::io::pdb::build_pose_as_is1(), 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::conformation::change_cys_state(), protocols::simple_filters::SidechainRmsdFilter::compute(), 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::swa::rna::Correctly_position_cutpoint_phosphate_torsions(), protocols::hotspot_hashing::HotspotStubSet::create_hotspot_after_pose(), core::pack::rotamer_set::create_oriented_water_rotamer(), protocols::simple_moves::HelicalPeptideLengthMover::create_residue_from_resname_(), create_rotamer(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::create_rotamers_from_chisets(), core::import_pose::atom_tree_diffs::dump_atom_tree_diff(), protocols::sic_dock::dump_loophash_linkers(), core::coarse::Translator::fix_coarsetype_geometry(), core::conformation::form_disulfide(), protocols::kinmatch::FunGroupTK::FunGroupTK(), protocols::toolbox::match_enzdes_util::TheozymeInvrotTree::generate_targets_and_inverse_rotamers(), protocols::simple_moves::AddCavitiesMover::get_suck_res(), protocols::hotspot_hashing::StubGenerator::getStubByName(), protocols::forge::methods::grow_left_rtype(), protocols::forge::methods::grow_right_rtype(), core::conformation::idealize_position(), protocols::simple_moves::sidechain_moves::SidechainMoverBase::idealize_sidechains(), protocols::motifs::MotifSearch::incorporate_motifs(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), core::pack::dunbrack::SingleLigandRotamerLibrary::init_from_file(), core::conformation::insert_ideal_bonds_at_polymer_junction(), core::conformation::insert_ideal_mainchain_bonds(), core::conformation::is_ideal_position(), core::scoring::methods::IdealParametersDatabase::lookup_angle_legacy(), core::scoring::methods::IdealParametersDatabase::lookup_bondangle_buildideal(), core::scoring::methods::IdealParametersDatabase::lookup_bondlength_buildideal(), core::scoring::methods::IdealParametersDatabase::lookup_length_legacy(), core::scoring::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_saccharide_sequence(), core::pose::make_pose_from_sequence(), core::fragment::make_pose_from_sequence_(), protocols::rotamer_recovery::RRComparerAutomorphicRMSD::measure_rotamer_recovery(), protocols::forge::build::BuildManager::modify(), protocols::flexpep_docking::FlexPepDockingProtocol::polyAla(), core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff(), protocols::motifs::MotifSearch::protein_dna_motif(), protocols::motifs::LigandMotifSearch::protein_dna_motif(), protocols::anchored_design::AnchoredDesignMover::randomize_input_sequence(), core::io::serialization::read_binary(), protocols::toolbox::pose_metric_calculators::ExplicitWaterUnsatisfiedPolarsCalculator::recompute(), core::scoring::constraints::BackboneStubConstraint::remapped_clone(), core::pose::remove_variant_type_from_residue(), core::conformation::replace_conformation_residue_copying_existing_coordinates(), core::pose::replace_pose_residue_copying_existing_coordinates(), protocols::rbsegment_relax::restore_pose_from_rbsegs(), protocols::flexpep_docking::FlexPepDockingAbInitio::restorePSER(), protocols::rbsegment_relax::setup_pose_from_rbsegs(), core::scoring::rna::RNA_LowResolutionPotential::setup_precise_zeta_cutoffs(), core::conformation::symmetry::setup_symmetric_conformation(), core::scoring::methods::setup_water_builders_for_residue_type(), protocols::motifs::single_residue_from_stream(), protocols::dna::substitute_residue(), and core::util::switch_to_residue_type_set().

ResidueOP core::conformation::ResidueFactory::create_residue ( chemical::ResidueType const &  rsd_type,
Residue const &  current_rsd,
Conformation const &  conformation,
bool  preserve_c_beta = false 
)
static

rotamer-style creation, uses backbone of existing residue (current_rsd)


The documentation for this class was generated from the following files: