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Rosetta 3.5
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All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
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Rosetta 3.5
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Classes | |
| class | AtomID |
| Atom identifier class. Defined by the atom number and the residue number. More... | |
| class | BondID |
| two more classes, temporary for testing purposes More... | |
| class | StubID |
| class | AtomID_Map |
| Map from Atom identifiers to contained values class. More... | |
| class | CacheableAtomID_MapVector |
| AtomID_Map< xyzVector< Real > > More... | |
| class | DOF_ID |
| Kinematics DOF identifier class. More... | |
| class | DOF_ID_Map |
| Map from Atom DOF identifiers to contained values class. More... | |
| class | DOF_ID_Range |
| Kinematics DOF identifier (with range) class. More... | |
| class | EXCN_AtomNotFound |
| class | JumpID |
| class | NamedAtomID |
| Atom identifier class. More... | |
| class | NamedStubID |
| class | SequenceMapping |
| class | TorsionID |
| class | TorsionID_Range |
| Kinematics DOF identifier (with range) class. More... | |
Typedefs | |
| typedef AtomID_Map< bool > | AtomID_Mask |
| typedef utility::pointer::owning_ptr < CacheableAtomID_MapVector > | CacheableAtomID_MapVectorOP |
| typedef utility::pointer::owning_ptr < CacheableAtomID_MapVector const > | CacheableAtomID_MapVectorCOP |
| typedef utility::pointer::access_ptr < CacheableAtomID_MapVector > | CacheableAtomID_MapVectorAP |
| typedef utility::pointer::access_ptr < CacheableAtomID_MapVector const > | CacheableAtomID_MapVectorCAP |
| typedef DOF_ID_Map< bool > | DOF_ID_Mask |
| typedef utility::pointer::owning_ptr < SequenceMapping > | SequenceMappingOP |
| typedef utility::pointer::owning_ptr < SequenceMapping const > | SequenceMappingCOP |
Enumerations | |
| enum | DOF_Type { PHI = 1, THETA, D, RB1, RB2, RB3, RB4, RB5, RB6 } |
| DOF (degrees of freedom) type. More... | |
| enum | TorsionType { BB = 1, CHI, JUMP } |
| Torsion type – used in the TorsionID class. More... | |
Functions | |
| static basic::Tracer | tr ("core.id.AtomID") |
| std::ostream & | operator<< (std::ostream &os, AtomID const &a) |
| stream << AtomID More... | |
| std::ostream & | operator<< (std::ostream &os, StubID const &stub) |
| stream << AtomID More... | |
| template<typename T > | |
| void | swap (AtomID_Map< T > &a, AtomID_Map< T > &b) |
| swap( AtomID_Map, AtomID_Map ) More... | |
| std::ostream & | operator<< (std::ostream &os, DOF_ID const &a) |
| stream << DOF_ID More... | |
| DOF_Type | get_rb_type (Size const k) |
| Size | get_rb_number (DOF_Type const t) |
| bool | DOF_type_is_rb (DOF_Type const t) |
| std::ostream & | operator<< (std::ostream &os, DOF_ID_Range const &a) |
| stream << DOF_ID_Range More... | |
| std::ostream & | operator<< (std::ostream &os, NamedAtomID const &a) |
| stream << NamedAtomID More... | |
| std::istream & | operator>> (std::istream &is, NamedAtomID &e) |
| input operator >> NamedAtomID More... | |
| std::ostream & | operator<< (std::ostream &os, NamedStubID const &a) |
| stream << NamedStubID More... | |
| std::istream & | operator>> (std::istream &is, NamedStubID &s) |
| input operator >> NamedAtomID More... | |
| core::id::SequenceMappingOP | combine_sequence_mappings (utility::vector1< core::id::SequenceMapping > const &smaps) |
| make one sequence mapping out of all input ones utility function added by flo, feb 2011 More... | |
| void | combine_sequence_mappings (core::id::SequenceMapping &smap, core::id::SequenceMapping const &smap_to_add) |
| combine the input sequence mappings into one utility function added by flo, feb 2011 More... | |
| std::ostream & | operator<< (std::ostream &out, SequenceMapping const &map) |
| std::ostream & | operator<< (std::ostream &os, TorsionID_Range const &a) |
| stream << TorsionID_Range More... | |
| static Size const | n_DOF_Type (9) |
| static Size const | phi_torsion (1) |
| static Size const | psi_torsion (2) |
| static Size const | omega_torsion (3) |
Variables | |
| AtomID const | BOGUS_ATOM_ID (0, 0) |
| Globals. More... | |
| AtomID const | CHAINBREAK_BOGUS_ATOM_ID (0, 0) |
| StubID const | BOGUS_STUB_ID (BOGUS_ATOM_ID, BOGUS_ATOM_ID, BOGUS_ATOM_ID) |
| Globals. More... | |
| DOF_ID const | BOGUS_DOF_ID (BOGUS_ATOM_ID, PHI) |
| Globals. More... | |
| NamedAtomID const | BOGUS_NAMED_ATOM_ID ("", 0) |
| Globals. More... | |
| NamedAtomID const | CHAINBREAK_BOGUS_NAMED_ATOM_ID ("", 0) |
| TorsionID const | BOGUS_TORSION_ID (0, BB, 0) |
| Globals. More... | |
| typedef AtomID_Map< bool > core::id::AtomID_Mask |
Definition at line 28 of file AtomID_Mask.fwd.hh.
| typedef utility::pointer::access_ptr< CacheableAtomID_MapVector > core::id::CacheableAtomID_MapVectorAP |
Definition at line 29 of file CacheableAtomID_MapVector.fwd.hh.
| typedef utility::pointer::access_ptr< CacheableAtomID_MapVector const > core::id::CacheableAtomID_MapVectorCAP |
Definition at line 30 of file CacheableAtomID_MapVector.fwd.hh.
| typedef utility::pointer::owning_ptr< CacheableAtomID_MapVector const > core::id::CacheableAtomID_MapVectorCOP |
Definition at line 28 of file CacheableAtomID_MapVector.fwd.hh.
| typedef utility::pointer::owning_ptr< CacheableAtomID_MapVector > core::id::CacheableAtomID_MapVectorOP |
Definition at line 26 of file CacheableAtomID_MapVector.fwd.hh.
| typedef DOF_ID_Map< bool > core::id::DOF_ID_Mask |
Definition at line 28 of file DOF_ID_Mask.fwd.hh.
| typedef utility::pointer::owning_ptr< SequenceMapping const > core::id::SequenceMappingCOP |
Definition at line 25 of file SequenceMapping.fwd.hh.
Definition at line 23 of file SequenceMapping.fwd.hh.
| enum core::id::DOF_Type |
| core::id::SequenceMappingOP core::id::combine_sequence_mappings | ( | utility::vector1< core::id::SequenceMapping > const & | smaps) |
make one sequence mapping out of all input ones utility function added by flo, feb 2011
combine all input sequence mappings into one. sequentially, that is
Definition at line 351 of file SequenceMapping.cc.
Referenced by protocols::seeded_abinitio::adjust_mm_to_length(), and core::pack::task::operation::ReadResfileAndObeyLengthEvents::apply().
| void core::id::combine_sequence_mappings | ( | core::id::SequenceMapping & | smap, |
| core::id::SequenceMapping const & | smap_to_add | ||
| ) |
combine the input sequence mappings into one utility function added by flo, feb 2011
combine smap_to_add into smap, i.e. smap[j] becomes smap_to_add[ smap[j] ]
Definition at line 376 of file SequenceMapping.cc.
References core::id::SequenceMapping::downstream_combine().
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Definition at line 160 of file DOF_ID.hh.
Referenced by core::optimization::symmetry::SymMinimizerMap::reset_jump_rb_deltas(), and core::optimization::MinimizerMap::reset_jump_rb_deltas().
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Definition at line 147 of file DOF_ID.hh.
Referenced by core::kinematics::tree::JumpAtom::dof(), core::kinematics::tree::JumpAtom::get_dof_axis_and_end_pos(), and core::kinematics::tree::JumpAtom::set_dof().
Definition at line 136 of file DOF_ID.hh.
References RB1.
Referenced by core::conformation::Conformation::dof_id_from_torsion_id(), and core::kinematics::tree::JumpAtom::setup_min_map().
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Referenced by protocols::anchored_design::AnchorMoversData::fix_anchor(), protocols::relax::fix_worst_bad_ramas(), protocols::forge::remodel::RemodelLoopMover::mark_loop_moveable(), protocols::forge::build::SegmentRebuild::movemap(), protocols::forge::build::SegmentInsert::movemap(), core::pose::Pose::omega(), protocols::anchored_design::AnchorMoversData::set_movemap(), and core::pose::Pose::set_omega().
| std::ostream& core::id::operator<< | ( | std::ostream & | os, |
| TorsionID_Range const & | a | ||
| ) |
stream << TorsionID_Range
Definition at line 27 of file TorsionID_Range.cc.
References core::id::TorsionID_Range::max(), core::id::TorsionID_Range::min(), and core::id::TorsionID_Range::torsion_id().
| std::ostream& core::id::operator<< | ( | std::ostream & | os, |
| DOF_ID_Range const & | a | ||
| ) |
stream << DOF_ID_Range
Definition at line 31 of file DOF_ID_Range.cc.
References core::id::DOF_ID_Range::dof_id(), core::id::DOF_ID_Range::max(), and core::id::DOF_ID_Range::min().
| std::ostream& core::id::operator<< | ( | std::ostream & | os, |
| DOF_ID const & | a | ||
| ) |
stream << DOF_ID
Definition at line 31 of file DOF_ID.cc.
References core::id::DOF_ID::atom_id(), and core::id::DOF_ID::type().
| std::ostream& core::id::operator<< | ( | std::ostream & | os, |
| NamedAtomID const & | a | ||
| ) |
stream << NamedAtomID
Definition at line 38 of file NamedAtomID.cc.
References protocols::comparative_modeling::features::A, core::id::NamedAtomID::atom(), and core::id::NamedAtomID::rsd().
| std::ostream& core::id::operator<< | ( | std::ostream & | os, |
| AtomID const & | a | ||
| ) |
stream << AtomID
Definition at line 50 of file AtomID.cc.
References core::id::AtomID::atomno(), and core::id::AtomID::rsd().
| std::ostream& core::id::operator<< | ( | std::ostream & | os, |
| StubID const & | stub | ||
| ) |
stream << AtomID
Definition at line 63 of file AtomID.cc.
References core::id::StubID::atom1, core::id::StubID::atom2, core::id::StubID::atom3, and core::id::StubID::center_.
| std::ostream& core::id::operator<< | ( | std::ostream & | os, |
| NamedStubID const & | a | ||
| ) |
stream << NamedStubID
output operator
Definition at line 91 of file NamedStubID.cc.
References core::id::NamedStubID::atom1, core::id::NamedStubID::atom2, core::id::NamedStubID::atom3, and core::id::NamedStubID::center_.
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Definition at line 160 of file SequenceMapping.hh.
References core::id::SequenceMapping::show().
| std::istream& core::id::operator>> | ( | std::istream & | is, |
| NamedAtomID & | e | ||
| ) |
input operator >> NamedAtomID
input operator
Definition at line 49 of file NamedAtomID.cc.
References core::id::NamedAtomID::atom(), and core::id::NamedAtomID::rsd().
| std::istream& core::id::operator>> | ( | std::istream & | is, |
| NamedStubID & | s | ||
| ) |
input operator >> NamedAtomID
input operator
Definition at line 100 of file NamedStubID.cc.
References core::id::NamedStubID::atom1, core::id::NamedStubID::atom2, core::id::NamedStubID::atom3, and core::id::NamedStubID::center_.
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Referenced by protocols::grafting::AnchoredGraftMover::apply(), protocols::idealize::basic_idealize(), protocols::simple_moves::SmallMover::dof_id_ranges(), protocols::simple_moves::ShearMover::dof_id_ranges(), protocols::loops::loop_closure::ccd::fast_ccd_loop_closure(), protocols::anchored_design::AnchorMoversData::fix_anchor(), protocols::relax::fix_worst_bad_ramas(), protocols::forge::build::SegmentRebuild::movemap(), protocols::forge::build::SegmentInsert::movemap(), core::pose::Pose::phi(), core::pose::Pose::set_phi(), protocols::simple_moves::BBGaussianMover::setup_list(), protocols::simple_moves::SmallMover::setup_list(), protocols::simple_moves::ShearMover::setup_list(), and core::kinematics::tree::BondedAtom::setup_min_map().
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Referenced by protocols::grafting::AnchoredGraftMover::apply(), protocols::simple_moves::SmallMover::dof_id_ranges(), protocols::simple_moves::ShearMover::dof_id_ranges(), protocols::loops::loop_closure::ccd::fast_ccd_loop_closure(), protocols::anchored_design::AnchorMoversData::fix_anchor(), protocols::forge::build::SegmentRebuild::movemap(), protocols::forge::build::SegmentInsert::movemap(), core::pose::Pose::psi(), core::pose::Pose::set_psi(), protocols::simple_moves::BBGaussianMover::setup_list(), protocols::simple_moves::SmallMover::setup_list(), and protocols::simple_moves::ShearMover::setup_list().
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swap( AtomID_Map, AtomID_Map )
Definition at line 503 of file AtomID_Map.hh.
Referenced by core::chemical::IdealBondLengthSet::add_bond_length(), core::chemical::IdealBondLengthSet::contains_bond_length(), core::chemical::IdealBondLengthSet::get_bond_length(), core::pack::rotamer_set::symmetry::SymmetricRotamerSets::precompute_two_body_energies(), core::pack::rotamer_set::symmetry::SymmetricRotamerSets::prepare_symm_otf_interaction_graph(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::readMRCandResize(), core::scoring::electron_density::ElectronDensity::readMRCandResize(), protocols::cluster::Cluster::shuffle(), and protocols::noesy_assign::FragsToAtomDist::swap_atoms().
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| AtomID const core::id::BOGUS_ATOM_ID |
Globals.
Definition at line 148 of file AtomID.hh.
Referenced by protocols::loops::addScoresForLoopParts(), protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::align_all_pose(), protocols::hybridization::HybridizeProtocol::align_by_domain(), protocols::rna::RNA_ChunkLibrary::align_to_chunk(), protocols::antibody::Antibody::align_to_native(), protocols::antibody2::align_to_native(), protocols::antibody2::GraftOneCDRLoop::apply(), protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::apply(), protocols::comparative_modeling::ExtraThreadingMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::antibody::GraftOneMover::apply(), core::scoring::constraints::NonResidueTypeConstraint::atom(), core::scoring::constraints::ResidueTypeConstraint::atom(), core::scoring::constraints::ResidueTypeLinkingConstraint::atom(), protocols::constraints_additional::SequenceCouplingConstraint::atom(), core::scoring::constraints::SequenceProfileConstraint::atom(), core::chemical::ICoorAtomID::atom_id(), core::chemical::atom_id_from_icoor_line(), core::scoring::calpha_superimpose_pose(), core::sequence::calpha_superimpose_with_mapping(), protocols::swa::create_alignment_id_map(), protocols::swa::rna::create_alignment_id_map(), protocols::backrub::BackrubSegment::end_bond_angle_key(), protocols::hybridization::InsertChunkMover::get_local_sequence_mapping(), core::conformation::get_residue_connections(), protocols::loops::loop_rmsd_with_superimpose_core(), core::pose::named_atom_id_to_atom_id(), protocols::hybridization::DomainAssembly::run(), protocols::simple_moves::SuperimposeMover::superimpose(), protocols::fldsgn::MatchResidues::superimpose_comb(), protocols::grafting::GraftMoverBase::superimpose_overhangs_heavy(), protocols::fibril::superimpose_pose_on_subset_bb(), protocols::toolbox::pose_manipulation::superimpose_pose_on_subset_CA(), protocols::hybridization::FoldTreeHybridize::superimpose_strand_pairings_to_templates(), protocols::docking::ConformerSwitchMover::switch_conformer(), protocols::hybridization::TMalign_poses(), and protocols::hybridization::update_atom_map().
| DOF_ID const core::id::BOGUS_DOF_ID |
Globals.
Definition at line 129 of file DOF_ID.hh.
Referenced by core::optimization::symmetry::SymMinimizerMap::add_torsion(), core::kinematics::AtomTree::bond_angle_dof_id(), core::kinematics::AtomTree::bond_length_dof_id(), core::conformation::Conformation::dof_id_from_torsion_id(), protocols::swa::rna::RNA_AnalyticLoopCloser::figure_out_offset(), protocols::coarse_rna::CoarseRNA_LoopCloser::figure_out_offset(), protocols::coarse_rna::CoarseRNA_LoopCloser::fill_solution(), core::optimization::symmetry::numerical_derivative_check(), core::optimization::numerical_derivative_check(), core::optimization::CartesianMinimizerMap::setup(), core::optimization::MinimizerMap::setup(), core::optimization::symmetry::SymMinimizerMap::SymMinimizerMap(), and core::kinematics::AtomTree::torsion_angle_dof_id().
| NamedAtomID const core::id::BOGUS_NAMED_ATOM_ID |
Globals.
Definition at line 150 of file NamedAtomID.hh.
Referenced by core::conformation::Conformation::append_residue_by_bond(), core::conformation::Conformation::append_residue_by_jump(), protocols::noesy_assign::ResonanceList::operator[](), and protocols::noesy_assign::ResonanceList::resonances_at_residue().
| TorsionID const core::id::BOGUS_TORSION_ID |
Globals.
Definition at line 180 of file TorsionID.hh.
Referenced by core::optimization::symmetry::SymMinimizerMap::assign_rosetta_torsions(), core::optimization::MinimizerMap::assign_rosetta_torsions(), core::optimization::CartesianMinimizerMap::assign_rosetta_torsions_and_trim(), core::pose::setup_dof_to_torsion_map(), core::pack::scmin::CartSCMinMinimizerMap::tor_for_dof(), and core::pack::scmin::AtomTreeSCMinMinimizerMap::tor_for_dof().
| NamedAtomID const core::id::CHAINBREAK_BOGUS_NAMED_ATOM_ID |
Definition at line 151 of file NamedAtomID.hh.
1.8.4