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core::id Namespace Reference

Classes

class  AtomID
 Atom identifier class. Defined by the atom number and the residue number. More...
 
class  AtomID_Map
 Map from Atom identifiers to contained values class. More...
 
class  AtomID_Map_AtomID
 
class  AtomID_Map_bool
 
class  AtomID_Map_Real
 
class  BondID
 two more classes, temporary for testing purposes 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  NamedAtomID_Map
 Map from Atom identifiers to contained values class. More...
 
class  NamedAtomID_Map_NamedAtomID
 
class  NamedStubID
 
class  SequenceMapping
 
class  StubID
 
class  TorsionID
 Torsion identifier class. More...
 
class  TorsionID_Range
 Kinematics DOF identifier (with range) class. More...
 

Typedefs

typedef AtomID_Map< boolAtomID_Mask
 
typedef
utility::pointer::shared_ptr
< CacheableAtomID_MapVector
CacheableAtomID_MapVectorOP
 
typedef
utility::pointer::shared_ptr
< CacheableAtomID_MapVector
const > 
CacheableAtomID_MapVectorCOP
 
typedef
utility::pointer::weak_ptr
< CacheableAtomID_MapVector
CacheableAtomID_MapVectorAP
 
typedef
utility::pointer::weak_ptr
< CacheableAtomID_MapVector
const > 
CacheableAtomID_MapVectorCAP
 
typedef DOF_ID_Map< boolDOF_ID_Mask
 
typedef NamedAtomID_Map< boolNamedAtomID_Mask
 
typedef
utility::pointer::shared_ptr
< SequenceMapping
SequenceMappingOP
 
typedef
utility::pointer::shared_ptr
< SequenceMapping const > 
SequenceMappingCOP
 

Enumerations

enum  DOF_Type {
  INVALID_DOF = 0, PHI = 1, THETA, D,
  RB1, RB2, RB3, RB4,
  RB5, RB6
}
 DOF (degrees of freedom) type. More...
 
enum  TorsionType {
  BB = 1, CHI, NU, BRANCH,
  JUMP
}
 Torsion type – used in the TorsionID class. More...
 
enum  MainchainTorsionType {
  phi_dihedral = 1, psi_dihedral, omega_dihedral, omega2_dihedral,
  omega3_dihedral
}
 

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...
 
AtomID const GLOBAL_BOGUS_ATOM_ID (AtomID::BOGUS_ATOM_ID())
 
AtomID const GLOBAL_CHAINBREAK_BOGUS_ATOM_ID (AtomID::CHAINBREAK_BOGUS_ATOM_ID())
 
StubID const GLOBAL_BOGUS_STUB_ID (StubID::BOGUS_STUB_ID())
 
DOF_ID const GLOBAL_BOGUS_DOF_ID (AtomID::BOGUS_ATOM_ID(), PHI)
 
NamedAtomID const GLOBAL_BOGUS_NAMED_ATOM_ID (NamedAtomID::BOGUS_NAMED_ATOM_ID())
 
NamedAtomID const GLOBAL_CHAINBREAK_BOGUS_NAMED_ATOM_ID (NamedAtomID::CHAINBREAK_BOGUS_NAMED_ATOM_ID())
 
TorsionID const GLOBAL_BOGUS_TORSION_ID (TorsionID::BOGUS_TORSION_ID())
 Globals. More...
 
void initialize_core_id_globals ()
 Calling this function ensures that all of the global variables in core::id are initialize before they are needed. 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, JumpID const &a)
 
std::ostream & operator<< (std::ostream &os, NamedAtomID const &a)
 stream << NamedAtomID More...
 
std::istream & operator>> (std::istream &is, NamedAtomID &e)
 input operator >> NamedAtomID More...
 
template<typename T >
void swap (NamedAtomID_Map< T > &a, NamedAtomID_Map< T > &b)
 swap( NamedAtomID_Map, NamedAtomID_Map ) 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...
 
static basic::Tracer TR ("core.id.SequenceMapping")
 
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 const &a)
 
std::ostream & operator<< (std::ostream &os, TorsionID_Range const &a)
 stream << TorsionID_Range More...
 
static Size const n_DOF_Type (9)
 
std::string to_string (DOF_Type const &type)
 
std::string to_string (TorsionType const &type)
 
static Size const phi_torsion (1)
 
static Size const psi_torsion (2)
 
static Size const omega_torsion (3)
 
static Size const omega2_torsion (4)
 
static Size const phi_torsion_beta_aa (1)
 
static Size const theta_torsion_beta_aa (2)
 
static Size const psi_torsion_beta_aa (3)
 
static Size const omega_torsion_beta_aa (4)
 
static Size const phi_torsion_oligourea (1)
 
static Size const theta_torsion_oligourea (2)
 
static Size const psi_torsion_oligourea (3)
 
static Size const mu_torsion_oligourea (4)
 
static Size const omega_torsion_oligourea (5)
 
static Size const phi_torsion_ortho_aramid (1)
 
static Size const theta_torsion_ortho_aramid (2)
 
static Size const psi_torsion_ortho_aramid (3)
 
static Size const omega_torsion_ortho_aramid (4)
 
static Size const phi_torsion_pre_methylene_ortho_aramid (1)
 
static Size const eta_torsion_pre_methylene_ortho_aramid (2)
 
static Size const theta_torsion_pre_methylene_ortho_aramid (3)
 
static Size const psi_torsion_pre_methylene_ortho_aramid (4)
 
static Size const omega_torsion_pre_methylene_ortho_aramid (5)
 
static Size const phi_torsion_post_methylene_ortho_aramid (1)
 
static Size const eta_torsion_post_methylene_ortho_aramid (2)
 
static Size const theta_torsion_post_methylene_ortho_aramid (3)
 
static Size const psi_torsion_post_methylene_ortho_aramid (4)
 
static Size const omega_torsion_post_methylene_ortho_aramid (5)
 
static Size const phi_torsion_pre_methylene_post_methylene_ortho_aramid (1)
 
static Size const zeta_torsion_pre_methylene_post_methylene_ortho_aramid (2)
 
static Size const eta_torsion_pre_methylene_post_methylene_ortho_aramid (3)
 
static Size const theta_torsion_pre_methylene_post_methylene_ortho_aramid (4)
 
static Size const psi_torsion_pre_methylene_post_methylene_ortho_aramid (5)
 
static Size const omega_torsion_pre_methylene_post_methylene_ortho_aramid (6)
 
static Size const phi_torsion_meta_aramid (1)
 
static Size const eta_torsion_meta_aramid (2)
 
static Size const theta_torsion_meta_aramid (3)
 
static Size const psi_torsion_meta_aramid (4)
 
static Size const omega_torsion_meta_aramid (5)
 
static Size const phi_torsion_pre_methylene_meta_aramid (1)
 
static Size const zeta_torsion_pre_methylene_meta_aramid (2)
 
static Size const eta_torsion_pre_methylene_meta_aramid (3)
 
static Size const theta_torsion_pre_methylene_meta_aramid (4)
 
static Size const psi_torsion_pre_methylene_meta_aramid (5)
 
static Size const omega_torsion_pre_methylene_meta_aramid (6)
 
static Size const phi_torsion_post_methylene_meta_aramid (1)
 
static Size const zeta_torsion_post_methylene_meta_aramid (2)
 
static Size const eta_torsion_post_methylene_meta_aramid (3)
 
static Size const theta_torsion_post_methylene_meta_aramid (4)
 
static Size const psi_torsion_post_methylene_meta_aramid (5)
 
static Size const omega_torsion_post_methylene_meta_aramid (6)
 
static Size const phi_torsion_pre_methylene_post_methylene_meta_aramid (1)
 
static Size const epsilon_torsion_pre_methylene_post_methylene_meta_aramid (2)
 
static Size const zeta_torsion_pre_methylene_post_methylene_meta_aramid (3)
 
static Size const eta_torsion_pre_methylene_post_methylene_meta_aramid (4)
 
static Size const theta_torsion_pre_methylene_post_methylene_meta_aramid (5)
 
static Size const psi_torsion_pre_methylene_post_methylene_meta_aramid (6)
 
static Size const omega_torsion_pre_methylene_post_methylene_meta_aramid (7)
 
static Size const phi_torsion_para_aramid (1)
 
static Size const zeta_torsion_para_aramid (2)
 
static Size const eta_torsion_para_aramid (3)
 
static Size const theta_torsion_para_aramid (4)
 
static Size const psi_torsion_para_aramid (5)
 
static Size const omega_torsion_para_aramid (6)
 
static Size const phi_torsion_pre_methylene_para_aramid (1)
 
static Size const epsilon_torsion_pre_methylene_para_aramid (2)
 
static Size const zeta_torsion_pre_methylene_para_aramid (3)
 
static Size const eta_torsion_pre_methylene_para_aramid (4)
 
static Size const theta_torsion_pre_methylene_para_aramid (5)
 
static Size const psi_torsion_pre_methylene_para_aramid (6)
 
static Size const omega_torsion_pre_methylene_para_aramid (7)
 
static Size const phi_torsion_post_methylene_para_aramid (1)
 
static Size const epsilon_torsion_post_methylene_para_aramid (2)
 
static Size const zeta_torsion_post_methylene_para_aramid (3)
 
static Size const eta_torsion_post_methylene_para_aramid (4)
 
static Size const theta_torsion_post_methylene_para_aramid (5)
 
static Size const psi_torsion_post_methylene_para_aramid (6)
 
static Size const omega_torsion_post_methylene_para_aramid (7)
 
static Size const phi_torsion_pre_methylene_post_methylene_para_aramid (1)
 
static Size const epsilon_torsion_pre_methylene_post_methylene_para_aramid (2)
 
static Size const zeta_torsion_pre_methylene_post_methylene_para_aramid (3)
 
static Size const eta_torsion_pre_methylene_post_methylene_para_aramid (4)
 
static Size const iota_torsion_pre_methylene_post_methylene_para_aramid (5)
 
static Size const theta_torsion_pre_methylene_post_methylene_para_aramid (6)
 
static Size const psi_torsion_pre_methylene_post_methylene_para_aramid (7)
 
static Size const omega_torsion_pre_methylene_post_methylene_para_aramid (8)
 

Variables

AtomID const GLOBAL_BOGUS_ATOM_ID
 Globals – may not be used until after core::init is called. More...
 
AtomID const GLOBAL_CHAINBREAK_BOGUS_ATOM_ID
 
StubID const GLOBAL_BOGUS_STUB_ID
 Global – may not be used until after core::init is called. More...
 
DOF_ID const GLOBAL_BOGUS_DOF_ID
 Global – may not be used until after core::init is called. More...
 
NamedAtomID const GLOBAL_BOGUS_NAMED_ATOM_ID
 Globals – may not be used until after core::init is called. More...
 
NamedAtomID const GLOBAL_CHAINBREAK_BOGUS_NAMED_ATOM_ID
 
TorsionID const GLOBAL_BOGUS_TORSION_ID
 Global – may not be used until after core::init is called. More...
 

Typedef Documentation

typedef utility::pointer::weak_ptr< CacheableAtomID_MapVector const > core::id::CacheableAtomID_MapVectorCAP
typedef utility::pointer::shared_ptr< CacheableAtomID_MapVector const > core::id::CacheableAtomID_MapVectorCOP
typedef utility::pointer::shared_ptr< CacheableAtomID_MapVector > core::id::CacheableAtomID_MapVectorOP
typedef utility::pointer::shared_ptr< SequenceMapping const > core::id::SequenceMappingCOP
typedef utility::pointer::shared_ptr< SequenceMapping > core::id::SequenceMappingOP

Enumeration Type Documentation

DOF (degrees of freedom) type.

  • PHI : torsion or improper angle
  • THETA : bond angle
  • D : distance
  • RB1-RB6 : rigid-body jump translation and rotation
Enumerator
INVALID_DOF 
PHI 
THETA 
RB1 
RB2 
RB3 
RB4 
RB5 
RB6 
Enumerator
phi_dihedral 
psi_dihedral 
omega_dihedral 
omega2_dihedral 
omega3_dihedral 

Torsion type – used in the TorsionID class.

  • BB : "backbone" torsion (Actually, this is a main-chain torsion.)
  • CHI : sidechain torsion
  • NU : internal ring torsion
  • BRANCH : torsions at branch connection points which are CHEMICAL edges of the FoldTree
  • JUMP : rigid-body transformation
Enumerator
BB 
CHI 
NU 
BRANCH 
JUMP 

Function Documentation

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

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] ]

References core::id::SequenceMapping::downstream_combine().

bool core::id::DOF_type_is_rb ( DOF_Type const  t)
inline
static Size const core::id::epsilon_torsion_post_methylene_para_aramid ( )
static
static Size const core::id::epsilon_torsion_pre_methylene_para_aramid ( )
static
static Size const core::id::epsilon_torsion_pre_methylene_post_methylene_meta_aramid ( )
static
static Size const core::id::epsilon_torsion_pre_methylene_post_methylene_para_aramid ( )
static
static Size const core::id::eta_torsion_meta_aramid ( )
static
static Size const core::id::eta_torsion_para_aramid ( )
static
static Size const core::id::eta_torsion_post_methylene_meta_aramid ( )
static
static Size const core::id::eta_torsion_post_methylene_ortho_aramid ( )
static
static Size const core::id::eta_torsion_post_methylene_para_aramid ( )
static
static Size const core::id::eta_torsion_pre_methylene_meta_aramid ( )
static
static Size const core::id::eta_torsion_pre_methylene_ortho_aramid ( )
static
static Size const core::id::eta_torsion_pre_methylene_para_aramid ( )
static
static Size const core::id::eta_torsion_pre_methylene_post_methylene_meta_aramid ( )
static
static Size const core::id::eta_torsion_pre_methylene_post_methylene_ortho_aramid ( )
static
static Size const core::id::eta_torsion_pre_methylene_post_methylene_para_aramid ( )
static
Size core::id::get_rb_number ( DOF_Type const  t)
inline
DOF_Type core::id::get_rb_type ( Size const  k)
inline
AtomID const core::id::GLOBAL_BOGUS_ATOM_ID ( AtomID::  BOGUS_ATOM_ID())
DOF_ID const core::id::GLOBAL_BOGUS_DOF_ID ( AtomID::  BOGUS_ATOM_ID(),
PHI   
)
NamedAtomID const core::id::GLOBAL_BOGUS_NAMED_ATOM_ID ( NamedAtomID::  BOGUS_NAMED_ATOM_ID())
StubID const core::id::GLOBAL_BOGUS_STUB_ID ( StubID::  BOGUS_STUB_ID())
TorsionID const core::id::GLOBAL_BOGUS_TORSION_ID ( TorsionID::  BOGUS_TORSION_ID())

Globals.

AtomID const core::id::GLOBAL_CHAINBREAK_BOGUS_ATOM_ID ( AtomID::  CHAINBREAK_BOGUS_ATOM_ID())
NamedAtomID const core::id::GLOBAL_CHAINBREAK_BOGUS_NAMED_ATOM_ID ( NamedAtomID::  CHAINBREAK_BOGUS_NAMED_ATOM_ID())
void core::id::initialize_core_id_globals ( )

Calling this function ensures that all of the global variables in core::id are initialize before they are needed.

Referenced by core::init::init().

static Size const core::id::iota_torsion_pre_methylene_post_methylene_para_aramid ( )
static
static Size const core::id::mu_torsion_oligourea ( )
static
static Size const core::id::n_DOF_Type ( )
static
static Size const core::id::omega2_torsion ( )
static
static Size const core::id::omega_torsion ( )
static
static Size const core::id::omega_torsion_beta_aa ( )
static
static Size const core::id::omega_torsion_meta_aramid ( )
static
static Size const core::id::omega_torsion_oligourea ( )
static
static Size const core::id::omega_torsion_ortho_aramid ( )
static
static Size const core::id::omega_torsion_para_aramid ( )
static
static Size const core::id::omega_torsion_post_methylene_meta_aramid ( )
static
static Size const core::id::omega_torsion_post_methylene_ortho_aramid ( )
static
static Size const core::id::omega_torsion_post_methylene_para_aramid ( )
static
static Size const core::id::omega_torsion_pre_methylene_meta_aramid ( )
static
static Size const core::id::omega_torsion_pre_methylene_ortho_aramid ( )
static
static Size const core::id::omega_torsion_pre_methylene_para_aramid ( )
static
static Size const core::id::omega_torsion_pre_methylene_post_methylene_meta_aramid ( )
static
static Size const core::id::omega_torsion_pre_methylene_post_methylene_ortho_aramid ( )
static
static Size const core::id::omega_torsion_pre_methylene_post_methylene_para_aramid ( )
static
std::ostream& core::id::operator<< ( std::ostream &  os,
JumpID const &  a 
)
std::ostream& core::id::operator<< ( std::ostream &  os,
TorsionID const &  a 
)
std::ostream& core::id::operator<< ( std::ostream &  os,
TorsionID_Range const &  a 
)
std::ostream& core::id::operator<< ( std::ostream &  os,
DOF_ID_Range const &  a 
)
std::ostream& core::id::operator<< ( std::ostream &  os,
DOF_ID const &  a 
)
std::ostream& core::id::operator<< ( std::ostream &  os,
NamedAtomID const &  a 
)
std::ostream& core::id::operator<< ( std::ostream &  os,
AtomID const &  a 
)
std::ostream& core::id::operator<< ( std::ostream &  os,
StubID const &  stub 
)
std::ostream& core::id::operator<< ( std::ostream &  os,
NamedStubID const &  a 
)
std::ostream& core::id::operator<< ( std::ostream &  out,
SequenceMapping const &  map 
)
inline
std::istream& core::id::operator>> ( std::istream &  is,
NamedAtomID &  e 
)

input operator >> NamedAtomID

input operator

References core::id::NamedAtomID::atom(), and core::id::NamedAtomID::rsd().

std::istream& core::id::operator>> ( std::istream &  is,
NamedStubID &  s 
)
static Size const core::id::phi_torsion ( )
static
static Size const core::id::phi_torsion_beta_aa ( )
static
static Size const core::id::phi_torsion_meta_aramid ( )
static
static Size const core::id::phi_torsion_oligourea ( )
static
static Size const core::id::phi_torsion_ortho_aramid ( )
static
static Size const core::id::phi_torsion_para_aramid ( )
static
static Size const core::id::phi_torsion_post_methylene_meta_aramid ( )
static
static Size const core::id::phi_torsion_post_methylene_ortho_aramid ( )
static
static Size const core::id::phi_torsion_post_methylene_para_aramid ( )
static
static Size const core::id::phi_torsion_pre_methylene_meta_aramid ( )
static
static Size const core::id::phi_torsion_pre_methylene_ortho_aramid ( )
static
static Size const core::id::phi_torsion_pre_methylene_para_aramid ( )
static
static Size const core::id::phi_torsion_pre_methylene_post_methylene_meta_aramid ( )
static
static Size const core::id::phi_torsion_pre_methylene_post_methylene_ortho_aramid ( )
static
static Size const core::id::phi_torsion_pre_methylene_post_methylene_para_aramid ( )
static
static Size const core::id::psi_torsion ( )
static
static Size const core::id::psi_torsion_beta_aa ( )
static
static Size const core::id::psi_torsion_meta_aramid ( )
static
static Size const core::id::psi_torsion_oligourea ( )
static
static Size const core::id::psi_torsion_ortho_aramid ( )
static
static Size const core::id::psi_torsion_para_aramid ( )
static
static Size const core::id::psi_torsion_post_methylene_meta_aramid ( )
static
static Size const core::id::psi_torsion_post_methylene_ortho_aramid ( )
static
static Size const core::id::psi_torsion_post_methylene_para_aramid ( )
static
static Size const core::id::psi_torsion_pre_methylene_meta_aramid ( )
static
static Size const core::id::psi_torsion_pre_methylene_ortho_aramid ( )
static
static Size const core::id::psi_torsion_pre_methylene_para_aramid ( )
static
static Size const core::id::psi_torsion_pre_methylene_post_methylene_meta_aramid ( )
static
static Size const core::id::psi_torsion_pre_methylene_post_methylene_ortho_aramid ( )
static
static Size const core::id::psi_torsion_pre_methylene_post_methylene_para_aramid ( )
static
template<typename T >
void core::id::swap ( NamedAtomID_Map< T > &  a,
NamedAtomID_Map< T > &  b 
)
inline

swap( NamedAtomID_Map, NamedAtomID_Map )

template<typename T >
void core::id::swap ( AtomID_Map< T > &  a,
AtomID_Map< T > &  b 
)
inline

swap( AtomID_Map, AtomID_Map )

Referenced by core::chemical::IdealBondLengthSet::add_bond_length(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::add_to_twobody(), core::pack::rotamer_set::symmetry::SymmetricRotamerSets::append_two_body_energy_computations_to_work_vector(), core::chemical::IdealBondLengthSet::contains_bond_length(), core::conformation::parametric::RealValuedParameter::correct_range(), core::pack::hbonds::HBondGraphInitializerIG::eval_rot_pair(), core::scoring::rna::TNA_SuitePotential::eval_score(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty::evaluate_rotamer_pair_energies(), core::chemical::gasteiger::PossibleAtomTypesForAtom::FinalizeUnhybridized(), core::chemical::find_chi_bonds(), protocols::jd3::JobGenealogist::garbage_collection(), core::chemical::IdealBondLengthSet::get_bond_length(), protocols::indexed_structure_store::FragmentStoreManager::load_grouped_fragment_store(), protocols::pockets::SmallMol::operator=(), protocols::hotspot_hashing::HotspotStubSet::operator=(), protocols::hbnet::HBondNetStruct::operator=(), core::scoring::nmr::order_tensor_parameters(), core::pack::rotamer_set::symmetry::SymmetricRotamerSets::prepare_symm_otf_interaction_graph(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::prestore_sc_oversat(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::readMRCandResize(), core::scoring::electron_density::ElectronDensity::readMRCandResize(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty::residue_pair_energy(), core::scoring::motif::ResPairMotif::reverse_in_place_unsafe(), protocols::cluster::Cluster::shuffle(), core::scoring::nmr::pcs::PCSSingleSet::solve_tensor_and_compute_score_by_nls(), core::scoring::nmr::rdc::RDCMultiSet::solve_tensor_and_compute_score_by_nls(), and protocols::noesy_assign::FragsToAtomDist::swap_atoms().

static Size const core::id::theta_torsion_beta_aa ( )
static
static Size const core::id::theta_torsion_meta_aramid ( )
static
static Size const core::id::theta_torsion_oligourea ( )
static
static Size const core::id::theta_torsion_ortho_aramid ( )
static
static Size const core::id::theta_torsion_para_aramid ( )
static
static Size const core::id::theta_torsion_post_methylene_meta_aramid ( )
static
static Size const core::id::theta_torsion_post_methylene_ortho_aramid ( )
static
static Size const core::id::theta_torsion_post_methylene_para_aramid ( )
static
static Size const core::id::theta_torsion_pre_methylene_meta_aramid ( )
static
static Size const core::id::theta_torsion_pre_methylene_ortho_aramid ( )
static
static Size const core::id::theta_torsion_pre_methylene_para_aramid ( )
static
static Size const core::id::theta_torsion_pre_methylene_post_methylene_meta_aramid ( )
static
static Size const core::id::theta_torsion_pre_methylene_post_methylene_ortho_aramid ( )
static
static Size const core::id::theta_torsion_pre_methylene_post_methylene_para_aramid ( )
static
std::string core::id::to_string ( DOF_Type const &  type)
inline

References D, PHI, RB1, RB2, RB3, RB4, RB5, RB6, and THETA.

Referenced by protocols::features::InterfaceDdGMover::add_chain_id(), protocols::antibody::clusters::add_cluster_comments_to_pose(), protocols::abinitio::AbrelaxApplication::add_constraints(), protocols::seeded_abinitio::add_coordinate_constraints(), protocols::legacy_sewing::SewGraph::add_edges_from_binary(), protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator::add_helix_update_moves(), protocols::constraint_movers::CstInfoMover::add_info_for_csts(), protocols::features::InterfaceDdGMover::add_jump_id(), core::chemical::MutableResidueType::add_metapatch_connect(), protocols::sewing::movers::LigandBindingAssemblyMover::add_motif_scorers_to_score_file(), protocols::sewing::movers::AssemblyMover::add_motif_scorers_to_score_file(), protocols::relax::membrane::add_mutant_to_vectors(), protocols::pack_daemon::DaemonSet::add_npd_property_calculator_for_state(), core::pose::rna::add_number_base_pairs(), core::pose::rna::add_number_native_base_pairs(), protocols::pack_daemon::DaemonSet::add_pack_daemon(), protocols::sewing::hashing::AlignmentFileGeneratorMover::add_pose_segments_to_segment_vector(), core::scoring::methods::NMerSVMEnergy::add_pssm_features(), core::pack::interaction_graph::add_rotamers_to_pose(), core::io::mmtf::add_xbond_information(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::align_and_calculate_rmsd(), protocols::helical_bundle_predict::HelicalBundlePredictApplication::align_to_native_pose(), core::scoring::MembraneTopology::allow_scoring(), protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::alter_rotamer_set(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::append_metal_vsites(), protocols::simple_filters::ResidueBurialFilter::apply(), protocols::simple_moves::AddResidueLabelMover::apply(), protocols::protein_interface_design::movers::ShoveResidueMover::apply(), protocols::ligand_docking::WriteLigandMolFile::apply(), protocols::symmetry::DetectSymmetry::apply(), protocols::simple_moves::DumpPdb::apply(), protocols::simple_moves::CombinePoseMover::apply(), protocols::fold_from_loops::movers::ResidueLabelsToPymolSelectionMover::apply(), protocols::symmetry::SetupForSequenceSymmetryMover::apply(), protocols::loophash::LoopHashMoverWrapper::apply(), protocols::struct_fragment::StructFragmentMover::apply(), protocols::task_operations::InteractingRotamerExplosion::apply(), protocols::hbnet::ConstrainHBondNetwork::apply(), protocols::splice::SpliceIn::apply(), protocols::splice::SpliceInTail::apply(), protocols::enzdes::SetCatalyticResPackBehavior::apply(), protocols::splice::SpliceOut::apply(), protocols::simple_moves::BBDihedralSamplerMover::apply(), protocols::pose_creation::MakePolyXMover::apply(), protocols::task_operations::SequenceMotifTaskOperation::apply(), protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::apply(), protocols::calc_taskop_filters::ConservedPosMutationFilter::apply(), protocols::loop_grower::FragmentExtension::apply(), protocols::antibody::AntibodyNumberingConverterMover::apply(), core::select::residue_selector::SliceResidueSelector::apply(), protocols::carbohydrates::GlycanSampler::apply(), protocols::splice::Splice::apply(), protocols::simple_moves::SimpleThreadingMover::apply(), protocols::docking::membrane::QuickRelaxPartnersSeparately::apply(), protocols::carbohydrates::CreateGlycanSequonMover::apply(), protocols::simple_moves::PeriodicBoxMover::apply(), protocols::protein_interface_design::Revert::apply(), protocols::sewing::hashing::AlignmentFileGeneratorMover::apply(), protocols::simple_filters::SimpleMetricFilter::apply(), protocols::ligand_docking::HighResEnsemble::apply(), protocols::membrane::MPQuickRelaxMover::apply(), protocols::ligand_docking::ProtLigEnsemble::apply(), protocols::antibody::design::AntibodyDesignMover::apply(), protocols::dna_dock::DNAClashCheckFilter::apply(), protocols::dna_dock::PropagateClashCheckFilter::apply(), protocols::carbohydrates::GlycanTreeModeler::apply(), protocols::membrane::TransformIntoMembraneMover::apply(), protocols::nmr::pre::PREMover::apply(), protocols::enzdes::RepackLigandSiteWithoutLigandMover::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::apply(), protocols::loop_grower::LoopGrower::apply(), core::chemical::AddConnectAndTrackingVirt::apply(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply_coord_cst_to_sctip(), protocols::electron_density::DockIntoDensityMover::apply_multi(), protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::apply_multi_sequence(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_randomize_backbone_by_rama_prepro(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_set_bondangle(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_set_bondlength(), protocols::antibody::design::AntibodyDesignMover::apply_to_cdr(), protocols::match::output::PDBWriter::assemble_outtag(), protocols::toolbox::match_enzdes_util::assemble_remark_line(), protocols::match::output::PDBWriter::assemble_remark_lines(), protocols::fold_from_loops::utils::Nub::assign_disulfides(), core::chemical::ResidueType::atom_name(), 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::dunbrack::SingleResidueDunbrackLibrary::bin_rotameric_chi(), protocols::pack_daemon::EntityCorrespondence::bounds_check_entity(), protocols::pack_daemon::EntityCorrespondence::bounds_check_residue(), protocols::hbnet::HBNet::branch_overlapping_networks(), protocols::abinitio::abscript::FragmentJumpCM::build_claims(), core::pack::rotamer_set::build_optimal_hyp_H_for_acceptor(), core::pack::rotamer_set::build_optimal_hyp_H_for_donor(), protocols::loophash::LoopHashSampler::build_structures(), core::pack::rotamer_set::build_water_O_on_donor(), core::scoring::sc::ShapeComplementarityCalculator::Calc(), protocols::symmetric_docking::SymDockProtocol::calc_fnat(), protocols::nmr::pcs::PCSEnergy::calcualate_total_score_and_tensors(), core::simple_metrics::metrics::SelectedResiduesPyMOLMetric::calculate(), core::simple_metrics::metrics::SelectedResiduesMetric::calculate(), core::simple_metrics::metrics::SecondaryStructureMetric::calculate(), core::simple_metrics::metrics::DihedralDistanceMetric::calculate(), protocols::analysis::simple_metrics::SequenceRecoveryMetric::calculate(), protocols::nmr::pre::PREEnergy::calculate_total_score(), protocols::antibody::clusters::CDRClusterEnumManager::cdr_cluster_enum_to_string(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::check_backbones_match(), protocols::docking::DockingEnsemblePrepackProtocol::check_ensemble_member_compatibility(), protocols::helical_bundle_predict::HelicalBundlePredictApplication::check_ignore_residues_reasonable(), protocols::antibody::CDRSetOptionsParser::check_line_len(), protocols::antibody::design::CDRSeqDesignOptionsParser::check_line_len(), protocols::antibody::design::CDRGraftDesignOptionsParser::check_line_len(), protocols::relax::membrane::check_mutants_ok(), protocols::features::FeaturesReporter::check_relevant_residues(), protocols::features::FeaturesReporter::check_relevant_residues_range(), protocols::loop_grower::LoopPartialSolutionStore::cluster_check(), protocols::pockets::GenPharmacophore::cluster_KeyFeatures(), protocols::toolbox::match_enzdes_util::InvrotTarget::collect_all_inverse_rotamers(), protocols::optimize_weights::IterativeOptEDriver::collect_decoy_discrimination_data(), core::pack::task::ResfileContents::commands_for_residue(), protocols::simple_filters::SimpleMetricFilter::compare_composites(), core::pack::compare_mingraph_and_energy_graph(), core::pack::compare_simple_inteaction_graph_alt_state_and_energy_graph(), protocols::rigid::UniformRigidBodyMover::complex_type_gen(), core::chemical::sdf::MolWriter::compose_atoms(), core::chemical::sdf::MolWriter::compose_nbr_atom(), protocols::simple_filters::NMerSVMEnergyFilter::compute(), protocols::frag_picker::FragmentScoreFilter::compute(), protocols::simple_filters::BuriedUnsatHbondFilter::compute(), protocols::features::InterfaceDdGMover::compute(), core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::compute_burial(), core::pack::rotamer_set::symmetry::SymmetricRotamerSets::compute_energies(), core::pack::rotamer_set::RotamerSets::compute_energies(), protocols::simple_moves::ConcatenatePosesMover::concatenate_poses(), protocols::forge::remodel::RemodelMover::confirm_sequence(), protocols::enzdes::PoseFoundResiduesCombination::construct_and_dump_outpose(), protocols::jd3::job_distributors::VanillaJobDistributor::construct_job_result_input_list(), protocols::frag_picker::convert_binary_checkpoint(), core::chemical::ResidueType::copy_other_info(), core::chemical::correct_conn(), core::pack::rotamers::SingleNCAARotamerLibraryCreator::create(), core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::create_atom_id_map(), protocols::calc_taskop_movers::ConsensusDesignMover::create_consensus_design_task(), core::pack::annealer::SequenceSymmetricAnnealer::create_corresponding_mress_for_mres(), core::pack::dunbrack::RotamerLibrary::create_fa_dunbrack_libraries_10_from_ASCII(), protocols::toolbox::ResidueNetwork::create_from_pose(), core::scoring::ScoringManager::create_nmer_pssm(), protocols::match::output::ProcessorFactory::create_output_writer(), core::io::pdb::create_records_from_sfr(), core::pack::dunbrack::RotamerLibrary::create_rotameric_dunlib(), core::pack::dunbrack::RotamerLibrary::create_semi_rotameric_dunlib(), protocols::pack_daemon::DynamicAggregateFunction::create_variable_vector_expressions(), core::chemical::gasteiger::PossibleAtomTypesForAtom::CreateAtomicEnvironmentToTypesMap(), protocols::ligand_docking::ga_ligand_dock::crossover(), protocols::ligand_docking::ga_ligand_dock::crossover_ft(), protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::debug_note_projected_deltaE_of_considered_substitution(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_active_virtual_sites(), core::chemical::MutableResidueType::delete_child_proton(), protocols::loophash::LoopHashLibrary::delete_db(), core::io::HeaderInformation::deposition_date(), protocols::match::Matcher::desymmeterize_upstream_restype_for_constraint(), protocols::antibody::AntibodyInfo::detect_and_set_regular_CDR_H3_stem_type_new_rule(), protocols::match::MatcherTask::determine_all_match_relevant_downstream_atoms(), protocols::match::output::OutputWriter::determine_redundant_upstream_matchres(), protocols::multistage_rosetta_scripts::MRSJobQueen::determine_validity_of_stage_tags(), protocols::pack_daemon::DynamicAggregateFunctionDriver::distribute_jobs_to_remote_daemons(), core::optimization::AtomTreeMultifunc::dump(), core::optimization::CartesianMultifunc::dump(), protocols::normalmode::NormalModeMultifunc::dump(), core::optimization::symmetry::SymAtomTreeMultifunc::dump(), core::io::mmcif::dump_cif(), protocols::toolbox::match_enzdes_util::InvrotTree::dump_invrots_tree_as_multimodel_pdbs(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::dump_pdbs(), protocols::grafting::simple_movers::KeepRegionMover::end(), core::scoring::ScoringManager::energy_method(), protocols::simple_moves::DumpSingleResidueRotamers::enumerate_aa_rotamer(), protocols::enzdes::EnzdesFlexibleRegion::EnzdesFlexibleRegion(), protocols::enzdes::EnzdesScorefileFilter::examine_pose(), protocols::hotspot_hashing::movers::PlaceProbeMover::execute_one_search(), protocols::match::upstream::FullChiSampleSet::expand_non_dunbrack_chi(), protocols::match::upstream::FullChiSampleSet::expand_samples_for_nrchi_wi_nrchi_bin(), core::scoring::ScoringManager::factory_register(), protocols::jd2::EnsembleJobInputter::fill_jobs(), protocols::features::DatabaseJobInputter::fill_jobs(), protocols::loop_grower::LoopPartialSolutionStore::filter(), protocols::docking::membrane::MPDockingMover::finalize_setup(), protocols::splice::SpliceIn::find_dbase_entry(), protocols::splice::SpliceInTail::find_dbase_entry(), protocols::splice::Splice::find_dbase_entry(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface_arg_sweep(), core::scoring::hbonds::find_hb_paths(), protocols::denovo_design::components::find_orientations_and_lengths(), core::chemical::gasteiger::PossibleAtomTypesForAtom::FindPossibleAtomTypesForAtom(), protocols::noesy_assign::CrossPeak::fold_resonance(), protocols::noesy_assign::CrossPeak::folder(), core::kinematics::Stub::from_four_points(), protocols::pack_daemon::DynamicAggregateFunction::function_expression(), protocols::pack_daemon::EntityFunc::function_expression(), protocols::legacy_sewing::LegacyEnumerateAssemblyMover::generate_assembly(), protocols::sewing::hashing::EdgeMapGenerator::generate_edge_file(), core::pack::interaction_graph::generate_rotamers_from_packer_solution_description(), protocols::match::output::WriteUpstreamHitKinemage::geom_id(), protocols::features::InterfaceFeatures::get_all_pose_chains(), core::pack::interaction_graph::get_annealable_graph_summary(), core::import_pose::libraries::ChunkSet::get_atom_id_domain_map_for_rosetta_library_chunk(), protocols::analysis::GlycanInfoMover::get_attachment_point_string(), protocols::antibody::AntibodyInfo::get_CDR_end(), protocols::antibody::AntibodyInfo::get_CDR_start(), core::pose::get_chain_id_from_chain(), protocols::sewing::data_storage::SmartAssembly::get_comprehensive_assembly_string(), protocols::sewing::data_storage::SmartAssembly::get_comprehensive_forward_assembly(), protocols::sewing::data_storage::SmartAssembly::get_comprehensive_reverse_assembly(), protocols::hbnet::HBNet::get_file_name(), core::kinematics::get_foldtree_which_partitions(), protocols::sewing::data_storage::SmartAssembly::get_forward_assembly(), protocols::qsar::scoring_grid::GridManager::get_grids(), protocols::jd3::dag_node_managers::get_index_of_last_element_with_token(), core::pose::get_jump_id_from_chain_id(), protocols::antibody::AntibodyInfo::get_landmark_resnum(), protocols::ligand_docking::InterfaceScoreCalculator::get_ligand_docking_scores(), protocols::ligand_docking::get_ligand_grid_scores(), protocols::ligand_docking::get_ligand_travel(), core::conformation::carbohydrates::get_linkage_position_of_saccharide_residue(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::get_loop_index(), protocols::legacy_sewing::SewGraph::get_model_node(), protocols::motif_grafting::movers::MotifMatch::get_motif_ranges(), protocols::stepwise::monte_carlo::get_move_type_string(), protocols::abinitio::abscript::AbscriptStageMover::get_name(), protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSampler::get_name(), protocols::stepwise::sampler::StepWiseSamplerOneDOF::get_name(), protocols::stepwise::sampler::StepWiseSamplerOneTorsion::get_name(), protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler::get_name(), protocols::stepwise::sampler::rna::RNA_KIC_Sampler::get_name(), protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::get_name(), protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::get_name(), protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::get_name(), protocols::optimize_weights::IterativeOptEDriver::get_nat_rot_opte_data(), core::conformation::carbohydrates::GlycanTree::get_node(), core::conformation::carbohydrates::GlycanTreeSet::get_node(), protocols::legacy_sewing::SewGraph::get_node_indices_from_model_id(), protocols::fold_from_loops::utils::Nub::get_nub_pieces(), protocols::jobdist::PlainPdbJobDistributor::get_output_filename(), protocols::jobdist::PlainRawJobDistributor::get_output_filename(), protocols::jobdist::PlainSilentFileJobDistributor::get_output_filename(), core::pose::get_pdb2pose_numbering_as_stdmap(), protocols::pdbinfo_manipulations::get_pose_sequences(), core::select::get_pymol_selection_for_atoms(), protocols::ligand_docking::get_radius_of_gyration(), core::pack::task::get_resfile_commands(), core::pose::carbohydrates::get_resnums_from_glycan_positions(), protocols::sewing::data_storage::SmartAssembly::get_reverse_assembly(), core::chemical::rna::get_rna_base_coordinate_system(), core::scoring::carbohydrates::OmegaPreferencesFunction::get_sampling_data(), core::scoring::carbohydrates::CHIEnergyFunction::get_sampling_data(), protocols::motif_grafting::movers::MotifMatch::get_scaffold2motif_size_change(), protocols::motif_grafting::movers::MotifMatch::get_scaffold_ranges(), core::pose::get_sha1_hash_excluding_chain(), core::pose::get_sha1_hash_excluding_chains(), core::pose::get_sha1_hash_from_chain(), core::pose::get_sha1_hash_from_chains(), protocols::antibody::PDBLandmark::get_string(), protocols::features::get_struct_id_with_highest_score_from_score_data(), protocols::features::get_struct_id_with_nth_lowest_score_from_job_data(), protocols::features::get_struct_id_with_nth_lowest_score_from_score_data(), protocols::simple_moves::bb_sampler::SugarBBSampler::get_torsion(), protocols::canonical_sampling::MetricRecorder::get_torsion_ids(), core::conformation::carbohydrates::GlycanTreeSet::get_tree(), core::pose::Pose::glycan_tree_branch_sequence(), protocols::jd2::JobDistributor::go_main(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_pose_energies_table(), core::kinematics::FoldTree::hash_value(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::identical_info_consistency_check(), protocols::optimize_weights::WrapperOptEMultifunc::init(), protocols::membrane::MPQuickRelaxMover::init_from_cmd(), protocols::carbohydrates::GlycanSampler::init_objects(), core::scoring::nmr::pcs::PCSData::init_pcs_data_from_file(), core::scoring::nmr::pre::PREData::init_pre_data_from_file(), core::scoring::nmr::rdc::RDCData::init_rdc_data_from_file(), protocols::abinitio::abscript::RigidChunkCM::initialize(), protocols::fldsgn::topology::HelixPairing::initialize(), protocols::pack_daemon::IterativeVectorExpression::initialize(), protocols::fldsgn::topology::StrandPairing::initialize(), protocols::match::downstream::LigandConformerBuilder::initialize_conformers(), protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst::initialize_from_command_line(), protocols::pack_daemon::EntityCorrespondence::initialize_from_correspondence_file(), protocols::match::Matcher::initialize_from_file(), protocols::match::downstream::ActiveSiteGrid::initialize_from_gridlig_file(), core::scoring::hbonds::HBondDatabase::initialize_HBEval(), core::conformation::membrane::ImplicitLipidInfo::initialize_implicit_lipid_parameters(), core::pose::datacache::CacheableDataType::initialize_name_map(), protocols::calc_taskop_movers::CreateSequenceMotifMover::initialize_objects(), protocols::qsar::scoring_grid::PCSMultiGrid::initialize_pcs_data_from_input_file(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::initialize_rotamer_set_and_scores(), protocols::match::MatcherTask::initialize_scaffold_active_site_residue_list_from_command_line(), protocols::pack_daemon::EntityFunc::initialize_scanner_and_function_names(), protocols::tcr::initialize_template_db_files(), core::environment::FoldTreeSketch::insert_cut(), core::environment::FoldTreeSketch::insert_jump(), core::scoring::methods::EnergyMethodOptions::insert_score_function_method_options_rows(), protocols::features::ScoreTypeFeatures::insert_score_type_rows(), core::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator::InterfaceDeltaEnergeticsCalculator(), protocols::environment::introduce_datamap_cuts(), protocols::sewing::hashing::Hasher::iterate_over_basis_pairs(), protocols::sewing::data_storage::SmartAssembly::iterate_over_basis_pairs(), protocols::fold_from_loops::utils::Nub::join_pieces(), protocols::optimize_weights::load_component_weights(), protocols::loophash::LoopHashLibrary::load_db(), protocols::loophash::LoopHashLibrary::load_mergeddb(), protocols::denovo_design::components::SheetDB::load_sheetlist_from_file(), core::scoring::mm::MMBondAngleLibrary::lookup(), core::scoring::mm::MMTorsionLibrary::lookup(), protocols::loophash::LoopHashLibrary::LoopHashLibrary(), protocols::motifs::IRCollection::make_motif_filename(), protocols::membrane::MPMutateRelaxMover::make_mutations(), protocols::task_operations::RestrictToInterfaceOperation::make_name(), protocols::task_operations::RestrictToNeighborhoodOperation::make_name(), protocols::denovo_design::components::make_strand_info_str(), protocols::fold_from_loops::utils::map_by_residue_subsets(), protocols::fldsgn::MatchResidues::map_ss_segments(), core::conformation::map_string_to_torsion_bin_string(), protocols::jd2::MPIFileBufJobDistributor::master_go(), protocols::splice::min_seg(), protocols::legacy_sewing::Model::model_begin(), protocols::legacy_sewing::Model::model_end(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::legacy_sewing::HashEdge::model_resnum(), protocols::match::SecondaryStructureMPM::modified_match_positions(), protocols::match::NumNeighborsMPM::modified_match_positions(), protocols::match::BfactorMPM::modified_match_positions(), protocols::ligand_docking::ga_ligand_dock::mutate(), core::chemical::ICoorAtomID::name(), protocols::jd3::chunk_library::ChunkLibraryJobQueen::next_batch_of_larval_jobs_from_prelim(), protocols::jd3::full_model::FullModelJobQueen::next_batch_of_larval_jobs_from_prelim(), protocols::jd3::standard::StandardJobQueen::next_batch_of_larval_jobs_from_prelim(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::next_generation(), protocols::canonical_sampling::TrialCounterObserver::observe_after_metropolis(), protocols::canonical_sampling::TemperingBase::observe_after_metropolis(), core::environment::LengthChecker::operator()(), core::scoring::func::FourPointsFunc::operator()(), operator<<(), protocols::relax::LocalRelax::optimization_loop(), protocols::membrane::OptimizeMembranePositionMover::optimize_membrane_center(), protocols::membrane::OptimizeMembranePositionMover::optimize_membrane_normal(), protocols::optimize_weights::IterativeOptEDriver::optimize_weights(), protocols::membrane::MPMutateRelaxMover::output_filename(), protocols::score_filters::ScoreCutoffFilter::output_residue_pair_energies(), core::scoring::rna::output_rna_motifs(), protocols::match::output::WriteUpstreamHitKinemage::output_upstream_coordinates(), protocols::loop_grower::LoopPartialSolutionStore::parametercheck_filter(), protocols::constraint_generator::parse_custom_torsion(), protocols::sewing::hashing::AlignmentFileGeneratorMover::parse_ligands_tag(), protocols::abinitio::abscript::AbscriptMover::parse_my_tag(), protocols::ligand_docking::Rotate::parse_my_tag(), core::scoring::constraints::ConstraintIO::parse_residue(), core::pack::task::operation::ExtraRotamers::parse_tag(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_1_merge_residues_as_necessary(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_2_resolve_residue_types(), core::scoring::nmr::pcs::PCSSingle::PCSSingle(), protocols::ligand_docking::ga_ligand_dock::Pharmacophore::Pharmacophore(), protocols::cyclic_peptide_predict::PNearCalculator::PNearCalculator(), protocols::flxbb::LayerDesignOperation::pos2select(), protocols::legacy_sewing::Assembly::pose_num(), protocols::legacy_sewing::Model::pose_number(), protocols::task_operations::RestrictConservedLowDdgOperation::position_ala_ddG(), protocols::task_operations::RestrictConservedLowDdgOperation::position_untouchable(), protocols::jd3::job_distributors::VanillaJobDistributor::potentially_discard_some_job_results(), protocols::jd3::job_distributors::VanillaJobDistributor::potentially_output_some_job_results(), core::scoring::nmr::pre::PRESingle::PRESingle(), protocols::pose_metric_calculators::HPatchCalculator::print(), protocols::pose_metric_calculators::ResidueDecompositionCalculator::print(), protocols::pose_metric_calculators::SurfaceCalculator::print(), core::pose::metrics::simple_calculators::SasaCalculatorLegacy::print(), protocols::mean_field::EnergiesByTaskCalculator::print(), core::pose::metrics::simple_calculators::InterfaceNeighborDefinitionCalculator::print(), core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator::print(), core::pose::metrics::simple_calculators::SasaCalculator2::print(), core::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator::print(), protocols::pose_metric_calculators::PackstatCalculator::print(), protocols::pose_metric_calculators::NeighborsByDistanceCalculator::print(), protocols::denovo_design::calculators::CavityCalculator::print(), protocols::pose_metric_calculators::RotamerBoltzCalculator::print(), protocols::pose_metric_calculators::NeighborhoodByDistanceCalculator::print(), protocols::pose_metric_calculators::SaltBridgeCalculator::print(), protocols::pose_metric_calculators::CatPiCalculator::print(), protocols::pose_metric_calculators::PiPiCalculator::print(), protocols::simple_pose_metric_calculators::NumberHBondsCalculator::print(), protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::print(), protocols::pose_metric_calculators::InterGroupNeighborsCalculator::print(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::print(), protocols::fldsgn::NcontactsCalculator::print(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::print(), protocols::pose_metric_calculators::FragQualCalculator::print(), protocols::match::downstream::AtomDistanceSecMatchRPE::print(), protocols::match::downstream::AtomAngleSecMatchRPE::print(), protocols::match::downstream::AtomDihedralSecMatchRPE::print(), protocols::vardist_solaccess::VarSolDistSasaCalculator::print(), protocols::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator::print(), protocols::ligand_docking::ProtLigPair_info::print_mut_string(), protocols::antibody::design::AntibodyDesignMover::print_str_vec(), protocols::ligand_docking::ProtLigPair_info::print_string(), protocols::pockets::FingerprintBase::print_to_pdb(), protocols::pack_daemon::EntityFunc::process_AA_SET_line(), protocols::pack_daemon::DynamicAggregateFunction::process_ENTITY_FUNCTION_line(), protocols::pack_daemon::DynamicAggregateFunction::process_FITNESS_line(), protocols::pack_daemon::DynamicAggregateFunction::process_NPD_PROPERTY_line(), protocols::toolbox::match_enzdes_util::EnzConstraintIO::process_pdb_header(), protocols::pack_daemon::DynamicAggregateFunction::process_POSE_ENERGY_line(), protocols::pack_daemon::DynamicAggregateFunction::process_POSE_ENERGY_VECTOR_line(), protocols::pack_daemon::DynamicAggregateFunction::process_SCALAR_EXPRESSION_line(), protocols::pack_daemon::EntityFunc::process_SCORE_line(), protocols::pack_daemon::EntityFunc::process_SET_CONDITION_line(), protocols::pack_daemon::DynamicAggregateFunction::process_STATE_line(), protocols::pack_daemon::DynamicAggregateFunction::process_STATE_VECTOR_line(), protocols::pack_daemon::EntityFunc::process_SUB_EXPRESSION_line(), protocols::pack_daemon::DynamicAggregateFunction::process_VECTOR_EXPRESSION_line(), protocols::pack_daemon::DynamicAggregateFunction::process_VECTOR_VARIABLE_line(), protocols::network::NetworkQueue::process_work_unit(), protocols::recon_design::FitnessFilter::provide_xml_schema(), protocols::struct_fragment::StructFragmentMover::provide_xml_schema(), protocols::fold_from_loops::movers::SavePDBInfoMover::provide_xml_schema(), protocols::fold_from_loops::movers::LabelPoseFromResidueSelectorMover::provide_xml_schema(), protocols::fold_from_loops::constraint_generator::AutomaticSheetConstraintGenerator::provide_xml_schema(), protocols::fold_from_loops::selectors::CutpointResidueSelector::provide_xml_schema(), protocols::fold_from_loops::movers::ResidueLabelsToPymolSelectionMover::provide_xml_schema(), protocols::fold_from_loops::selectors::ConstraintResidueSelector::provide_xml_schema(), protocols::fold_from_loops::filters::ScorePoseSegmentFromResidueSelectorFilter::provide_xml_schema(), protocols::fold_from_loops::filters::ConstraintFulfilmentFilter::provide_xml_schema(), protocols::coupled_moves::CoupledMovesProtocol::provide_xml_schema(), protocols::mean_field::GenMeanFieldMover::provide_xml_schema(), protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::provide_xml_schema(), protocols::fold_from_loops::movers::DisplayPoseLabelsMover::provide_xml_schema(), core::simple_metrics::composite_metrics::ElectrostaticComplementarityMetric::provide_xml_schema(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::provide_xml_schema(), protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::provide_xml_schema(), protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::provide_xml_schema(), protocols::fold_from_loops::movers::SplitAndMixPoseMover::provide_xml_schema(), core::select::residue_selector::ResiduePropertySelector::provide_xml_schema(), core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::provide_xml_schema(), core::simple_metrics::metrics::RMSDMetric::provide_xml_schema(), protocols::simple_filters::SimpleMetricFilter::provide_xml_schema(), core::simple_metrics::metrics::ResidueSummaryMetric::provide_xml_schema(), core::pack::task::operation::ExtraChiCutoffRLT::provide_xml_schema(), protocols::enzdes::EnzScoreFilter::provide_xml_schema(), protocols::fold_from_loops::NubInitioMover::provide_xml_schema(), protocols::backrub::BackrubMover::provide_xml_schema(), protocols::moves::PyMOLMover::provide_xml_schema(), protocols::motif_grafting::movers::MotifGraftMover::provide_xml_schema(), core::conformation::parametric::SizeValuedParameter::provide_xsd_information(), core::conformation::parametric::RealValuedParameter::provide_xsd_setting_information(), protocols::loop_grower::LoopPartialSolutionStore::push(), protocols::jd3::job_distributors::JobExtractor::query_job_queen_for_more_jobs_for_current_node(), core::environment::FoldTreeSketch::range_check(), core::scoring::nmr::rdc::RDCSingle::RDCSingle(), core::chemical::gasteiger::GasteigerAtomTypeSet::read_bond_file(), core::sequence::SequenceProfile::read_from_checkpoint(), core::sequence::SequenceProfile::read_from_file(), protocols::noesy_assign::PeakFileFormat::read_header(), core::chemical::carbohydrates::read_linkage_conformers_from_database_file(), core::scoring::methods::NMerRefEnergy::read_nmer_table(), protocols::pack_daemon::DynamicAggregateFunction::read_state_vector_file(), core::conformation::symmetry::SymmetricConformation::recalculate_transforms(), protocols::pose_metric_calculators::ResidueDecompositionByChainCalculator::recompute(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), protocols::match::output::PDBWriter::record_match(), protocols::match::output::CloudPDBWriter::record_match(), protocols::match::upstream::ProteinUpstreamBuilder::recover_hits(), protocols::pack_daemon::MPIMultistateFitnessFunction::recover_poses_from_states(), protocols::loop_grower::LoopGrower::refine_cycle(), core::environment::FoldTreeSketch::remove_cycles(), protocols::legacy_sewing::remove_models_from_dssp(), protocols::toolbox::match_enzdes_util::EnzdesCstParamCache::remove_seqpos_from_template_res(), core::chemical::rename_atoms(), core::environment::FoldTreeSketch::render(), protocols::toolbox::pose_manipulation::repack_this_residue(), protocols::simple_filters::TotalSasaFilter::report(), protocols::indexed_structure_store::filters::FragmentLookupFilter::report(), protocols::mean_field::GenMeanFieldMover::report_aa_matrix(), protocols::legacy_sewing::SewGraph::report_binary_stats(), protocols::features::ModelFeatures::report_features(), protocols::indexed_structure_store::filters::FragmentLookupFilter::report_sm(), core::scoring::symmetry::SymmetricEnergies::require_context_graph_(), core::scoring::Energies::require_context_graph_(), core::pack::task::IGEdgeReweightContainer::res_res_weight(), protocols::loop_grower::LoopGrower::rescoresolutionset(), core::pose::residue_types_from_sequence(), protocols::enzdes::SecondaryMatchProtocol::residues_compatible(), core::pose::ResidueIndexDescriptionPoseNum::resolve_index(), core::pose::ResidueIndexDescriptionPDB::resolve_index(), core::pose::ResidueIndexDescriptionChainEnd::resolve_index(), core::io::pose_to_sfr::restrict_prec(), core::pack::task::operation::rotamer_sampling_data_xml_schema_attributes(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::run(), protocols::antibody::design::AntibodyDesignMover::run_basic_mc_algorithm(), protocols::frag_picker::run_command(), core::io::external::PsiPredInterface::run_psipred(), core::io::external::PsiPredInterface::run_psipred_prob(), protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::sample_loops(), protocols::match::upstream::DunbrackSCSampler::samples(), protocols::monte_carlo::GenericSimulatedAnnealer::save_checkpoint_file(), protocols::loophash::LoopHashLibrary::save_db(), protocols::pack_daemon::PackDaemon::select_rotamer_subset(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), protocols::moves::PyMOLMover::send_any(), protocols::moves::PyMOLMover::send_foldtree(), protocols::moves::PyMOLMover::send_hbonds(), protocols::moves::PyMOLMover::send_membrane_planes(), protocols::moves::PyMOLMover::send_movemap(), protocols::moves::PyMOLMover::send_polars(), protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst::seqpos_for_geomcst(), protocols::features::serialize_ids(), protocols::hbnet::HBNet::set_constraints(), protocols::antibody::AntibodyInfo::set_default(), protocols::splice::Splice::set_fold_tree(), core::select::residue_selector::ResidueIndexSelector::set_index(), core::select::residue_selector::ResidueIndexSelector::set_index_range(), protocols::match::set_ligpose_rotamer(), protocols::frag_picker::FragmentPicker::set_max_threads(), core::scoring::Energies::set_owner(), protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::set_rmsd_residues_to_ignore_native(), protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::set_rmsd_residues_to_ignore_prediction(), protocols::features::DatabaseJobInputter::set_struct_ids_from_sql(), protocols::environment::ProtectedConformation::set_stub_transform(), core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix::set_thresh(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_up_terminal_disulfide_variants(), protocols::rna::setup::RNA_CSA_JobDistributor::set_updates(), core::simple_metrics::SimpleMetricData::set_value(), protocols::antibody::AntibodyInfo::setup_CDRsInfo(), core::scoring::carbohydrates::OmegaPreferencesFunction::setup_for_sampling(), core::scoring::carbohydrates::CHIEnergyFunction::setup_for_sampling(), core::conformation::carbohydrates::GlycanTree::setup_glycan_nodes(), protocols::optimize_weights::IterativeOptEDriver::setup_pdbnames_next_round(), protocols::simple_moves::PeriodicBoxMover::setup_pose(), protocols::enzdes::EnzdesScorefileFilter::setup_pose_metric_calculators(), protocols::tcr::TCRmodel::setup_templates(), protocols::cryst::MakeLayerMover::setup_xtal_symminfo(), protocols::cryst::MakeLatticeMover::setup_xtal_symminfo(), protocols::ligand_docking::ga_ligand_dock::AtomProperties::show(), protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::show(), protocols::antibody::design::AntibodyDesignMover::show(), core::simple_metrics::SimpleMetricData::show(), core::kinematics::MoveMap::show(), core::select::residue_selector::SliceResidueSelector::show_selection_logic(), protocols::match::output::PDBWriter::signature_string(), protocols::loop_grower::LoopGrower::single_grow(), protocols::loop_grower::LoopPartialSolutionStore::skeleton_filter(), protocols::task_operations::ConservativeDesignOperation::skip_resid(), protocols::enzdes::EnzdesFlexibleRegion::sort_ensemble_by_designability(), core::pose::RID_FileSource::source_string(), core::pack::task::ResfileContents::specialized_commands_exist_for_residue(), protocols::splice::SpliceOut::SpliceOutFilter(), core::sequence::split_sequence_motif(), protocols::grafting::simple_movers::KeepRegionMover::start(), core::id::TorsionID::str(), protocols::docking::membrane::MPFindInterfaceMover::superimpose_upstream_partner(), core::pack::interaction_graph::DensePDEdge::swap_edge_energies(), core::pack::interaction_graph::FASTEREdge::swap_edge_energies(), protocols::optimize_weights::IterativeOptEDriver::test_weight_sensitivity(), core::select::residue_selector::ResidueRange::to_string(), core::pack::annealer::Value::to_string(), protocols::noesy_assign::CrossPeak::tolerance(), protocols::antibody::design::transform_sequence_to_mutation_set(), protocols::motifs::IRCollection::try_for_more(), protocols::moves::UDPSocketClient::UDPSocketClient(), core::kinematics::tree::BondedAtom::update_internal_coords(), core::conformation::symmetry::SymmetryInfo::update_nmonomer_jumps(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::update_tags(), protocols::pack_daemon::DynamicAggregateFunction::variable_expression(), protocols::pack_daemon::EntityFunc::variable_expression(), protocols::pack_daemon::IterativeVectorExpression::vector_values(), protocols::pack_daemon::DynamicAggregateFunctionDriver::verify_remote_daemon_set_initialization_successful(), protocols::pack_daemon::DynamicAggregateFunction::verify_variable_name_or_throw(), protocols::pack_daemon::DynamicAggregateFunction::verify_vector_arguments(), core::select::residue_selector::SelectorLogicParser::visit(), core::select::residue_selector::SliceResidueSelector::wrap_index(), protocols::sewing::hashing::BasisMapGenerator::write_alignments_to_file(), protocols::sewing::hashing::EdgeMapGenerator::write_edges_for_segment(), protocols::noesy_assign::PeakFileFormat::write_header(), protocols::match::output::CloudPDBWriter::write_match_groups(), protocols::simple_moves::DumpSingleResidueRotamers::write_poses_to_pdbs(), protocols::loop_grower::LoopGrower::write_to_disk(), protocols::loop_grower::LoopPartialSolutionStore::writelpsstore(), core::scoring::func::FourPointsFunc::xyz(), protocols::loops::loop_mover::LoopCM::yield_claims(), and protocols::abinitio::abscript::RigidChunkCM::yield_claims().

std::string core::id::to_string ( TorsionType const &  type)
inline

References BB, BRANCH, CHI, JUMP, and NU.

static basic::Tracer core::id::tr ( "core.id.AtomID"  )
static
static basic::Tracer core::id::TR ( "core.id.SequenceMapping"  )
static
static Size const core::id::zeta_torsion_para_aramid ( )
static
static Size const core::id::zeta_torsion_post_methylene_meta_aramid ( )
static
static Size const core::id::zeta_torsion_post_methylene_para_aramid ( )
static
static Size const core::id::zeta_torsion_pre_methylene_meta_aramid ( )
static
static Size const core::id::zeta_torsion_pre_methylene_para_aramid ( )
static
static Size const core::id::zeta_torsion_pre_methylene_post_methylene_meta_aramid ( )
static
static Size const core::id::zeta_torsion_pre_methylene_post_methylene_ortho_aramid ( )
static
static Size const core::id::zeta_torsion_pre_methylene_post_methylene_para_aramid ( )
static

Variable Documentation

AtomID const core::id::GLOBAL_BOGUS_ATOM_ID
DOF_ID const core::id::GLOBAL_BOGUS_DOF_ID
NamedAtomID const core::id::GLOBAL_BOGUS_NAMED_ATOM_ID

Globals – may not be used until after core::init is called.

StubID const core::id::GLOBAL_BOGUS_STUB_ID

Global – may not be used until after core::init is called.

TorsionID const core::id::GLOBAL_BOGUS_TORSION_ID

Global – may not be used until after core::init is called.

AtomID const core::id::GLOBAL_CHAINBREAK_BOGUS_ATOM_ID
NamedAtomID const core::id::GLOBAL_CHAINBREAK_BOGUS_NAMED_ATOM_ID