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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  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< boolAtomID_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< boolDOF_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 Documentation

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
PHI 
THETA 
D 
RB1 
RB2 
RB3 
RB4 
RB5 
RB6 

Torsion type – used in the TorsionID class.

  • BB: backbone torsion
  • CHI: sidechain torsion
  • JUMP: rigid-body transformation
Enumerator
BB 
CHI 
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
Size core::id::get_rb_number ( DOF_Type const  t)
inline
DOF_Type core::id::get_rb_type ( Size const  k)
inline
static Size const core::id::n_DOF_Type ( )
static
static Size const core::id::omega_torsion ( )
static
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::psi_torsion ( )
static
template<typename T >
void core::id::swap ( AtomID_Map< T > &  a,
AtomID_Map< T > &  b 
)
inline
static basic::Tracer core::id::tr ( "core.id.AtomID"  )
static

Variable Documentation

AtomID const core::id::BOGUS_ATOM_ID

Globals.

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
NamedAtomID const core::id::BOGUS_NAMED_ATOM_ID
StubID const core::id::BOGUS_STUB_ID

Globals.

TorsionID const core::id::BOGUS_TORSION_ID
AtomID const core::id::CHAINBREAK_BOGUS_ATOM_ID
NamedAtomID const core::id::CHAINBREAK_BOGUS_NAMED_ATOM_ID