Rosetta Core  2014.35
Classes | Typedefs | Enumerations | Functions | Variables
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::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 NamedAtomID_Map< boolNamedAtomID_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, NU, JUMP }
 Torsion type – used in the TorsionID class. More...
 

Functions

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...
 
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...
 
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)
 
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)
 

Variables

static basic::Tracer tr ("core.id.AtomID")
 
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 
RB1 
RB2 
RB3 
RB4 
RB5 
RB6 

Torsion type – used in the TorsionID class.

  • BB: backbone torsion
  • CHI: sidechain torsion
  • NU: internal ring torsion
  • JUMP: rigid-body transformation
Enumerator
BB 
CHI 
NU 
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 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(), core::id::NamedAtomID::rsd(), and tag.

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

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

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

References BB, CHI, JUMP, and NU.

Variable Documentation

AtomID const core::id::BOGUS_ATOM_ID
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
basic::Tracer core::id::tr("core.id.AtomID")
static