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	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	NamedStubID

class	SequenceMapping

class	StubID

class	TorsionID
	Torsion identifier class. More...

class	TorsionID_Range
	Kinematics DOF identifier (with range) class. More...

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...

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

typedef AtomID_Map< bool > core::id::AtomID_Mask

typedef utility::pointer::access_ptr< CacheableAtomID_MapVector > core::id::CacheableAtomID_MapVectorAP

typedef utility::pointer::access_ptr< CacheableAtomID_MapVector const > core::id::CacheableAtomID_MapVectorCAP

typedef utility::pointer::owning_ptr< CacheableAtomID_MapVector const > core::id::CacheableAtomID_MapVectorCOP

typedef utility::pointer::owning_ptr< CacheableAtomID_MapVector > core::id::CacheableAtomID_MapVectorOP

typedef DOF_ID_Map< bool > core::id::DOF_ID_Mask

typedef utility::pointer::owning_ptr< SequenceMapping const > core::id::SequenceMappingCOP

typedef utility::pointer::owning_ptr< SequenceMapping > core::id::SequenceMappingOP

Enumeration Type Documentation

enum core::id::DOF_Type

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

enum core::id::TorsionType

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

References RB1, and RB6.

Referenced by core::optimization::symmetry::SymMinimizerMap::reset_jump_rb_deltas(), and core::optimization::MinimizerMap::reset_jump_rb_deltas().

Size core::id::get_rb_number ( DOF_Type const t )

inline

References RB1, and RB6.

Referenced by core::kinematics::tree::JumpAtom::dof(), core::kinematics::tree::JumpAtom::get_dof_axis_and_end_pos(), and core::kinematics::tree::JumpAtom::set_dof().

DOF_Type core::id::get_rb_type ( Size const k )

inline

References RB1.

Referenced by core::conformation::Conformation::dof_id_from_torsion_id(), and core::kinematics::tree::JumpAtom::setup_min_map().

static Size const core::id::n_DOF_Type ( 9 )

static

Referenced by core::id::DOF_ID_Map< utility::pointer::owning_ptr >::clear(), core::id::DOF_ID_Map< utility::pointer::owning_ptr >::default_value(), core::id::DOF_ID_Map< utility::pointer::owning_ptr >::resize(), and core::id::DOF_ID_Map< utility::pointer::owning_ptr >::shrink().

static Size const core::id::omega_torsion ( 3 )

static

Referenced by core::pose::carbohydrates::get_reference_atoms(), core::pose::Pose::omega(), and core::pose::Pose::set_omega().

std::ostream& core::id::operator<<	(	std::ostream &	os,
		TorsionID_Range const &	a
	)

stream << TorsionID_Range

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

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

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

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

std::ostream& core::id::operator<<	(	std::ostream &	os,
		AtomID const &	a
	)

stream << AtomID

References core::id::AtomID::atomno(), and core::id::AtomID::rsd().

std::ostream& core::id::operator<<	(	std::ostream &	os,
		StubID const &	stub
	)

stream << AtomID

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

References core::id::NamedStubID::atom1, core::id::NamedStubID::atom2, core::id::NamedStubID::atom3, and core::id::NamedStubID::center_.

std::ostream& core::id::operator<<	(	std::ostream &	out,
		SequenceMapping const &	map
	)

inline

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

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
	)

input operator >> NamedAtomID

input operator

References core::id::NamedStubID::atom1, core::id::NamedStubID::atom2, core::id::NamedStubID::atom3, core::id::NamedStubID::center_, and tag.

static Size const core::id::phi_torsion ( 1 )

static

Referenced by core::pose::carbohydrates::get_reference_atoms(), core::pose::Pose::phi(), core::pose::Pose::set_phi(), and core::kinematics::tree::BondedAtom::setup_min_map().

static Size const core::id::psi_torsion ( 2 )

static

Referenced by core::pose::carbohydrates::get_reference_atoms(), core::pose::Pose::psi(), and core::pose::Pose::set_psi().

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::chemical::IdealBondLengthSet::contains_bond_length(), core::chemical::gasteiger::PossibleAtomTypesForAtom::FinalizeUnhybridized(), 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(), and core::scoring::electron_density::ElectronDensity::readMRCandResize().

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

Globals.

Referenced by core::scoring::constraints::NonResidueTypeConstraint::atom(), core::scoring::constraints::ResidueTypeConstraint::atom(), core::scoring::constraints::ResidueTypeLinkingConstraint::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(), core::pose::convert_from_std_map(), core::conformation::get_residue_connections(), and core::pose::named_atom_id_to_atom_id().

DOF_ID const core::id::BOGUS_DOF_ID

Globals.

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(), 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.

Referenced by core::conformation::Conformation::append_residue_by_bond(), and core::conformation::Conformation::append_residue_by_jump().

StubID const core::id::BOGUS_STUB_ID

Globals.

TorsionID const core::id::BOGUS_TORSION_ID

Globals.

Referenced by core::optimization::symmetry::SymMinimizerMap::add_new_dof_node(), 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().

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

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

Classes

Typedefs

Enumerations

Functions

Variables

Typedef Documentation

Enumeration Type Documentation

Function Documentation

Variable Documentation