core::conformation::symmetry Namespace Reference

Classes
class	SymDof
class	SymmData
class	SymmDataFactory
class	SymmDataLoader
class	SymmDataLoaderCreator
class	SymmDataOptions
class	SymmDataOptionsCreator
class	SymmetricConformation
	A symmetric conformation: has an additional data member "SymmetryInfo" class. More...
class	SymmetryInfo
class	SymSlideInfo
class	VirtualCoordinate
class	VirtualCoordinates

Typedefs
typedef utility::pointer::owning_ptr < SymDof >	SymDofOP
typedef utility::pointer::owning_ptr < SymDof const >	SymDofCOP
typedef numeric::xyzTransform < Real >	Xform
typedef numeric::xyzVector< Real >	Vec
typedef numeric::xyzMatrix< Real >	Mat
typedef vector1< pair< Size, Real > >	WtedClones
typedef utility::pointer::owning_ptr < SymmData >	SymmDataOP
typedef utility::pointer::owning_ptr < SymmData const >	SymmDataCOP
typedef utility::pointer::owning_ptr < SymmDataLoader >	SymmDataLoaderOP
typedef utility::pointer::owning_ptr < SymmDataLoader const >	SymmDataLoaderCOP
typedef utility::pointer::owning_ptr < SymmDataOptions >	SymmDataOptionsOP
typedef utility::pointer::owning_ptr < SymmDataOptions const >	SymmDataOptionsCOP
typedef utility::pointer::owning_ptr < SymmetricConformation >	SymmetricConformationOP
typedef utility::pointer::owning_ptr < SymmetricConformation const >	SymmetricConformationCOP
typedef utility::pointer::owning_ptr < SymmetryInfo >	SymmetryInfoOP
typedef utility::pointer::owning_ptr < SymmetryInfo const >	SymmetryInfoCOP
typedef utility::pointer::owning_ptr < SymSlideInfo >	SymSlideInfoOP
typedef utility::pointer::owning_ptr < SymSlideInfo const >	SymSlideInfoCOP
typedef utility::pointer::owning_ptr < VirtualCoordinate >	VirtualCoordinateOP
typedef utility::pointer::owning_ptr < VirtualCoordinate const >	VirtualCoordinateCOP

Enumerations
enum	dof_type {   X_DOF = 1, Y_DOF, Z_DOF, X_ANGLE_DOF,   Y_ANGLE_DOF, Z_ANGLE_DOF }
enum	SlideType { SEQUENTIAL = 1, ORDERED_SEQUENTIAL, RANDOM }
enum	SlideCriteriaType { CEN_DOCK_SCORE = 1, FA_REP_SCORE, CONTACTS, TOTAL_NUM_CRITERIA }

Functions
std::ostream &	operator<< (std::ostream &s, const SymDof &dof)
bool	operator== (SymDof const &a, SymDof const &b)
bool	operator!= (SymDof const &a, SymDof const &b)
bool	operator== (SymmData const &a, SymmData const &b)
template<class S , class T >
void	comma_strings_to_vector_map (std::istream &is, Size const nbase, std::map< S, utility::vector1< T > > &clones, std::string tag="")
template<class S , class T , class U >
void	comma_strings_to_pair_map (std::istream &is, Size const nbase, std::map< S, std::pair< T, U > > &clones, std::string tag="")
template<class S , class T >
void	comma_strings_to_map (std::istream &is, Size const nbase, std::map< S, T > &clones, std::string tag="")
template<class S >
void	comma_strings_to_vector (std::istream &is, Size const nbase, utility::vector1< S > &clones, std::string tag="")
void	comma_strings_to_map (std::istream &is, Size const nbase, std::map< Size, SymDof > &clones, std::string tag="")
template<class S , class T >
void	vector_map_to_comma_strings (std::ostream &out, std::map< S, utility::vector1< T > > clones, std::string tag="")
template<class S , class T >
void	map_to_comma_strings (std::ostream &out, std::map< S, T > clones, std::string tag="")
template<class S , class T , class U >
void	pair_map_to_comma_strings (std::ostream &out, std::map< S, std::pair< T, U > > clones, std::string tag="")
template<class S >
void	vector_to_comma_strings (std::ostream &out, utility::vector1< S > clones, std::string tag="")
id::TorsionType	guess_torsion_type_of_dof_id (id::DOF_ID const &id, Conformation const &conf)
std::istream &	operator>> (std::istream &s, SymmetryInfo &symminfo)
std::ostream &	operator<< (std::ostream &s, const SymmetryInfo &symminfo)
bool	operator== (SymSlideInfo const &a, SymSlideInfo const &b)
bool	operator!= (SymSlideInfo const &a, SymSlideInfo const &b)
static std::string const	chr_chains ("ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789!@#$&.<>?]{}|-_\\~=%zyxwvutsrqponmlkjihgfedcbaABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789!@#$&.<>?]{}|-_\\~=%zyxwvutsrqponmlkjihgfedcbaABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789!@#$&.<>?]{}|-_\\~=%zyxwvutsrqponmlkjihgfedcbaABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789!@#$&.<>?]{}|-_\\~=%zyxwvutsrqponmlkjihgfedcbaABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789!@#$&.<>?]{}|-_\\~=%zyxwvutsrqponmlkjihgfedcbaABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789!@#$&.<>?]{}|-_\\~=%zyxwvutsrqponmlkjihgfedcbaABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789!@#$&.<>?]{}|-_\\~=%zyxwvutsrqponmlkjihgfedcbaABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789!@#$&.<>?]{}|-_\\~=%zyxwvutsrqponmlkjihgfedcba")
Size	fold_tree_entry_point (core::kinematics::FoldTree const &ft, Size lb_resi=0, Size ub_resi=0)
Size	process_residue_request (conformation::Conformation const &src_conf, std::string input, Size lb_resi=0, Size ub_resi=0)
bool	is_jump_intracomponent (std::map< char, std::pair< Size, Size > > chain2range, Size up, Size dn)
char	which_component (std::map< char, std::pair< Size, Size > > chain2range, Size resi)
core::kinematics::FoldTree	get_component_contiguous_foldtree (core::kinematics::FoldTree const &f_orig, std::map< char, std::pair< Size, Size > > const &)
std::map< char, std::pair < Size, Size > >	get_chain2range (Conformation const &src_conf, std::map< int, char > src_conf2pdb_chain)
bool	is_symmetric (conformation::Conformation const &conf)
bool	is_symmetric (conformation::symmetry::SymmetryInfo const &symminfo)
conformation::symmetry::SymmetricConformationOP	setup_symmetric_conformation (conformation::Conformation &src_conformation, conformation::symmetry::SymmData &symmdata, std::map< int, char > src_conf2pdb_chain)
kinematics::FoldTree	set_fold_tree_from_symm_data (conformation::Conformation &src_conformation, conformation::symmetry::SymmData &symmdata, std::map< int, char > src_conf2pdb_chain)
kinematics::FoldTree	replaced_symmetric_foldtree_with_new_monomer (kinematics::FoldTree symm_f, conformation::symmetry::SymmetryInfo symmetry_info, kinematics::FoldTree monomer_f)
void	recenter (conformation::Conformation &src_conformation, conformation::symmetry::SymmData &symmdata)
void	shift_jump_numbers_in_dofs (conformation::Conformation &conformation, Size shift)
kinematics::FoldTree	get_asymm_unit_fold_tree (core::conformation::Conformation const &conf)
void	symmetrize_fold_tree (core::conformation::Conformation const &conf, kinematics::FoldTree &f)
void	set_asymm_unit_fold_tree (core::conformation::Conformation &conf, kinematics::FoldTree const &f)
int	residue_center_of_mass (conformation::Conformation const &conformation, int const start, int const stop)
int	return_nearest_residue (conformation::Conformation const &conformation, int const begin, int const end, Vector center)
std::string	show_foldtree (core::conformation::symmetry::SymmetricConformation const &symm_conf, SymmData const &symmdata, std::map< char, std::pair< Size, Size > > const &chain2range)
bool	operator== (VirtualCoordinate const &a, VirtualCoordinate const &b)
bool	operator!= (VirtualCoordinate const &a, VirtualCoordinate const &b)

Variables
static basic::Tracer	TR ("core.conformation.symmetry.SymmData")
static std::string const	NOPARENT = "NOPARENT"
static basic::Tracer	TR ("core.conformation.symmetry.symmdatafactory")
static basic::Tracer	TR ("core.conformation.symmetry.Conformation")
static basic::Tracer	TR ("core.conformation.symmetry.util")
static numeric::random::RandomGenerator	RG (408529)

Typedef Documentation

typedef numeric::xyzMatrix<Real> core::conformation::symmetry::Mat

typedef utility::pointer::owning_ptr< SymDof const > core::conformation::symmetry::SymDofCOP

typedef utility::pointer::owning_ptr< SymDof > core::conformation::symmetry::SymDofOP

typedef utility::pointer::owning_ptr< SymmData const > core::conformation::symmetry::SymmDataCOP

typedef utility::pointer::owning_ptr< SymmDataLoader const > core::conformation::symmetry::SymmDataLoaderCOP

typedef utility::pointer::owning_ptr< SymmDataLoader > core::conformation::symmetry::SymmDataLoaderOP

typedef utility::pointer::owning_ptr< SymmData > core::conformation::symmetry::SymmDataOP

typedef utility::pointer::owning_ptr< SymmDataOptions const > core::conformation::symmetry::SymmDataOptionsCOP

typedef utility::pointer::owning_ptr< SymmDataOptions > core::conformation::symmetry::SymmDataOptionsOP

typedef utility::pointer::owning_ptr< SymmetricConformation const > core::conformation::symmetry::SymmetricConformationCOP

typedef utility::pointer::owning_ptr< SymmetricConformation > core::conformation::symmetry::SymmetricConformationOP

typedef utility::pointer::owning_ptr< SymmetryInfo const > core::conformation::symmetry::SymmetryInfoCOP

typedef utility::pointer::owning_ptr< SymmetryInfo > core::conformation::symmetry::SymmetryInfoOP

typedef utility::pointer::owning_ptr< SymSlideInfo const > core::conformation::symmetry::SymSlideInfoCOP

typedef utility::pointer::owning_ptr< SymSlideInfo > core::conformation::symmetry::SymSlideInfoOP

typedef numeric::xyzVector<Real> core::conformation::symmetry::Vec

typedef utility::pointer::owning_ptr< VirtualCoordinate const > core::conformation::symmetry::VirtualCoordinateCOP

typedef utility::pointer::owning_ptr< VirtualCoordinate > core::conformation::symmetry::VirtualCoordinateOP

typedef vector1< pair<Size,Real> > core::conformation::symmetry::WtedClones

typedef numeric::xyzTransform<Real> core::conformation::symmetry::Xform

Enumeration Type Documentation

enum core::conformation::symmetry::dof_type

Enumerator
X_DOF
Y_DOF
Z_DOF
X_ANGLE_DOF
Y_ANGLE_DOF
Z_ANGLE_DOF

enum core::conformation::symmetry::SlideCriteriaType

Enumerator
CEN_DOCK_SCORE
FA_REP_SCORE
CONTACTS
TOTAL_NUM_CRITERIA

enum core::conformation::symmetry::SlideType

Enumerator
SEQUENTIAL
ORDERED_SEQUENTIAL
RANDOM

Function Documentation

static std::string const core::conformation::symmetry::chr_chains ( )

static

Referenced by get_chain2range().

template<class S , class T >

void core::conformation::symmetry::comma_strings_to_map	(	std::istream &	is,
		Size const	nbase,
		std::map< S, T > &	clones,
		std::string	tag = ""
	)

helper function for symminfo serialization

References l, tag, and TR.

Referenced by operator>>().

void core::conformation::symmetry::comma_strings_to_map	(	std::istream &	is,
		Size const	nbase,
		std::map< Size, SymDof > &	clones,
		std::string	tag = ""
	)

References l, tag, and TR.

template<class S , class T , class U >

void core::conformation::symmetry::comma_strings_to_pair_map	(	std::istream &	is,
		Size const	nbase,
		std::map< S, std::pair< T, U > > &	clones,
		std::string	tag = ""
	)

helper function for symminfo serialization

References l, tag, and TR.

Referenced by operator>>().

template<class S >

void core::conformation::symmetry::comma_strings_to_vector	(	std::istream &	is,
		Size const	nbase,
		utility::vector1< S > &	clones,
		std::string	tag = ""
	)

helper function for symminfo serialization

References j, l, tag, and TR.

Referenced by operator>>().

template<class S , class T >

void core::conformation::symmetry::comma_strings_to_vector_map	(	std::istream &	is,
		Size const	nbase,
		std::map< S, utility::vector1< T > > &	clones,
		std::string	tag = ""
	)

helper function for symminfo serialization

References j, l, core::io::serialization::size(), tag, and TR.

Referenced by operator>>().

Size core::conformation::symmetry::fold_tree_entry_point	(	core::kinematics::FoldTree const &	ft,
		Size	lb_resi = 0,
		Size	ub_resi = 0
	)

References core::kinematics::FoldTree::downstream_jump_residue(), core::kinematics::FoldTree::nres(), core::kinematics::FoldTree::num_jump(), resi, core::kinematics::FoldTree::root(), core::kinematics::FoldTree::upstream_jump_residue(), and utility_exit_with_message.

Referenced by get_component_contiguous_foldtree(), and process_residue_request().

kinematics::FoldTree core::conformation::symmetry::get_asymm_unit_fold_tree

(

core::conformation::Conformation const &

conf

)

References core::kinematics::FoldTree::add_edge(), core::kinematics::FoldTree::begin(), core::kinematics::FoldTree::end(), core::conformation::Conformation::fold_tree(), is_symmetric(), core::kinematics::FoldTree::renumber_jumps(), core::kinematics::Edge::start(), and core::conformation::symmetry::SymmetricConformation::Symmetry_Info().

Referenced by core::conformation::symmetry::SymmetricConformation::append_residue_by_jump(), core::pose::symmetry::extract_asymmetric_unit(), core::conformation::symmetry::SymmetricConformation::fold_tree(), and core::conformation::symmetry::SymmetricConformation::insert_conformation_by_jump().

std::map<char,std::pair<Size,Size> > core::conformation::symmetry::get_chain2range	(	Conformation const &	src_conf,
		std::map< int, char >	src_conf2pdb_chain
	)

get a mapping of chain chars to resi ranges

References chain, core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), chr_chains(), j, core::conformation::Conformation::num_chains(), and utility_exit_with_message.

Referenced by set_fold_tree_from_symm_data(), and setup_symmetric_conformation().

core::kinematics::FoldTree core::conformation::symmetry::get_component_contiguous_foldtree	(	core::kinematics::FoldTree const &	f_orig,
		std::map< char, std::pair< Size, Size > > const &
	)

References core::kinematics::FoldTree::cutpoint(), core::kinematics::FoldTree::downstream_atom(), fold_tree_entry_point(), jumps, core::kinematics::FoldTree::nres(), core::kinematics::FoldTree::num_cutpoint(), core::kinematics::FoldTree::num_jump(), core::kinematics::FoldTree::reorder(), core::kinematics::FoldTree::set_jump_atoms(), core::kinematics::FoldTree::tree_from_jumps_and_cuts(), and utility_exit_with_message.

Referenced by setup_symmetric_conformation().

id::TorsionType core::conformation::symmetry::guess_torsion_type_of_dof_id	(	id::DOF_ID const &	id,
		Conformation const &	conf
	)

This is a helper function for some of the DOF_ID routines below. Really just a best guess... this is a little tricky: the mapping from a DOF_ID to a TorsionID is not straightforward to construct (see kinematics/util.cc:setup_dof_to_torsion_map) So we don't really know whether a dof_id is a bb degree of freedom or a chi degree of freedom... or even which residue it should be attached to, eg the phi of residue i might be dof_id with rsd i-1 So we take a guess based on whether id.atomno is a backbone or sidechain atom

References core::conformation::Conformation::atom_is_backbone_norefold(), core::id::BB, core::id::CHI, core::id::JUMP, core::id::RB1, core::id::RB6, and type.

Referenced by core::conformation::symmetry::SymmetryInfo::dependent_dofs(), core::conformation::symmetry::SymmetryInfo::dof_is_independent(), and core::conformation::symmetry::SymmetryInfo::get_dof_derivative_weight().

bool core::conformation::symmetry::is_jump_intracomponent	(	std::map< char, std::pair< Size, Size > >	chain2range,
		Size	up,
		Size	dn
	)

Referenced by set_fold_tree_from_symm_data().

bool core::conformation::symmetry::is_symmetric

(

conformation::Conformation const &

conf

)

Attempt to detect whether a conformation is symmetric

Referenced by core::optimization::symmetry::SymMinimizerMap::add_torsion(), core::pack::task::operation::RestrictToInterface::apply(), core::optimization::symmetry::atom_tree_dfunc(), core::optimization::symmetry::atom_tree_get_atompairE_deriv(), core::optimization::cartesian_collect_atompairE_deriv(), core::optimization::cartesian_dfunc(), core::scoring::methods::MetalloPlacementEnergy::finalize_total_energy(), get_asymm_unit_fold_tree(), core::pose::symmetry::is_symmetric(), core::optimization::symmetry::SymAtomTreeMinimizer::make_assymetric_movemap(), core::optimization::symmetry::SymAtomTreeMinimizer::make_semisymmetric_movemap(), core::optimization::symmetry::SymAtomTreeMinimizer::run(), core::pose::symmetry::scorefxn_is_symmetric(), set_asymm_unit_fold_tree(), shift_jump_numbers_in_dofs(), and symmetrize_fold_tree().

bool core::conformation::symmetry::is_symmetric

(

conformation::symmetry::SymmetryInfo const &

symminfo

)

References core::conformation::symmetry::SymmetryInfo::get_use_symmetry().

template<class S , class T >

void core::conformation::symmetry::map_to_comma_strings	(	std::ostream &	out,
		std::map< S, T >	clones,
		std::string	tag = ""
	)

helper function for symminfo serialization

References tag.

Referenced by operator<<().

bool core::conformation::symmetry::operator!=	(	SymSlideInfo const &	a,
		SymSlideInfo const &	b
	)

bool core::conformation::symmetry::operator!=	(	VirtualCoordinate const &	a,
		VirtualCoordinate const &	b
	)

bool core::conformation::symmetry::operator!=	(	SymDof const &	a,
		SymDof const &	b
	)

std::ostream& core::conformation::symmetry::operator<<	(	std::ostream &	s,
		const SymDof &	dof
	)

References core::conformation::symmetry::SymDof::allow_dof(), core::conformation::symmetry::SymDof::jump_direction(), core::conformation::symmetry::SymDof::range1_lower(), core::conformation::symmetry::SymDof::range1_upper(), core::conformation::symmetry::SymDof::range2_lower(), and core::conformation::symmetry::SymDof::range2_upper().

std::ostream& core::conformation::symmetry::operator<<	(	std::ostream &	s,
		const SymmetryInfo &	symminfo
	)

References core::conformation::symmetry::SymmetryInfo::bb_clones_, core::conformation::symmetry::SymmetryInfo::bb_follows_, core::conformation::symmetry::SymmetryInfo::chi_clones_, core::conformation::symmetry::SymmetryInfo::chi_follows_, core::conformation::symmetry::SymmetryInfo::component_bounds_, core::conformation::symmetry::SymmetryInfo::components_, core::conformation::symmetry::SymmetryInfo::dofname2jnum_, core::conformation::symmetry::SymmetryInfo::dofs_, core::conformation::symmetry::SymmetryInfo::jname2components_, core::conformation::symmetry::SymmetryInfo::jname2subunits_, core::conformation::symmetry::SymmetryInfo::jnum2dofname_, core::conformation::symmetry::SymmetryInfo::jump_clone_wts_, core::conformation::symmetry::SymmetryInfo::jump_clones_, core::conformation::symmetry::SymmetryInfo::jump_follows_, map_to_comma_strings(), core::conformation::symmetry::SymmetryInfo::name2component_, core::conformation::symmetry::SymmetryInfo::njump_monomer_, core::conformation::symmetry::SymmetryInfo::npseudo_, core::conformation::symmetry::SymmetryInfo::nres_monomer_, core::conformation::symmetry::SymmetryInfo::num_components_, core::conformation::symmetry::SymmetryInfo::num_interfaces(), pair_map_to_comma_strings(), core::conformation::symmetry::SymmetryInfo::score_multiply_, core::conformation::symmetry::SymmetryInfo::scoring_subunit_, core::conformation::symmetry::SymmetryInfo::subunits(), core::conformation::symmetry::SymmetryInfo::type_, vector_map_to_comma_strings(), and vector_to_comma_strings().

bool core::conformation::symmetry::operator==	(	SymSlideInfo const &	a,
		SymSlideInfo const &	b
	)

References core::conformation::symmetry::SymSlideInfo::score_criteria_, core::conformation::symmetry::SymSlideInfo::slide_order_, core::conformation::symmetry::SymSlideInfo::slide_type_, and core::conformation::symmetry::SymSlideInfo::SlideCriteriaVal_.

bool core::conformation::symmetry::operator==	(	VirtualCoordinate const &	a,
		VirtualCoordinate const &	b
	)

References core::conformation::symmetry::VirtualCoordinate::axis_origin_, core::conformation::symmetry::VirtualCoordinate::axis_x_, and core::conformation::symmetry::VirtualCoordinate::axis_y_.

bool core::conformation::symmetry::operator==	(	SymDof const &	a,
		SymDof const &	b
	)

References core::conformation::symmetry::SymDof::allowed_dof_jumps_, core::conformation::symmetry::SymDof::has_range1_lower_, core::conformation::symmetry::SymDof::has_range1_upper_, core::conformation::symmetry::SymDof::has_range2_lower_, core::conformation::symmetry::SymDof::has_range2_upper_, core::conformation::symmetry::SymDof::jump_dir_, core::conformation::symmetry::SymDof::lower_range_dof_jumps1_, core::conformation::symmetry::SymDof::lower_range_dof_jumps2_, core::conformation::symmetry::SymDof::upper_range_dof_jumps1_, and core::conformation::symmetry::SymDof::upper_range_dof_jumps2_.

bool core::conformation::symmetry::operator==	(	SymmData const &	a,
		SymmData const &	b
	)

References core::conformation::symmetry::SymmData::allow_virtual_, core::conformation::symmetry::SymmData::anchor_residue_, core::conformation::symmetry::SymmData::components_, core::conformation::symmetry::SymmData::dofs_, core::conformation::symmetry::SymmData::include_subunit_, core::conformation::symmetry::SymmData::interfaces_, core::conformation::symmetry::SymmData::jname2components_, core::conformation::symmetry::SymmData::jname2subunits_, core::conformation::symmetry::SymmData::jump_clones_, core::conformation::symmetry::SymmData::jump_string_to_jump_num_, core::conformation::symmetry::SymmData::jump_string_to_virtual_pair_, core::conformation::symmetry::SymmData::name2component_, core::conformation::symmetry::SymmData::num_components_, core::conformation::symmetry::SymmData::output_subunit_, core::conformation::symmetry::SymmData::recenter_, core::conformation::symmetry::SymmData::root_, core::conformation::symmetry::SymmData::rotation_matrices_, core::conformation::symmetry::SymmData::score_multiply_subunit_, core::conformation::symmetry::SymmData::score_subunit_, core::conformation::symmetry::SymmData::slide_info_, core::conformation::symmetry::SymmData::slide_order_string_, core::conformation::symmetry::SymmData::subunit_num_to_virt_id_, core::conformation::symmetry::SymmData::subunits_, core::conformation::symmetry::SymmData::symm_transforms_, core::conformation::symmetry::SymmData::symmetry_name_, core::conformation::symmetry::SymmData::symmetry_type_, core::conformation::symmetry::SymmData::translation_matrices_, core::conformation::symmetry::SymmData::virt_id_to_subunit_chain_, core::conformation::symmetry::SymmData::virt_id_to_subunit_num_, core::conformation::symmetry::SymmData::virt_id_to_subunit_residue_, core::conformation::symmetry::SymmData::virt_id_to_virt_num_, core::conformation::symmetry::SymmData::virt_num_to_virt_id_, and core::conformation::symmetry::SymmData::virtual_coordinates_.

std::istream& core::conformation::symmetry::operator>>	(	std::istream &	s,
		SymmetryInfo &	symminfo
	)

References core::conformation::symmetry::SymmetryInfo::bb_clones_, core::conformation::symmetry::SymmetryInfo::bb_follows_, core::conformation::symmetry::SymmetryInfo::bb_is_independent(), core::conformation::symmetry::SymmetryInfo::chi_clones_, core::conformation::symmetry::SymmetryInfo::chi_follows_, comma_strings_to_map(), comma_strings_to_pair_map(), comma_strings_to_vector(), comma_strings_to_vector_map(), core::conformation::symmetry::SymmetryInfo::component_bounds_, core::conformation::symmetry::SymmetryInfo::components_, core::conformation::symmetry::SymmetryInfo::dofname2jnum_, core::conformation::symmetry::SymmetryInfo::dofs_, core::conformation::symmetry::SymmetryInfo::interfaces_, core::conformation::symmetry::SymmetryInfo::jname2components_, core::conformation::symmetry::SymmetryInfo::jname2subunits_, core::conformation::symmetry::SymmetryInfo::jnum2dofname_, core::conformation::symmetry::SymmetryInfo::jump_clone_wts_, core::conformation::symmetry::SymmetryInfo::jump_clones_, core::conformation::symmetry::SymmetryInfo::jump_follows_, core::conformation::symmetry::SymmetryInfo::last_indep_residue_, core::conformation::symmetry::SymmetryInfo::name2component_, core::conformation::symmetry::SymmetryInfo::njump_monomer_, core::conformation::symmetry::SymmetryInfo::npseudo_, core::conformation::symmetry::SymmetryInfo::nres_monomer_, core::conformation::symmetry::SymmetryInfo::num_components_, core::conformation::symmetry::SymmetryInfo::num_total_residues_without_pseudo(), core::conformation::symmetry::SymmetryInfo::score_multiply_, core::conformation::symmetry::SymmetryInfo::scoring_subunit_, core::conformation::symmetry::SymmetryInfo::set_use_symmetry(), tag, TR, and core::conformation::symmetry::SymmetryInfo::type_.

template<class S , class T , class U >

void core::conformation::symmetry::pair_map_to_comma_strings	(	std::ostream &	out,
		std::map< S, std::pair< T, U > >	clones,
		std::string	tag = ""
	)

helper function for symminfo serialization

References tag.

Referenced by operator<<().

Size core::conformation::symmetry::process_residue_request	(	conformation::Conformation const &	src_conf,
		std::string	input,
		Size	lb_resi = 0,
		Size	ub_resi = 0
	)

get residue index

References core::conformation::Conformation::fold_tree(), fold_tree_entry_point(), resi, residue_center_of_mass(), core::conformation::Conformation::size(), utility::string2int(), and utility_exit_with_message.

Referenced by recenter(), and set_fold_tree_from_symm_data().

void core::conformation::symmetry::recenter	(	conformation::Conformation &	src_conformation,
		conformation::symmetry::SymmData &	symmdata
	)

References anchor, core::conformation::symmetry::SymmData::get_anchor_residue(), j, core::chemical::ResidueType::natoms(), process_residue_request(), core::conformation::Conformation::residue(), core::conformation::Conformation::residue_type(), core::conformation::Conformation::set_xyz(), core::conformation::Conformation::size(), and core::conformation::Conformation::xyz().

Referenced by setup_symmetric_conformation().

kinematics::FoldTree core::conformation::symmetry::replaced_symmetric_foldtree_with_new_monomer	(	kinematics::FoldTree	symm_f,
		conformation::symmetry::SymmetryInfo	symmetry_info,
		kinematics::FoldTree	monomer_f
	)

References begin, core::sequence::end, core::conformation::symmetry::SymmetryInfo::num_independent_residues(), and core::conformation::symmetry::SymmetryInfo::subunits().

int core::conformation::symmetry::residue_center_of_mass	(	conformation::Conformation const &	conformation,
		int const	start,
		int const	stop
	)

References core::conformation::Residue::atom(), center(), core::conformation::Residue::is_protein(), core::conformation::Residue::nbr_atom_xyz(), core::conformation::Conformation::residue(), return_nearest_residue(), and core::conformation::Atom::xyz().

Referenced by core::membrane::MembraneProteinFactory::build_pose(), and process_residue_request().

int core::conformation::symmetry::return_nearest_residue	(	conformation::Conformation const &	conformation,
		int const	begin,
		int const	end,
		Vector	center
	)

References core::conformation::Residue::atom(), core::sequence::end, core::conformation::Residue::is_protein(), numeric::xyzVector< class >::length_squared(), core::conformation::Residue::nbr_atom_xyz(), core::conformation::Conformation::residue(), and core::conformation::Atom::xyz().

Referenced by residue_center_of_mass().

void core::conformation::symmetry::set_asymm_unit_fold_tree	(	core::conformation::Conformation &	conf,
		kinematics::FoldTree const &	f
	)

References core::conformation::Conformation::fold_tree(), is_symmetric(), and symmetrize_fold_tree().

Referenced by core::pose::symmetry::set_asymm_unit_fold_tree().

kinematics::FoldTree core::conformation::symmetry::set_fold_tree_from_symm_data	(	conformation::Conformation &	src_conformation,
		conformation::symmetry::SymmData &	symmdata,
		std::map< int, char >	src_conf2pdb_chain
	)

References anchor, core::conformation::Residue::atom_name(), chain, core::kinematics::FoldTree::clear(), core::sequence::end, core::conformation::Conformation::fold_tree(), core::conformation::symmetry::SymmData::get_anchor_residue(), get_chain2range(), core::conformation::symmetry::SymmData::get_num_components(), core::conformation::symmetry::SymmData::get_subunits(), core::conformation::symmetry::SymmData::get_virt_id_to_subunit_chain(), core::conformation::symmetry::SymmData::get_virt_id_to_subunit_num(), core::conformation::symmetry::SymmData::get_virt_id_to_subunit_residue(), core::conformation::symmetry::SymmData::get_virtual_connects(), core::conformation::symmetry::SymmData::get_virtual_coordinates(), core::conformation::symmetry::SymmData::get_virtual_id_to_num(), core::conformation::symmetry::SymmData::get_virtual_num_to_id(), is_jump_intracomponent(), j, jumps, njumps, core::scoring::pair, process_residue_request(), resi, core::conformation::Conformation::residue(), core::conformation::Conformation::size(), TR, and utility_exit_with_message.

Referenced by setup_symmetric_conformation().

conformation::symmetry::SymmetricConformationOP core::conformation::symmetry::setup_symmetric_conformation	(	conformation::Conformation &	src_conformation,
		conformation::symmetry::SymmData &	symmdata,
		std::map< int, char >	src_conf2pdb_chain
	)

Generate a symmetric conformation from a monomeric pose and symmetry information stored in the SymmData object

References core::conformation::Conformation::append_residue_by_jump(), chain, core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::conformation::symmetry::SymmData::components_moved_by_jump(), core::conformation::ResidueFactory::create_residue(), core::conformation::Conformation::fold_tree(), get_chain2range(), core::conformation::symmetry::SymmetryInfo::get_component_bounds(), get_component_contiguous_foldtree(), core::conformation::symmetry::SymmetryInfo::get_components(), core::conformation::symmetry::SymmData::get_components(), core::conformation::symmetry::SymmetryInfo::get_dofs(), core::conformation::symmetry::SymmetryInfo::get_jump_name(), core::conformation::symmetry::SymmData::get_jump_name_to_components(), core::conformation::symmetry::SymmData::get_jump_name_to_subunits(), core::conformation::symmetry::SymmData::get_num_components(), core::conformation::symmetry::SymmData::get_recenter(), core::conformation::symmetry::SymmData::get_root(), core::conformation::symmetry::SymmetryInfo::get_subunit_name_to_component(), core::conformation::symmetry::SymmData::get_subunit_name_to_component(), core::conformation::symmetry::SymmData::get_subunits(), core::conformation::symmetry::SymmData::get_virtual_connects(), core::conformation::symmetry::SymmData::get_virtual_coordinates(), core::conformation::symmetry::SymmData::get_virtual_num_to_id(), core::conformation::Conformation::insert_conformation_by_jump(), j, core::conformation::Conformation::jump(), core::conformation::symmetry::SymmetryInfo::jump_is_independent(), core::conformation::Conformation::num_chains(), core::kinematics::FoldTree::num_jump(), recenter(), core::conformation::Conformation::residue(), core::conformation::Residue::residue_type_set(), set_fold_tree_from_symm_data(), shift_jump_numbers_in_dofs(), show_foldtree(), core::conformation::Conformation::size(), core::conformation::symmetry::SymmData::subunits_moved_by_jump(), tag, TR, utility_exit_with_message, and core::kinematics::visualize_fold_tree().

Referenced by core::pose::symmetry::make_symmetric_pose().

void core::conformation::symmetry::shift_jump_numbers_in_dofs	(	conformation::Conformation &	conformation,
		Size	shift
	)

References is_symmetric(), runtime_assert, and core::conformation::symmetry::SymmetricConformation::Symmetry_Info().

Referenced by setup_symmetric_conformation().

std::string core::conformation::symmetry::show_foldtree	(	core::conformation::symmetry::SymmetricConformation const &	symm_conf,
		SymmData const &	symmdata,
		std::map< char, std::pair< Size, Size > > const &	chain2range
	)

References core::conformation::symmetry::SymmetricConformation::fold_tree(), core::conformation::symmetry::SymmData::get_virtual_num_to_id(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), and core::kinematics::visualize_fold_tree().

Referenced by setup_symmetric_conformation().

void core::conformation::symmetry::symmetrize_fold_tree	(	core::conformation::Conformation const &	conf,
		kinematics::FoldTree &	f
	)

References core::kinematics::FoldTree::clear(), core::kinematics::FoldTree::cutpoints(), core::kinematics::FoldTree::downstream_jump_residue(), core::conformation::Conformation::fold_tree(), is_symmetric(), j, jumps, core::kinematics::FoldTree::num_jump(), core::kinematics::FoldTree::root(), core::conformation::Conformation::size(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), TR, core::kinematics::FoldTree::tree_from_jumps_and_cuts(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by core::conformation::symmetry::SymmetricConformation::append_residue_by_jump(), core::conformation::symmetry::SymmetricConformation::insert_conformation_by_jump(), set_asymm_unit_fold_tree(), and core::pose::symmetry::symmetrize_fold_tree().

template<class S , class T >

void core::conformation::symmetry::vector_map_to_comma_strings	(	std::ostream &	out,
		std::map< S, utility::vector1< T > >	clones,
		std::string	tag = ""
	)

helper function for symminfo serialization

References l, and tag.

Referenced by operator<<().

template<class S >

void core::conformation::symmetry::vector_to_comma_strings	(	std::ostream &	out,
		utility::vector1< S >	clones,
		std::string	tag = ""
	)

helper function for symminfo serialization

References tag.

Referenced by operator<<().

char core::conformation::symmetry::which_component	(	std::map< char, std::pair< Size, Size > >	chain2range,
		Size	resi
	)

References utility_exit_with_message.

Variable Documentation

std::string const core::conformation::symmetry::NOPARENT = "NOPARENT"

static

Referenced by core::conformation::symmetry::SymmData::get_least_common_ancertor_jump(), core::conformation::symmetry::SymmData::get_least_common_ancertor_virtual(), core::conformation::symmetry::SymmData::get_parent_jump(), core::conformation::symmetry::SymmData::get_parent_virtual(), and core::conformation::symmetry::SymmData::is_ancestor_virtual().

numeric::random::RandomGenerator core::conformation::symmetry::RG(408529)

static

basic::Tracer core::conformation::symmetry::TR("core.conformation.symmetry.symmdatafactory")

static

basic::Tracer core::conformation::symmetry::TR("core.conformation.symmetry.Conformation")

static

basic::Tracer core::conformation::symmetry::TR("core.conformation.symmetry.util")

static

basic::Tracer core::conformation::symmetry::TR("core.conformation.symmetry.SymmData")

static

Referenced by core::conformation::symmetry::SymmetricConformation::append_residue_by_jump(), core::conformation::symmetry::SymmetricConformation::batch_set_xyz(), comma_strings_to_map(), comma_strings_to_pair_map(), comma_strings_to_vector(), comma_strings_to_vector_map(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::conformation::symmetry::SymmetricConformation::insert_conformation_by_jump(), operator>>(), core::conformation::symmetry::SymmData::read_symmetry_data_from_stream(), core::conformation::symmetry::SymmetricConformation::replace_residue(), core::conformation::symmetry::SymmetricConformation::set_bond_angle(), core::conformation::symmetry::SymmetricConformation::set_bond_length(), core::conformation::symmetry::SymmetricConformation::set_dof(), set_fold_tree_from_symm_data(), core::conformation::symmetry::SymmetricConformation::set_jump(), core::conformation::symmetry::SymmetricConformation::set_secstruct(), core::conformation::symmetry::SymmetricConformation::set_torsion(), core::conformation::symmetry::SymmetricConformation::set_torsion_angle(), core::conformation::symmetry::SymmetricConformation::set_xyz(), setup_symmetric_conformation(), core::conformation::symmetry::SymmData::show(), symmetrize_fold_tree(), and core::conformation::symmetry::SymmetryInfo::SymmetryInfo().