core::conformation::symmetry Namespace Reference

Classes
class	MirrorSymmetricConformation
	Mirror symmetric conformation contains the same symminfo logic, but also includes special logic for mirror symmetries. More...
class	SymDof
class	SymmData
class	SymmDataLoader
class	SymmDataLoaderCreator
class	SymmetricConformation
	A symmetric conformation: has an additional data member "SymmetryInfo" class. More...
class	SymmetryInfo
class	SymmetryTransform
class	SymSlideInfo
class	VirtualCoordinate

Typedefs
typedef utility::pointer::shared_ptr < MirrorSymmetricConformation >	MirrorSymmetricConformationOP
typedef utility::pointer::shared_ptr < MirrorSymmetricConformation const >	MirrorSymmetricConformationCOP
typedef utility::pointer::shared_ptr < SymDof >	SymDofOP
typedef utility::pointer::shared_ptr < SymDof const >	SymDofCOP
using	Xform = numeric::xyzTransform< Real >
using	Vec = numeric::xyzVector< Real >
using	Mat = numeric::xyzMatrix< Real >
typedef vector1< pair< Size, Real > >	WtedClones
typedef utility::pointer::shared_ptr < SymmData >	SymmDataOP
typedef utility::pointer::shared_ptr < SymmData const >	SymmDataCOP
typedef utility::pointer::shared_ptr < SymmDataLoader >	SymmDataLoaderOP
typedef utility::pointer::shared_ptr < SymmDataLoader const >	SymmDataLoaderCOP
typedef utility::pointer::shared_ptr < SymmDataOptions >	SymmDataOptionsOP
typedef utility::pointer::shared_ptr < SymmDataOptions const >	SymmDataOptionsCOP
typedef utility::pointer::shared_ptr < SymmetricConformation >	SymmetricConformationOP
typedef utility::pointer::shared_ptr < SymmetricConformation const >	SymmetricConformationCOP
typedef utility::pointer::shared_ptr < SymmetryInfo >	SymmetryInfoOP
typedef utility::pointer::shared_ptr < SymmetryInfo const >	SymmetryInfoCOP
typedef utility::pointer::shared_ptr < SymmetryTransform >	SymmetryTransformOP
typedef utility::pointer::shared_ptr < SymmetryTransform const >	SymmetryTransformCOP
typedef utility::pointer::shared_ptr < SymSlideInfo >	SymSlideInfoOP
typedef utility::pointer::shared_ptr < SymSlideInfo const >	SymSlideInfoCOP
typedef utility::pointer::shared_ptr < VirtualCoordinate >	VirtualCoordinateOP
typedef utility::pointer::shared_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
static basic::Tracer	TR ("core.conformation.symmetry.Conformation")
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)
static basic::Tracer	TR ("core.conformation.symmetry.SymmData")
bool	operator== (SymmData const &a, SymmData const &b)
static basic::Tracer	TR ("core.conformation.symmetry.Conformation")
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 const &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 const &tag="")
template<class S , class T >
void	comma_strings_to_map (std::istream &is, Size const nbase, std::map< S, T > &clones, std::string const &tag="")
template<class S >
void	comma_strings_to_vector (std::istream &is, Size const nbase, utility::vector1< S > &clones, std::string const &tag="")
void	comma_strings_to_map (std::istream &is, Size const nbase, std::map< Size, SymDof > &clones, std::string const &tag="")
template<class S , class T >
void	vector_map_to_comma_strings (std::ostream &out, std::map< S, utility::vector1< T > > clones, std::string const &tag="")
template<class S , class T >
void	map_to_comma_strings (std::ostream &out, std::map< S, T > clones, std::string const &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 const &tag="")
template<class S >
void	vector_to_comma_strings (std::ostream &out, utility::vector1< S > clones, std::string const &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")
std::string	get_chain_id_string ()
static basic::Tracer	TR ("core.conformation.symmetry.util")
void	calculate_inverting_virtuals (core::kinematics::FoldTree const &ft, Conformation const &conf, SymmetryInfo const &symm_info, utility::vector1< bool > &mirrored_subs, utility::vector1< std::pair< bool, bool > > &mirrored_jumps)
	A very specific helper function that counts the number of mirror ops from root->each subunit More...
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< core::Size, char > src_conf2pdb_chain)
bool	is_symmetric (conformation::Conformation const &conf)
bool	is_mirror_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< core::Size, char > src_conf2pdb_chain)
kinematics::FoldTree	set_fold_tree_from_symm_data (conformation::Conformation &src_conformation, conformation::symmetry::SymmData &symmdata, std::map< core::Size, 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)
	Converts an asymmetric foldtree (f) with virtual root into a symmetric foldtree compatible with symmetric conformation (conf) More...
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 std::string const	NOPARENT = "NOPARENT"

Typedef Documentation

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

typedef utility::pointer::shared_ptr< MirrorSymmetricConformation const > core::conformation::symmetry::MirrorSymmetricConformationCOP

typedef utility::pointer::shared_ptr< MirrorSymmetricConformation > core::conformation::symmetry::MirrorSymmetricConformationOP

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

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

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

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

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

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

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

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

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

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

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

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

typedef utility::pointer::shared_ptr< SymmetryTransform const > core::conformation::symmetry::SymmetryTransformCOP

typedef utility::pointer::shared_ptr< SymmetryTransform > core::conformation::symmetry::SymmetryTransformOP

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

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

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

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

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

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

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

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

void core::conformation::symmetry::calculate_inverting_virtuals	(	core::kinematics::FoldTree const &	ft,
		Conformation const &	conf,
		SymmetryInfo const &	symm_info,
		utility::vector1< bool > &	mirrored_subs,
		utility::vector1< std::pair< bool, bool > > &	inverted_jumps
	)

A very specific helper function that counts the number of mirror ops from root->each subunit

A very specific helper function that counts the number of mirror ops from root->each subunit returns: a bool vector 'mirrored_subs' that defines which subunits are mirrored w.r.t. master a bool pair vector 'mirrored_jumps' that defines which jumps are mirrored w.r.t. master (upstream/downstream)

References core::chemical::ResidueType::is_inverted_virtual_residue(), core::conformation::symmetry::SymmetryInfo::num_total_residues_without_pseudo(), core::conformation::Conformation::residue_type(), and core::conformation::symmetry::SymmetryInfo::subunit_index().

Referenced by core::conformation::symmetry::MirrorSymmetricConformation::update_njumps_nres().

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

static

Referenced by get_chain2range(), and get_chain_id_string().

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 const &	tag = ""
	)

helper function for symminfo serialization

References protocols::forge::methods::replace(), core::chemical::element::S, 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 const &	tag = ""
	)

References protocols::forge::methods::replace(), 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 const &	tag = ""
	)

helper function for symminfo serialization

References protocols::forge::methods::replace(), core::chemical::element::S, TR(), and core::chemical::element::U.

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 const &	tag = ""
	)

helper function for symminfo serialization

References protocols::forge::methods::replace(), core::chemical::element::S, 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 const &	tag = ""
	)

helper function for symminfo serialization

References protocols::forge::methods::replace(), core::chemical::element::S, 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(), core::kinematics::FoldTree::root(), and core::kinematics::FoldTree::upstream_jump_residue().

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::conformation::Conformation::fold_tree(), is_symmetric(), core::kinematics::FoldTree::renumber_jumps_ordered(), core::kinematics::Edge::start(), and core::conformation::symmetry::SymmetricConformation::Symmetry_Info().

Referenced by core::conformation::symmetry::SymmetricConformation::append_polymer_residue_after_seqpos(), core::conformation::symmetry::SymmetricConformation::append_residue_by_jump(), protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::cryst::MakeLayerMover::apply(), protocols::cryst::MakeLatticeMover::apply(), protocols::loop_grower::LoopGrower::apply(), core::pose::symmetry::extract_asymmetric_unit(), core::conformation::symmetry::SymmetricConformation::fold_tree(), protocols::loops::fold_tree_from_loops(), protocols::hybridization::HybridizeFoldtreeDynamic::initialize(), core::conformation::symmetry::MirrorSymmetricConformation::insert_conformation_by_jump(), core::conformation::symmetry::SymmetricConformation::insert_conformation_by_jump(), core::conformation::symmetry::SymmetricConformation::prepend_polymer_residue_before_seqpos(), protocols::rbsegment_relax::setup_disconnected(), protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops(), and protocols::hybridization::HybridizeFoldtreeDynamic::update().

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

get a mapping of chain chars to resi ranges

References core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), chr_chains(), protocols::mean_field::max(), protocols::mean_field::min(), and core::conformation::Conformation::num_chains().

Referenced by set_fold_tree_from_symm_data(), and setup_symmetric_conformation().

std::string core::conformation::symmetry::get_chain_id_string

(

)

References chr_chains().

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(), core::kinematics::FoldTree::nres(), core::kinematics::FoldTree::num_cutpoint(), core::kinematics::FoldTree::num_jump(), core::kinematics::FoldTree::reorder(), core::kinematics::FoldTree::set_jump_atoms(), and core::kinematics::FoldTree::tree_from_jumps_and_cuts().

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, and core::id::RB6.

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_mirror_symmetric

(

conformation::Conformation const &

conf

)

Attempt to detect whether a conformation is mirror symmetric

Referenced by protocols::cryst::MakeLatticeMover::apply(), and core::pose::symmetry::is_mirror_symmetric().

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(), protocols::forge::remodel::RemodelGlobalFrame::align_segment(), protocols::topology_broker::FibrilModelingClaimer::allow_claim(), protocols::matdes::MotifHitsRotamersOperation::alter_rotamer_set(), protocols::task_operations::SelectByDeltaScoreOperation::apply(), protocols::task_operations::CrystalContactsOperation::apply(), protocols::cyclic_peptide::CrosslinkerMover::apply(), protocols::symmetric_docking::membrane::MPSymDockMover::apply(), protocols::fldsgn::CircularPermutation::apply(), protocols::topology_broker::TopologyBroker::apply(), protocols::forge::remodel::RemodelLoopMover::apply(), core::optimization::symmetry::atom_tree_dfunc(), core::optimization::symmetry::atom_tree_get_atompairE_deriv(), protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::calculate(), core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::calculate(), core::simple_metrics::metrics::RMSDMetric::calculate(), protocols::scoring::Interface::calculate(), core::optimization::cartesian_collect_atompairE_deriv(), core::optimization::cartesian_dfunc(), protocols::score_filters::GeometryFilter::compute(), protocols::simple_filters::BuriedUnsatHbondFilter::compute(), protocols::matdes::SymUnsatHbondFilter::compute(), protocols::sasa_scores::compute_avge_scores(), protocols::forge::remodel::RemodelMover::design_refine_cart_relax(), protocols::forge::remodel::RemodelMover::design_refine_seq_relax(), core::energy_methods::FastDensEnergy::eval_residue_pair_derivatives(), protocols::pose_creation::MergePDBMover::generate_overlaps(), get_asymm_unit_fold_tree(), protocols::fldsgn::potentials::SetSecStructEnergies::get_secstruct(), core::scoring::nmr::pre::PRESingleSet::init_from_filedata(), core::scoring::nmr::pcs::PCSSingleSet::init_from_pcs_filedata(), core::scoring::nmr::pre::PREMultiSet::init_from_pre_singleset_vec(), core::scoring::nmr::rdc::RDCSingleSet::init_from_rdc_filedata(), core::scoring::nmr::rdc::RDCMultiSet::init_from_rdc_filedata(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::initialize_graph_for_packing(), core::pose::symmetry::is_symmetric(), core::optimization::symmetry::SymAtomTreeMinimizer::make_asymmetric_movemap(), core::optimization::symmetry::SymAtomTreeMinimizer::make_semisymmetric_movemap(), protocols::features::DatabaseJobInputter::pose_from_job(), protocols::denovo_design::DisulfidizeMover::process_pose(), core::optimization::symmetry::SymAtomTreeMinimizer::run(), core::optimization::CartesianMinimizer::run(), core::pose::symmetry::scorefxn_is_symmetric(), set_asymm_unit_fold_tree(), core::scoring::nmr::pcs::PCSSingleSet::set_atom_derivatives(), core::scoring::nmr::rdc::RDCMultiSet::set_atom_derivatives(), core::scoring::nmr::pre::PREMultiSet::set_atom_derivatives(), protocols::relax::RepeatProteinRelax::setup_repeat_pose(), protocols::relax::RepeatProteinRelax::setup_repeat_pose_jumping(), shift_jump_numbers_in_dofs(), protocols::forge::remodel::RemodelLoopMover::simultaneous_stage(), core::scoring::superimpose_pose(), protocols::topology_broker::TopologyBroker::switch_to_fullatom(), symmetrize_fold_tree(), core::scoring::nmr::pcs::PCSSingleSet::update_spin_coordinates(), core::scoring::nmr::rdc::RDCMultiSet::update_spin_coordinates(), and core::scoring::nmr::pre::PREMultiSet::update_spin_coordinates().

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 const &	tag = ""
	)

helper function for symminfo serialization

Referenced by operator<<().

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

References protocols::match::upstream::b.

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

References protocols::match::upstream::b.

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

References protocols::match::upstream::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_, core::conformation::symmetry::VirtualCoordinate::axis_y_, and core::conformation::symmetry::VirtualCoordinate::mirror_Z_.

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(), TR(), core::conformation::symmetry::SymmetryInfo::type_, and core::conformation::symmetry::SymmetryInfo::update_score_multiply_factor().

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 const &	tag = ""
	)

helper function for symminfo serialization

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(), residue_center_of_mass(), and core::conformation::Conformation::size().

Referenced by recenter(), and set_fold_tree_from_symm_data().

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

References core::conformation::symmetry::SymmData::get_anchor_residue(), 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(), trans(), 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 core::sequence::end, core::conformation::symmetry::SymmetryInfo::num_independent_residues(), and core::conformation::symmetry::SymmetryInfo::subunits().

Referenced by protocols::jumping::close_chainbreaks().

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

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

Referenced by protocols::protein_interface_design::movers::SetAtomTree::apply(), protocols::relax::RangeRelaxMover::finalize_setup(), protocols::floppy_tail::FloppyTailMover::init_on_new_input(), process_residue_request(), and protocols::relax::membrane::MPFastRelaxMover::setup_relax_foldtree().

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::conformation::membrane::center, core::sequence::end, core::conformation::Residue::is_protein(), 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< core::Size, char >	src_conf2pdb_chain
	)

References core::conformation::Residue::atom_name(), 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(), core::chemical::element::I, is_jump_intracomponent(), core::kinematics::Edge::keep_stub_in_residue(), protocols::mean_field::max(), protocols::mean_field::min(), core::scoring::pair, process_residue_request(), core::conformation::Conformation::residue(), core::conformation::Conformation::size(), protocols::loops::start, core::kinematics::Edge::start_atom(), protocols::loops::stop, core::kinematics::Edge::stop_atom(), and TR().

Referenced by setup_symmetric_conformation().

conformation::symmetry::SymmetricConformationOP core::conformation::symmetry::setup_symmetric_conformation	(	conformation::Conformation &	src_conformation,
		conformation::symmetry::SymmData &	symmdata,
		std::map< core::Size, 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(), core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::conformation::Conformation::clone(), core::conformation::symmetry::SymmData::components_moved_by_jump(), protocols::splice::coords(), 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::SymmData::get_components(), core::conformation::symmetry::SymmetryInfo::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::SymmData::get_subunit_name_to_component(), core::conformation::symmetry::SymmetryInfo::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(), core::conformation::inv_virtual_type_for_conf(), 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_type_set_for_conf(), 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(), TR(), core::conformation::virtual_type_for_conf(), 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(), 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
	)

Converts an asymmetric foldtree (f) with virtual root into a symmetric foldtree compatible with symmetric conformation (conf)

Parameters

conf	- A symmetric conformation
f	- An asymmetric foldtree. This foldtree MUST have a virtual root

This function does not require the symm data

References core::kinematics::FoldTree::clear(), core::kinematics::FoldTree::cutpoints(), core::kinematics::FoldTree::downstream_jump_residue(), core::conformation::Conformation::fold_tree(), is_symmetric(), protocols::mean_field::max(), protocols::mean_field::min(), 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_polymer_residue_after_seqpos(), core::conformation::symmetry::SymmetricConformation::append_residue_by_jump(), protocols::cryst::MakeLayerMover::apply(), protocols::cryst::MakeLatticeMover::apply(), protocols::loop_grower::LoopGrower::apply(), core::conformation::symmetry::MirrorSymmetricConformation::insert_conformation_by_jump(), core::conformation::symmetry::SymmetricConformation::insert_conformation_by_jump(), core::conformation::symmetry::SymmetricConformation::prepend_polymer_residue_before_seqpos(), set_asymm_unit_fold_tree(), and core::pose::symmetry::symmetrize_fold_tree().

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

static

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

static

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

static

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

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::declare_chemical_bond(), 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(), core::conformation::symmetry::SymmetryInfo::SymmetryInfo(), and core::conformation::symmetry::SymmetricConformation::update_noncanonical_connection().

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 const &	tag = ""
	)

helper function for symminfo serialization

Referenced by operator<<().

template<class S >

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

helper function for symminfo serialization

Referenced by operator<<().

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

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().