protocols::environment::EnvClaimBroker Class Reference

#include <EnvClaimBroker.hh>

Classes
struct	BrokerResult

Public Member Functions
	EnvClaimBroker (Environment const &env, MoverPassMap const &movers_and_passes, core::pose::Pose const &in_pose)
virtual	~EnvClaimBroker ()
BrokerResult const &	result () const

Private Types
typedef std::map < ClaimingMoverOP, core::environment::DofPassportOP >	MoverPassMap
typedef core::environment::SequenceAnnotationCOP	SequenceAnnotationCOP
typedef core::environment::SequenceAnnotationOP	SequenceAnnotationOP
typedef core::environment::FoldTreeSketch	FoldTreeSketch
typedef core::conformation::Conformation	Conformation
typedef core::conformation::ConformationOP	ConformationOP
typedef core::conformation::ConformationCOP	ConformationCOP
typedef std::map< core::Size, std::string >	SizeToStringMap
typedef std::map< std::string, std::pair< Size, Size > >	StringToSizePairMap
typedef std::map< std::string, std::pair< std::string, std::string > >	StringToStringPairMap
typedef utility::vector1 < core::Real >	BiasVector

Private Member Functions
void	broker_fold_tree (Conformation &, basic::datacache::BasicDataCache &)
void	broker_dofs (ProtectedConformationOP)
core::kinematics::FoldTreeOP	render_fold_tree (FoldTreeSketch &fts, std::set< Size > &unphysical_cuts, utility::vector1< core::Real > const &bias, basic::datacache::BasicDataCache &, core::Size const &hash)
void	annotate_fold_tree (core::kinematics::FoldTreeOP, StringToSizePairMap const &jump_labels, StringToStringPairMap const &jump_atoms, SequenceAnnotationOP=NULL)
void	add_virtual_residues (Conformation &, SizeToStringMap const &new_vrts, SequenceAnnotationOP)
void	process_elements (claims::ResidueElements const &elems, FoldTreeSketch &fts, SizeToStringMap &new_vrts)
void	process_elements (claims::JumpElements const &elems, FoldTreeSketch &fts, FoldTreeSketch &physical_fts, StringToSizePairMap &new_jumps, StringToStringPairMap &jump_atoms)
void	process_elements (claims::CutElements const &elems, FoldTreeSketch &fts, FoldTreeSketch &physical_fts, std::set< core::Size > &unphysical_cuts)
void	process_elements (claims::CutBiasElements const &elems, BiasVector &bias)
core::Size	resolve (claims::RTElement const &e) const
core::Size	resolve (claims::TorsionElement const &e) const
void	grant_access (claims::TorsionElement const &e, ProtectedConformationOP conf) const
void	grant_access (claims::RTElement const &e, ProtectedConformationOP conf) const
template<typename T >
void	setup_control_passports (utility::vector1< T > &elements, ProtectedConformationOP conf, core::Size n_dofs)
template<typename T >
void	setup_initialization_passports (utility::vector1< T > &elems, ProtectedConformationOP conf, core::Size n_dofs, std::set< ClaimingMoverOP > &initializers)
	iterate through all dof elements, determine who gets initialization right, and modify their DofPassport appropriately More...
template<typename T >
void	collect_elements (utility::vector1< T > &elements, FoldTreeSketch const &fts) const
claims::EnvClaims	collect_claims (MoverPassMap const &movers_and_passes, core::pose::Pose &pose) const
void	build_new_residues (claims::EnvClaims const &claims, FoldTreeSketch &fts, SequenceAnnotationOP ann)
	broker new residues More...
void	assign_passports (claims::EnvClaims const &, ProtectedConformation const &)
	use accepted claims to build DofPassport objects for movers. More...
void	add_chainbreak_variants (core::Size cut, core::conformation::Conformation &conf) const

Private Attributes
MoverPassMap const &	movers_and_passes_
SequenceAnnotationOP	ann_
claims::EnvClaims	claims_
BrokerResult	result_

Member Typedef Documentation

typedef utility::vector1< core::Real > protocols::environment::EnvClaimBroker::BiasVector

private

typedef core::conformation::Conformation protocols::environment::EnvClaimBroker::Conformation

private

typedef core::conformation::ConformationCOP protocols::environment::EnvClaimBroker::ConformationCOP

private

typedef core::conformation::ConformationOP protocols::environment::EnvClaimBroker::ConformationOP

private

typedef core::environment::FoldTreeSketch protocols::environment::EnvClaimBroker::FoldTreeSketch

private

typedef std::map< ClaimingMoverOP, core::environment::DofPassportOP > protocols::environment::EnvClaimBroker::MoverPassMap

private

typedef core::environment::SequenceAnnotationCOP protocols::environment::EnvClaimBroker::SequenceAnnotationCOP

private

typedef core::environment::SequenceAnnotationOP protocols::environment::EnvClaimBroker::SequenceAnnotationOP

private

typedef std::map< core::Size, std::string > protocols::environment::EnvClaimBroker::SizeToStringMap

private

typedef std::map< std::string, std::pair< Size, Size > > protocols::environment::EnvClaimBroker::StringToSizePairMap

private

typedef std::map< std::string, std::pair< std::string, std::string > > protocols::environment::EnvClaimBroker::StringToStringPairMap

private

Constructor & Destructor Documentation

protocols::environment::EnvClaimBroker::EnvClaimBroker	(	Environment const &	env,
		MoverPassMap const &	movers_and_passes,
		core::pose::Pose const &	in_pose
	)

References ann_, broker_dofs(), broker_fold_tree(), claims_, collect_claims(), core::pose::Pose::conformation(), core::pose::Pose::data(), utility::pointer::owning_ptr< T >::get(), basic::datacache::BasicDataCache::get_raw_ptr(), basic::datacache::BasicDataCache::has(), pair, protocols::environment::EnvClaimBroker::BrokerResult::pose, result(), result_, basic::datacache::BasicDataCache::set(), core::pose::Pose::set_new_conformation(), and core::pose::datacache::CacheableDataType::WRITEABLE_DATA.

protocols::environment::EnvClaimBroker::~EnvClaimBroker ( )

virtual

Member Function Documentation

void protocols::environment::EnvClaimBroker::add_chainbreak_variants ( core::Size  cut, core::conformation::Conformation &  conf  ) const

private

References copy_residue_coordinates_and_rebuild_missing_atoms(), CUTPOINT_LOWER, CUTPOINT_UPPER, core::conformation::Conformation::fold_tree(), core::kinematics::FoldTree::is_cutpoint(), core::conformation::Conformation::replace_residue(), and core::conformation::Conformation::residue().

Referenced by broker_fold_tree().

void protocols::environment::EnvClaimBroker::add_virtual_residues ( Conformation &  conf, SizeToStringMap const &  new_vrts, SequenceAnnotationOP  ann  )

private

References core::conformation::Conformation::append_residue_by_jump(), core::conformation::ResidueFactory::create_residue(), pair, core::conformation::Conformation::residue(), core::conformation::Residue::residue_type_set(), and core::conformation::Conformation::size().

Referenced by broker_fold_tree().

void protocols::environment::EnvClaimBroker::annotate_fold_tree ( core::kinematics::FoldTreeOP  ft, StringToSizePairMap const &  jump_labels, StringToStringPairMap const &  jump_atoms, SequenceAnnotationOP  ann = NULL  )

private

References pair.

Referenced by broker_fold_tree().

void protocols::environment::EnvClaimBroker::assign_passports ( claims::EnvClaims const &  , ProtectedConformation const &    )

private

use accepted claims to build DofPassport objects for movers.

void protocols::environment::EnvClaimBroker::broker_dofs ( ProtectedConformationOP  conf )

private

References collect_elements(), movers_and_passes_, pair, core::pose::Pose::set_new_conformation(), setup_control_passports(), and setup_initialization_passports().

Referenced by EnvClaimBroker().

void protocols::environment::EnvClaimBroker::broker_fold_tree ( Conformation &  conf, basic::datacache::BasicDataCache &  datacache  )

private

References add_chainbreak_variants(), add_virtual_residues(), ann_, annotate_fold_tree(), protocols::environment::EnvClaimBroker::BrokerResult::closer_ft, collect_elements(), protocols::environment::construct_hash(), core::conformation::Conformation::fold_tree(), protocols::environment::EnvClaimBroker::BrokerResult::inserted_cut_variants, protocols::environment::EnvClaimBroker::BrokerResult::new_vrts, process_elements(), render_fold_tree(), result_, core::conformation::Conformation::size(), and tr.

Referenced by EnvClaimBroker().

void protocols::environment::EnvClaimBroker::build_new_residues ( claims::EnvClaims const &  claims, FoldTreeSketch &  fts, SequenceAnnotationOP  ann  )

private

broker new residues

EnvClaims protocols::environment::EnvClaimBroker::collect_claims ( MoverPassMap const &  movers_and_passes, core::pose::Pose &  pose  ) const

private

References tr.

Referenced by EnvClaimBroker().

template<typename T >

void protocols::environment::EnvClaimBroker::collect_elements ( utility::vector1< T > &  elements, FoldTreeSketch const &  fts  ) const

private

References claims_, and tr.

Referenced by broker_dofs(), and broker_fold_tree().

void protocols::environment::EnvClaimBroker::grant_access ( claims::TorsionElement const &  e, ProtectedConformationOP  conf  ) const

private

References BB, movers_and_passes_, protocols::stepwise::sampling::protein::omega(), protocols::environment::claims::TorsionElement::owner, protocols::stepwise::sampling::protein::phi(), protocols::stepwise::sampling::protein::psi(), and resolve().

Referenced by setup_control_passports(), and setup_initialization_passports().

void protocols::environment::EnvClaimBroker::grant_access ( claims::RTElement const &  e, ProtectedConformationOP  conf  ) const

private

References jump_nr, movers_and_passes_, protocols::environment::claims::RTElement::owner, and resolve().

void protocols::environment::EnvClaimBroker::process_elements ( claims::ResidueElements const &  elems, FoldTreeSketch &  fts, SizeToStringMap &  new_vrts  )

private

References ann_, core::environment::FoldTreeSketch::append_residue(), and core::environment::FoldTreeSketch::nres().

Referenced by broker_fold_tree().

void protocols::environment::EnvClaimBroker::process_elements ( claims::JumpElements const &  elems, FoldTreeSketch &  fts, FoldTreeSketch &  physical_fts, StringToSizePairMap &  new_jumps, StringToStringPairMap &  jump_atoms  )

private

References ann_, protocols::environment::claims::JumpElement::atom1, protocols::environment::claims::JumpElement::atom2, core::environment::FoldTreeSketch::has_jump(), protocols::environment::claims::JumpElement::has_physical_cut, core::environment::FoldTreeSketch::insert_jump(), protocols::environment::claims::JumpElement::label, protocols::environment::claims::JumpElement::p1, protocols::environment::claims::JumpElement::p2, and tr.

void protocols::environment::EnvClaimBroker::process_elements ( claims::CutElements const &  elems, FoldTreeSketch &  fts, FoldTreeSketch &  physical_fts, std::set< core::Size > &  unphysical_cuts  )

private

References ann_, core::environment::FoldTreeSketch::insert_cut(), protocols::environment::claims::CutElement::p, and protocols::environment::claims::CutElement::physical.

void protocols::environment::EnvClaimBroker::process_elements ( claims::CutBiasElements const &  elems, BiasVector &  bias  )

private

References ann_, and utility::to_string().

core::kinematics::FoldTreeOP protocols::environment::EnvClaimBroker::render_fold_tree ( FoldTreeSketch &  fts, std::set< Size > &  unphysical_cuts, utility::vector1< core::Real > const &  bias, basic::datacache::BasicDataCache &  datacache, core::Size const &  hash  )

private

References utility::pointer::owning_ptr< T >::get(), basic::datacache::BasicDataCache::get_raw_ptr(), basic::datacache::BasicDataCache::has(), core::environment::FoldTreeSketch::insert_cut(), core::environment::FoldTreeSketch::remove_cycles(), core::environment::FoldTreeSketch::render(), basic::datacache::BasicDataCache::set(), and tr.

Referenced by broker_fold_tree().

core::Size protocols::environment::EnvClaimBroker::resolve ( claims::RTElement const &  e ) const

private

References ann_, and protocols::environment::claims::RTElement::label.

Referenced by grant_access(), setup_control_passports(), and setup_initialization_passports().

core::Size protocols::environment::EnvClaimBroker::resolve ( claims::TorsionElement const &  e ) const

private

References ann_, and protocols::environment::claims::TorsionElement::p.

EnvClaimBroker::BrokerResult const & protocols::environment::EnvClaimBroker::result

(

)

const

References result_.

Referenced by EnvClaimBroker().

template<typename T >

void protocols::environment::EnvClaimBroker::setup_control_passports ( utility::vector1< T > &  elements, ProtectedConformationOP  conf, core::Size  n_dofs  )

private

References protocols::environment::claims::DOES_NOT_CONTROL, protocols::environment::claims::EXCLUSIVE, grant_access(), protocols::environment::claims::MUST_CONTROL, resolve(), utility::to_string(), and tr.

Referenced by broker_dofs().

template<typename T >

void protocols::environment::EnvClaimBroker::setup_initialization_passports ( utility::vector1< T > &  elems, ProtectedConformationOP  conf, core::Size  n_dofs, std::set< ClaimingMoverOP > &  initializers  )

private

iterate through all dof elements, determine who gets initialization right, and modify their DofPassport appropriately

References protocols::environment::claims::DOES_NOT_INITIALIZE, grant_access(), protocols::environment::claims::MUST_INITIALIZE, resolve(), utility::to_string(), and tr.

Referenced by broker_dofs().

Member Data Documentation

SequenceAnnotationOP protocols::environment::EnvClaimBroker::ann_

private

Referenced by broker_fold_tree(), EnvClaimBroker(), process_elements(), and resolve().

claims::EnvClaims protocols::environment::EnvClaimBroker::claims_

private

Referenced by collect_elements(), and EnvClaimBroker().

MoverPassMap const& protocols::environment::EnvClaimBroker::movers_and_passes_

private

Referenced by broker_dofs(), and grant_access().

BrokerResult protocols::environment::EnvClaimBroker::result_

private

Referenced by broker_fold_tree(), EnvClaimBroker(), and result().

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The documentation for this class was generated from the following files:

• symlinks/rosetta/src/protocols/environment/EnvClaimBroker.hh
• symlinks/rosetta/src/protocols/environment/EnvClaimBroker.cc