#include <EnvClaimBroker.hh>

Inheritance diagram for protocols::environment::EnvClaimBroker:

Classes
class	BrokeredJumpData
	an inner class for tracking the properties of jumps that've been brokered. More...

struct	BrokerResult

Public Member Functions
	EnvClaimBroker (EnvironmentCAP env, MoverPassMap const &movers_and_passes, core::pose::Pose const &in_pose, SequenceAnnotationOP ann)

	~EnvClaimBroker () override

BrokerResult const &	result () const

Private Types
typedef std::map < ClientMoverOP, 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 utility::vector1 < std::pair < claims::ResidueElement, ClientMoverOP > >	ResElemVect

typedef utility::vector1 < std::pair < claims::JumpElement, ClientMoverOP > >	JumpElemVect

typedef utility::vector1 < std::pair < claims::CutElement, ClientMoverOP > >	CutElemVect

typedef utility::vector1 < std::pair < claims::CutBiasElement, ClientMoverOP > >	CutBiasElemVect

typedef utility::vector1 < std::pair < claims::DOFElement, ClientMoverOP > >	DOFElemVect

typedef std::map< core::Size, std::string >	SizeToStringMap

typedef std::map< std::string, std::pair< core::Size, core::Size > >	StringToSizePairMap

typedef std::map< std::string, std::pair< std::string, std::string > >	StringToStringPairMap

typedef utility::vector1 < core::Real >	BiasVector

typedef utility::pointer::shared_ptr < BrokeredJumpData >	BrokeredJumpDataOP

typedef utility::pointer::shared_ptr < BrokeredJumpData const >	BrokeredJumpDataCOP

typedef std::map< std::string, BrokeredJumpDataCOP >	JumpDataMap

Private Member Functions
void	broker_fold_tree (Conformation &, basic::datacache::BasicDataCache &)

void	broker_dofs (core::pose::Pose &)

core::kinematics::FoldTreeOP	render_fold_tree (FoldTreeSketch &fts, utility::vector1< core::Real > const &bias, basic::datacache::BasicDataCache &, core::conformation::Conformation const &input_conf)

void	annotate_fold_tree (core::kinematics::FoldTreeOP, JumpDataMap const &new_jumps, SequenceAnnotationOP=nullptr)

void	add_virtual_residues (Conformation &, SizeToStringMap const &new_vrts, SequenceAnnotationOP)

void	process_elements (ResElemVect const &elems, FoldTreeSketch &fts, SizeToStringMap &new_vrts)

void	process_elements (JumpElemVect const &elems, FoldTreeSketch &fts, JumpDataMap &new_jumps)

void	process_elements (CutElemVect const &elems, FoldTreeSketch &fts)

void	process_elements (CutBiasElemVect const &elems, BiasVector &bias)

void	grant_access (claims::DOFElement const &e, ClientMoverOP owner) const

void	setup_passports (DOFElemVect &elements, claims::ControlStrength const &(*str_access)(std::pair< claims::DOFElement, ClientMoverOP > const &))

template<typename T , typename I >
utility::vector1< std::pair< T, ClientMoverOP > >	collect_elements (I const &info) const

claims::EnvClaims	collect_claims (MoverPassMap const &movers_and_passes, core::pose::Pose &pose)

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_

EnvironmentCAP	env_

Member Typedef Documentation

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

private

typedef utility::pointer::shared_ptr< BrokeredJumpData const > protocols::environment::EnvClaimBroker::BrokeredJumpDataCOP

private

typedef utility::pointer::shared_ptr< BrokeredJumpData > protocols::environment::EnvClaimBroker::BrokeredJumpDataOP

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 utility::vector1< std::pair< claims::CutBiasElement, ClientMoverOP > > protocols::environment::EnvClaimBroker::CutBiasElemVect

private

typedef utility::vector1< std::pair< claims::CutElement, ClientMoverOP > > protocols::environment::EnvClaimBroker::CutElemVect

private

typedef utility::vector1< std::pair< claims::DOFElement, ClientMoverOP > > protocols::environment::EnvClaimBroker::DOFElemVect

private

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

private

typedef std::map< std::string, BrokeredJumpDataCOP > protocols::environment::EnvClaimBroker::JumpDataMap

private

typedef utility::vector1< std::pair< claims::JumpElement, ClientMoverOP > > protocols::environment::EnvClaimBroker::JumpElemVect

private

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

private

typedef utility::vector1< std::pair< claims::ResidueElement, ClientMoverOP > > protocols::environment::EnvClaimBroker::ResElemVect

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< core::Size, core::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	(	EnvironmentCAP	env,
		MoverPassMap const &	movers_and_passes,
		core::pose::Pose const &	in_pose,
		SequenceAnnotationOP	ann
	)

References protocols::environment::EnvClaimBroker::BrokerResult::ann, ann_, broker_dofs(), broker_fold_tree(), claims_, collect_claims(), core::pose::Pose::conformation(), core::pose::Pose::data(), core::pose::Pose::dump_pdb(), core::scoring::pair, core::pose::Pose::pdb_info(), protocols::environment::EnvClaimBroker::BrokerResult::pose, result(), result_, protocols::environment::safe_set_conf(), protocols::environment::tr(), protocols::environment::update_pdb_info(), and core::pose::datacache::CacheableDataType::WRITEABLE_DATA.

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

overridedefault

Member Function Documentation

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

private

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

Referenced by broker_fold_tree().

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

private

References core::conformation::Conformation::append_residue_by_jump(), core::conformation::ResidueFactory::create_residue(), core::scoring::pair, core::conformation::Conformation::size(), and core::conformation::virtual_type_for_conf().

Referenced by broker_fold_tree().

void protocols::environment::EnvClaimBroker::annotate_fold_tree	(	core::kinematics::FoldTreeOP	ft,
		JumpDataMap const &	new_jumps,
		SequenceAnnotationOP	ann = `nullptr`
	)

private

References core::scoring::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 ( core::pose::Pose & pose )

private

References core::pose::Pose::conformation(), protocols::environment::ctrl_str_selector(), core::conformation::Conformation::detect_disulfides(), protocols::environment::init_str_selector(), core::conformation::Conformation::is_centroid(), core::scoring::pair, and protocols::environment::tr().

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, core::conformation::Conformation::fold_tree(), protocols::environment::EnvClaimBroker::BrokerResult::new_vrts, process_elements(), render_fold_tree(), result(), result_, core::conformation::Conformation::size(), protocols::environment::tr(), and core::kinematics::visualize_fold_tree().

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
	)

private

References core::pose::Pose::data(), core::scoring::env, and protocols::environment::tr().

Referenced by EnvClaimBroker().

template<typename T , typename I >

utility::vector1< std::pair< T, ClientMoverOP > > protocols::environment::EnvClaimBroker::collect_elements ( I const & info ) const

private

References protocols::environment::tr().

void protocols::environment::EnvClaimBroker::grant_access	(	claims::DOFElement const &	e,
		ClientMoverOP	owner
	)		const

private

References protocols::environment::claims::DOFElement::id.

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

private

References protocols::environment::claims::ResidueElement::allow_duplicates, core::environment::FoldTreeSketch::append_residue(), protocols::environment::claims::ResidueElement::label, core::environment::FoldTreeSketch::nres(), and protocols::environment::tr().

Referenced by broker_fold_tree().

void protocols::environment::EnvClaimBroker::process_elements	(	JumpElemVect const &	elems,
		FoldTreeSketch &	fts,
		JumpDataMap &	new_jumps
	)

private

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

void protocols::environment::EnvClaimBroker::process_elements	(	CutElemVect const &	elems,
		FoldTreeSketch &	fts
	)

private

References core::scoring::env, core::environment::FoldTreeSketch::insert_cut(), protocols::environment::claims::CutElement::p, and core::scoring::pair.

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

private

References protocols::environment::claims::CutBiasElement::bias, protocols::environment::claims::CutBiasElement::p, and core::scoring::pair.

core::kinematics::FoldTreeOP protocols::environment::EnvClaimBroker::render_fold_tree	(	FoldTreeSketch &	fts,
		utility::vector1< core::Real > const &	bias,
		basic::datacache::BasicDataCache &	datacache,
		core::conformation::Conformation const &	input_conf
	)

private

References core::kinematics::FoldTree::cutpoints(), core::environment::FoldTreeSketch::cycle(), core::scoring::env, protocols::environment::find_implied_cut(), core::conformation::Conformation::fold_tree(), core::environment::FoldTreeSketch::has_jump(), protocols::environment::inherit_cuts(), core::environment::FoldTreeSketch::insert_cut(), protocols::environment::introduce_datamap_cuts(), core::environment::FoldTreeSketch::num_cuts(), core::environment::FoldTreeSketch::num_jumps(), core::environment::FoldTreeSketch::render(), and protocols::environment::tr().

Referenced by broker_fold_tree().

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

References result_.

Referenced by broker_fold_tree(), and EnvClaimBroker().

void protocols::environment::EnvClaimBroker::setup_passports	(	DOFElemVect &	elements,
		claims::ControlStrength const &(*)(std::pair< claims::DOFElement, ClientMoverOP > const &)	str_access
	)