#include <Environment.hh>

Inheritance diagram for protocols::environment::Environment:

Public Member Functions
	Environment (std::string name)

	~Environment () override

void	register_mover (moves::MoverOP)

template<class Iterator >
void	register_movers (Iterator start, Iterator end)

bool	is_registered (ClientMoverOP) const

core::pose::Pose	start (core::pose::Pose const &)

core::pose::Pose	end (core::pose::Pose const &)

EnvironmentCAP	superenv () const

EnvClaimBrokerCOP	broker () const

SequenceAnnotationCOP	annotations () const

bool	auto_cut () const

bool	inherit_cuts () const

bool	allow_pure_movers () const

void	auto_cut (bool)

void	inherit_cuts (bool)

void	allow_pure_movers (bool)

void	pconf_destruction (Conformation *ptr) const

void	pconf_creation (Conformation *ptr) const

EnvironmentCOP	get_self_ptr () const
	self pointers More...

EnvironmentOP	get_self_ptr ()

EnvironmentCAP	get_self_weak_ptr () const

EnvironmentAP	get_self_weak_ptr ()

Public Member Functions inherited from core::environment::EnvCore
	EnvCore (std::string const &env_name)

	~EnvCore () override

std::string const &	name () const

EnvCoreCAP	superenv () const

core::Size const &	id () const

Private Types
typedef core::environment::EnvCore	Parent

typedef core::environment::SequenceAnnotationCOP	SequenceAnnotationCOP

typedef core::environment::SequenceAnnotationOP	SequenceAnnotationOP

typedef core::environment::SequenceAnnotation	SequenceAnnotation

typedef core::conformation::Conformation	Conformation

typedef core::conformation::ConformationAP	ConformationAP

typedef core::conformation::ConformationOP	ConformationOP

typedef core::conformation::ConformationCOP	ConformationCOP

Private Member Functions
core::conformation::ConformationOP	end (ProtectedConformationCOP)

core::pose::Pose	broker (core::pose::Pose const &)

void	remove_nonpermenant_features (core::pose::Pose &)
	ENV OPEN/CLOSING. More...

void	assign_passport (ClientMoverOP, core::environment::DofPassportCOP)

void	cancel_passports ()

void	remove_chainbreak_variants (core::pose::Pose &, core::Size up_res, core::Size down_res) const

Private Attributes
EnvClaimBrokerOP	broker_

core::pose::Pose	input_pose_

std::set< ClientMoverOP >	registered_movers_

SequenceAnnotationOP	ann_

bool	bAutoCut_

bool	bInheritCuts_

bool	bAllowPureMovers_

std::set< Conformation * >	pconfs_

Additional Inherited Members
Protected Member Functions inherited from core::environment::EnvCore
DofPassportOP	issue_passport (std::string const &mover_name) const

void	set_superenv (EnvCoreCAP)

Member Typedef Documentation

typedef core::conformation::Conformation protocols::environment::Environment::Conformation

private

typedef core::conformation::ConformationAP protocols::environment::Environment::ConformationAP

private

typedef core::conformation::ConformationCOP protocols::environment::Environment::ConformationCOP

private

typedef core::conformation::ConformationOP protocols::environment::Environment::ConformationOP

private

typedef core::environment::EnvCore protocols::environment::Environment::Parent

private

typedef core::environment::SequenceAnnotation protocols::environment::Environment::SequenceAnnotation

private

typedef core::environment::SequenceAnnotationCOP protocols::environment::Environment::SequenceAnnotationCOP

private

typedef core::environment::SequenceAnnotationOP protocols::environment::Environment::SequenceAnnotationOP

private

Constructor & Destructor Documentation

protocols::environment::Environment::Environment ( std::string name )

protocols::environment::Environment::~Environment ( )

override

References cancel_passports(), protocols::environment::ProtectedConformation::env_destruction(), and pconfs_.

Member Function Documentation

bool protocols::environment::Environment::allow_pure_movers ( ) const

inline

References bAllowPureMovers_.

Referenced by register_mover().

void protocols::environment::Environment::allow_pure_movers ( bool setting )

References bAllowPureMovers_, broker(), and core::environment::EnvCore::name().

SequenceAnnotationCOP protocols::environment::Environment::annotations ( ) const

inline

References ann_.

void protocols::environment::Environment::assign_passport	(	ClientMoverOP	mover,
		core::environment::DofPassportCOP	passport
	)

private

References get_self_weak_ptr().

Referenced by broker().

bool protocols::environment::Environment::auto_cut ( ) const

inline

References bAutoCut_.

void protocols::environment::Environment::auto_cut ( bool setting )

References bAutoCut_, broker(), and core::environment::EnvCore::name().

EnvClaimBrokerCOP protocols::environment::Environment::broker ( ) const

inline

References broker_.

Referenced by allow_pure_movers(), auto_cut(), inherit_cuts(), remove_nonpermenant_features(), and start().

core::pose::Pose protocols::environment::Environment::broker ( core::pose::Pose const & in_pose )

private

References ann_, assign_passport(), broker_, cancel_passports(), get_self_weak_ptr(), core::environment::EnvCore::issue_passport(), core::environment::EnvCore::name(), registered_movers_, and protocols::environment::tr().

void protocols::environment::Environment::cancel_passports ( )

private

References core::environment::EnvCore::id(), registered_movers_, and protocols::environment::tr().

Referenced by broker(), end(), and ~Environment().

core::pose::Pose protocols::environment::Environment::end ( core::pose::Pose const & pose )

References core::pose::Pose::annotated_sequence(), broker_, core::pose::Pose::conformation_ptr(), core::pose::Pose::data(), core::pose::Pose::fold_tree(), input_pose_, core::environment::EnvCore::name(), core::pose::Pose::pdb_info(), core::pose::Pose::set_new_conformation(), core::pose::Pose::size(), protocols::environment::tr(), and core::pose::datacache::CacheableDataType::WRITEABLE_DATA.

Referenced by register_movers().

core::conformation::ConformationOP protocols::environment::Environment::end ( ProtectedConformationCOP conf )

private

References cancel_passports(), core::pose::Pose::conformation(), core::pose::Pose::fold_tree(), input_pose_, core::environment::EnvCore::name(), remove_nonpermenant_features(), core::pose::Pose::set_new_conformation(), superenv(), and protocols::environment::tr().

EnvironmentCOP protocols::environment::Environment::get_self_ptr ( ) const

inline

self pointers

EnvironmentOP protocols::environment::Environment::get_self_ptr ( )

inline

EnvironmentCAP protocols::environment::Environment::get_self_weak_ptr ( ) const

inline

Referenced by assign_passport(), and broker().

EnvironmentAP protocols::environment::Environment::get_self_weak_ptr ( )

inline

bool protocols::environment::Environment::inherit_cuts ( ) const

inline

References bInheritCuts_.

void protocols::environment::Environment::inherit_cuts ( bool setting )

References bInheritCuts_, broker(), and core::environment::EnvCore::name().

bool protocols::environment::Environment::is_registered ( ClientMoverOP mover ) const

References registered_movers_.

Referenced by register_mover().

void protocols::environment::Environment::pconf_creation ( Conformation * ptr ) const

inline

References pconfs_.

void protocols::environment::Environment::pconf_destruction ( Conformation * ptr ) const

inline

References pconfs_.

void protocols::environment::Environment::register_mover ( moves::MoverOP mover )

References allow_pure_movers(), is_registered(), register_movers(), registered_movers_, and protocols::environment::tr().

Referenced by register_movers().

template<class Iterator >

void protocols::environment::Environment::register_movers	(	Iterator	start,
		Iterator	end
	)

inline

References end(), and register_mover().

Referenced by register_mover().

void protocols::environment::Environment::remove_chainbreak_variants	(	core::pose::Pose &	pose,
		core::Size	up_res,
		core::Size	down_res
	)		const

private

References core::pose::Pose::conformation(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, and core::pose::remove_variant_type_from_residue().

Referenced by remove_nonpermenant_features().

void protocols::environment::Environment::remove_nonpermenant_features ( core::pose::Pose & pose )

private

ENV OPEN/CLOSING.

References core::pose::Pose::annotated_sequence(), broker(), core::pose::Pose::conformation(), core::conformation::Conformation::delete_residue_range_slow(), core::pose::Pose::fold_tree(), input_pose_, core::kinematics::FoldTree::nres(), remove_chainbreak_variants(), core::kinematics::FoldTree::set_jump_atoms(), core::pose::Pose::size(), and protocols::environment::tr().

Referenced by end().

core::pose::Pose protocols::environment::Environment::start ( core::pose::Pose const & in_pose )

References ann_, broker(), core::pose::Pose::conformation(), core::pose::Pose::data(), input_pose_, core::environment::EnvCore::name(), core::environment::EnvCore::set_superenv(), core::conformation::Conformation::size(), protocols::environment::tr(), and core::pose::datacache::CacheableDataType::WRITEABLE_DATA.

EnvironmentCAP protocols::environment::Environment::superenv ( ) const

References core::scoring::env, and core::environment::EnvCore::superenv().

Referenced by end().

Member Data Documentation

SequenceAnnotationOP protocols::environment::Environment::ann_

private

Referenced by annotations(), broker(), and start().

bool protocols::environment::Environment::bAllowPureMovers_

private

Referenced by allow_pure_movers().

bool protocols::environment::Environment::bAutoCut_

private

Referenced by auto_cut().

bool protocols::environment::Environment::bInheritCuts_

private

Referenced by inherit_cuts().

EnvClaimBrokerOP protocols::environment::Environment::broker_

private

Referenced by broker(), and end().

core::pose::Pose protocols::environment::Environment::input_pose_

private

Referenced by end(), remove_nonpermenant_features(), and start().

std::set< Conformation * > protocols::environment::Environment::pconfs_

mutableprivate

Referenced by pconf_creation(), pconf_destruction(), and ~Environment().

std::set<ClientMoverOP> protocols::environment::Environment::registered_movers_

private

Referenced by broker(), cancel_passports(), is_registered(), and register_mover().

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

src/protocols/environment/Environment.hh
src/protocols/environment/Environment.cc

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation