protocols::environment::Environment Class Reference

#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

Conformation

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

private

ConformationAP

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

private

ConformationCOP

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

private

ConformationOP

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

private

Parent

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

private

SequenceAnnotation

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

private

SequenceAnnotationCOP

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

private

SequenceAnnotationOP

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

private

Constructor & Destructor Documentation

Environment()

protocols::environment::Environment::Environment

(

std::string

name

)

~Environment()

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

override

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

Member Function Documentation

allow_pure_movers() [1/2]

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

inline

References bAllowPureMovers_.

Referenced by protocols::environment::EnvMover::apply(), and register_mover().

allow_pure_movers() [2/2]

void protocols::environment::Environment::allow_pure_movers

(

bool

setting

)

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

annotations()

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

inline

References ann_.

assign_passport()

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

private

References get_self_weak_ptr().

Referenced by broker().

auto_cut() [1/2]

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

inline

References bAutoCut_.

Referenced by protocols::environment::EnvMover::apply().

auto_cut() [2/2]

void protocols::environment::Environment::auto_cut

(

bool

setting

)

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

broker() [1/2]

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

inline

References broker_.

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

broker() [2/2]

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().

cancel_passports()

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

private

References registered_movers_, and protocols::environment::tr().

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

end() [1/2]

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 protocols::environment::EnvMover::apply(), and register_movers().

end() [2/2]

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().

get_self_ptr() [1/2]

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

inline

get_self_ptr() [2/2]

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

inline

self pointers

get_self_weak_ptr() [1/2]

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

inline

get_self_weak_ptr() [2/2]

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

inline

Referenced by assign_passport(), and broker().

inherit_cuts() [1/2]

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

inline

References bInheritCuts_.

Referenced by protocols::environment::EnvMover::apply().

inherit_cuts() [2/2]

void protocols::environment::Environment::inherit_cuts

(

bool

setting

)

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

is_registered()

bool protocols::environment::Environment::is_registered

(

ClientMoverOP

mover

)

const

References registered_movers_.

Referenced by register_mover().

pconf_creation()

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

inline

References pconfs_.

pconf_destruction()

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

inline

References pconfs_.

register_mover()

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 protocols::environment::EnvMover::apply(), and register_movers().

register_movers()

template<class Iterator >

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

inline

References end(), register_mover(), and start().

Referenced by register_mover().

remove_chainbreak_variants()

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, core::pose::remove_variant_type_from_residue(), core::conformation::Conformation::replace_residue(), core::conformation::Conformation::residue(), and core::conformation::Residue::seqpos().

Referenced by remove_nonpermenant_features().

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(), core::kinematics::FoldTree::num_jump(), remove_chainbreak_variants(), core::kinematics::FoldTree::set_jump_atoms(), core::pose::Pose::size(), and protocols::environment::tr().

Referenced by end().

start()

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.

Referenced by protocols::environment::EnvMover::apply(), and register_movers().

superenv()

EnvironmentCAP protocols::environment::Environment::superenv

(

)

const

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

Referenced by end().

Member Data Documentation

ann_

SequenceAnnotationOP protocols::environment::Environment::ann_

private

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

bAllowPureMovers_

bool protocols::environment::Environment::bAllowPureMovers_

private

Referenced by allow_pure_movers().

bAutoCut_

bool protocols::environment::Environment::bAutoCut_

private

Referenced by auto_cut().

bInheritCuts_

bool protocols::environment::Environment::bInheritCuts_

private

Referenced by inherit_cuts().

broker_

EnvClaimBrokerOP protocols::environment::Environment::broker_

private

Referenced by broker(), and end().

input_pose_

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

private

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

pconfs_

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

mutableprivate

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

registered_movers_

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

private

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

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

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