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protocols::environment::EnvClaimBroker Class Reference

#include <EnvClaimBroker.hh>

Inheritance diagram for protocols::environment::EnvClaimBroker:
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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

◆ BiasVector

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

◆ BrokeredJumpDataCOP

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

◆ BrokeredJumpDataOP

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

◆ Conformation

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

◆ ConformationCOP

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

◆ ConformationOP

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

◆ CutBiasElemVect

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

◆ CutElemVect

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

◆ DOFElemVect

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

◆ FoldTreeSketch

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

◆ JumpDataMap

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

◆ JumpElemVect

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

◆ MoverPassMap

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

◆ ResElemVect

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

◆ SequenceAnnotationCOP

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

◆ SequenceAnnotationOP

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

◆ SizeToStringMap

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

◆ StringToSizePairMap

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

◆ StringToStringPairMap

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

Constructor & Destructor Documentation

◆ EnvClaimBroker()

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::env, 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.

◆ ~EnvClaimBroker()

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

Member Function Documentation

◆ add_chainbreak_variants()

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::chemical::ResidueTypeBase::mode(), core::conformation::Conformation::replace_residue(), core::conformation::Conformation::residue(), core::conformation::Conformation::residue_type_set_for_conf(), core::conformation::Residue::seqpos(), and core::conformation::Residue::type().

Referenced by broker_fold_tree().

◆ add_virtual_residues()

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().

◆ annotate_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().

◆ assign_passports()

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

use accepted claims to build DofPassport objects for movers.

◆ broker_dofs()

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().

◆ broker_fold_tree()

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, core::environment::FoldTreeSketch::nres(), process_elements(), render_fold_tree(), result(), result_, core::conformation::Conformation::size(), protocols::environment::tr(), and core::kinematics::visualize_fold_tree().

Referenced by EnvClaimBroker().

◆ build_new_residues()

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

broker new residues

◆ collect_claims()

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().

◆ collect_elements()

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().

◆ grant_access()

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

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

◆ process_elements() [1/4]

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.

◆ process_elements() [2/4]

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.

◆ process_elements() [3/4]

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().

◆ process_elements() [4/4]

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().

◆ render_fold_tree()

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().

◆ result()

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

References result_.

Referenced by broker_fold_tree(), and EnvClaimBroker().

◆ setup_passports()

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

References protocols::environment::claims::DOES_NOT_CONTROL, protocols::environment::claims::EXCLUSIVE, protocols::environment::claims::DOFElement::id, protocols::environment::init_str_selector(), protocols::environment::claims::MUST_CONTROL, core::scoring::pair, protocols::environment::tr(), protocols::environment::claims::DOFElement::type, and core::id::DOF_ID::valid().

Member Data Documentation

◆ ann_

SequenceAnnotationOP protocols::environment::EnvClaimBroker::ann_
private

Referenced by broker_fold_tree(), and EnvClaimBroker().

◆ claims_

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

Referenced by EnvClaimBroker().

◆ env_

EnvironmentCAP protocols::environment::EnvClaimBroker::env_
private

◆ movers_and_passes_

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

◆ result_

BrokerResult protocols::environment::EnvClaimBroker::result_
private

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

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