#include <TopologyBroker.hh>

Inheritance diagram for protocols::topology_broker::TopologyBroker:

Public Types
typedef TopologyClaimers::const_iterator	const_iterator

Public Member Functions
	TopologyBroker ()
	constructor More...

	~TopologyBroker () override

	TopologyBroker (TopologyBroker const &)

TopologyBroker &	operator= (TopologyBroker const &)

TopologyBrokerCOP	get_self_ptr () const
	self pointers More...

TopologyBrokerOP	get_self_ptr ()

TopologyBrokerCAP	get_self_weak_ptr () const

TopologyBrokerAP	get_self_weak_ptr ()

void	add (TopologyClaimerOP cl)
	add new Claimers to the broker -— useful before a job is started More...

void	use_job_pose (bool setting)
	use the input pose from the job (i.e., call new_decoy( pose ) ) More...

bool	use_job_pose () const
	Returns true if we are using the input pose from the job (i.e. new_decoy(pose)), false otherwise. More...

const TopologyClaimerOP &	claimer (core::Size i) const
	Returns the ith topology claimer if it exists. More...

TopologyClaimers::const_iterator	begin () const

TopologyClaimers::const_iterator	end () const

core::Size	num_claimers () const
	Returns the number of claimers associated with the broker. More...

void	apply (core::pose::Pose &)
	at the start of a job this is called, e.g., by the AbrelaxMover it generates a pose with appropriate foldtree and initializes dofs, adds constraints, etc. More...

moves::MoverOP	mover (core::pose::Pose const &, abinitio::StageID, core::scoring::ScoreFunction const &scorefxn, core::Real progress) const
	return a set of Movers ( RandomMover, i.e. container of movers ) More...

void	apply_filter (core::pose::Pose const &, abinitio::StageID, core::Real progress) const
	apply filter (TopologyClaimer::passes_filter() ) and raise exception EXCN_FILTER_FAILED if failed More...

void	adjust_relax_movemap (core::kinematics::MoveMap &) const
	if some claimer wants to influence the movemap for relax he can do it here: More...

core::fragment::FragSetCOP	loop_frags (core::kinematics::MoveMap &) const
	the SlidingWindowLoopClosure needs pure fragments, because it changes the the residue number in the ShortLoopClosure part thus extra hook for this — > only some Claimers will answer More...

bool	has_chainbreaks_to_close () const
	do we need to close loops ( unphysical chainbreaks have been introduced? ) More...

void	add_chainbreak_variants (core::pose::Pose &pose, core::Size max_dist=0, core::kinematics::ShortestPathInFoldTreeCOP sp=nullptr) const
	add chainbreak variant residue to the unphysical chainbreaks More...

bool	check_chainbreak_variants (core::pose::Pose &pose) const
	check that each chainbreak residue has a chainbreak variant More...

void	switch_to_fullatom (core::pose::Pose &)
	switch to fullatom — some Claimers might help by providing template based side-chain information More...

bool	does_final_fold_tree_exist () const

core::kinematics::FoldTree &	final_fold_tree () const
	access for hacky claimers More...

claims::SequenceClaim &	resolve_sequence_label (std::string const &label) const
	get the sequence claim that is consistent with the label, throws EXCN_Unknown_SequenceLabel if not found More...

const SequenceNumberResolver &	sequence_number_resolver () const

void	relay_message (ClaimerMessage &msg) const

bool	has_sequence_claimer ()

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

Private Types
typedef core::Size	StageID

typedef utility::vector1< TopologyClaimerOP >	TopologyClaimers

Private Member Functions
void	generate_sequence_claims (claims::DofClaims &all_claims)
	first round claims are collected More...

void	generate_symmetry_claims (claims::SymmetryClaims &all_claims)
	collects symmetry claims More...

SymmetryClaimerOP	resolve_symmetry_claims (claims::SymmetryClaims &symm_claims)
	checks whether only one sequence claim is there, otherwise crashes. More...

void	make_sequence_symmetric (claims::DofClaims pre_accepted, core::pose::Pose &pose)

void	generate_round1 (claims::DofClaims &all_claims)
	first round claims are collected More...

void	generate_final_claims (claims::DofClaims &all_claims)
	second round claims are collected More...

void	accept_claims (claims::DofClaims &claims)
	notify owner of accepted claims More...

bool	broking (claims::DofClaims const &all_claims, claims::DofClaims &pre_accepted)
	run thru list of claims, ask all claimers if this claims is acceptable — > returns accepted claims in pre_accepted throws EXCN_ExclusiveClaimDeclined if the call to the owners TopologyClaimer::accept_declined_claim( declined_claim ) returns false More...

void	build_fold_tree (claims::DofClaims &claims, core::Size nres)
	creates a fold-tree from the Jump- and CutClaims throws EXCN_InvalidFoldTree at failure More...

void	build_fold_tree_from_claimer (core::pose::Pose &pose, core::kinematics::FoldTree &fold_tree)

void	initialize_sequence (claims::DofClaims &claims, core::pose::Pose &new_pose)
	create new pose from SeqClaims More...

void	initialize_cuts (claims::DofClaims &claims, core::pose::Pose &new_pose)
	creates the list "to_be_closed_cuts_" from current fold-tree and CutClaims More...

void	initialize_dofs (claims::DofClaims &claims, core::pose::Pose &new_pose)
	initialize dofs More...

void	add_constraints (core::pose::Pose &) const
	add constraints --> referred to Claimers ( e.g., ConstraintClaimer, RigidChunkClaimer ) More...

Private Attributes
TopologyClaimers	claimers_
	vector of Claimers — RigidChunkClaimer, FragmentClaimer, ConstraintClaimer, etc. More...

claims::DofClaims	current_claims_
	list of dof-claims currently active More...

core::Size	nres_
	current pose has nres total_residues More...

core::kinematics::FoldTreeOP	fold_tree_
	the current fold-tree More...

core::kinematics::FoldTreeOP	final_fold_tree_
	current final-fold-tree — after removal to_bel_closed_cuts_ More...

core::scoring::ScoreFunctionOP	repack_scorefxn_
	Scorefunction used in switch_to_fullatom. More...

utility::vector1< core::Size >	to_be_closed_cuts_
	these cuts are not physical and should be closed ( i.e., chainbreak energy, loop-closing ) More...

utility::vector1< core::Size >	start_pose_cuts_
	these cuts are not physical and should be closed ( i.e., chainbreak energy, loop-closing ) More...

claims::SequenceClaims	sequence_claims_

SequenceNumberResolverOP	sequence_number_resolver_

bool	bUseJobPose_
	we restart from the input pose... call steal( pose ) for all claimers More...

bool	use_fold_tree_from_claimer_

core::pose::PoseOP	current_pose_

Member Typedef Documentation

◆ const_iterator

typedef TopologyClaimers::const_iterator protocols::topology_broker::TopologyBroker::const_iterator

◆ StageID

typedef core::Size protocols::topology_broker::TopologyBroker::StageID

private

◆ TopologyClaimers

typedef utility::vector1< TopologyClaimerOP > protocols::topology_broker::TopologyBroker::TopologyClaimers

private

Constructor & Destructor Documentation

◆ TopologyBroker() [1/2]

protocols::topology_broker::TopologyBroker::TopologyBroker ( )

constructor

References sequence_number_resolver_.

◆ ~TopologyBroker()

protocols::topology_broker::TopologyBroker::~TopologyBroker ( )

overridedefault

◆ TopologyBroker() [2/2]

protocols::topology_broker::TopologyBroker::TopologyBroker ( TopologyBroker const & tp )

References current_claims_, current_pose_, final_fold_tree_, fold_tree_, nres_, repack_scorefxn_, sequence_number_resolver_, start_pose_cuts_, to_be_closed_cuts_, and use_fold_tree_from_claimer_.

Member Function Documentation

◆ accept_claims()

void protocols::topology_broker::TopologyBroker::accept_claims ( claims::DofClaims & claims )

private

notify owner of accepted claims

Referenced by apply().

◆ add()

void protocols::topology_broker::TopologyBroker::add ( TopologyClaimerOP cl )

add new Claimers to the broker -— useful before a job is started

-------------— Application Setup ---------------------------------—

References claimers_, and get_self_weak_ptr().

Referenced by protocols::topology_broker::add_claims_from_stream(), and protocols::topology_broker::add_cmdline_claims().

◆ add_chainbreak_variants()

void protocols::topology_broker::TopologyBroker::add_chainbreak_variants	(	core::pose::Pose &	pose,
		core::Size	max_dist = `0`,
		core::kinematics::ShortestPathInFoldTreeCOP	sp = `nullptr`
	)		const

add chainbreak variant residue to the unphysical chainbreaks

References core::pose::add_variant_type_to_pose_residue(), core::pose::Pose::constraint_set(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_cutpoint(), to_be_closed_cuts_, and tr().

Referenced by apply().

◆ add_constraints()

void protocols::topology_broker::TopologyBroker::add_constraints ( core::pose::Pose & pose ) const

private

add constraints --> referred to Claimers ( e.g., ConstraintClaimer, RigidChunkClaimer )

References claimer(), claimers_, core::pose::Pose::constraint_set(), and tr().

Referenced by apply(), and switch_to_fullatom().

◆ adjust_relax_movemap()

void protocols::topology_broker::TopologyBroker::adjust_relax_movemap ( core::kinematics::MoveMap & mm ) const

if some claimer wants to influence the movemap for relax he can do it here:

References claimer(), and claimers_.

◆ apply()

void protocols::topology_broker::TopologyBroker::apply ( core::pose::Pose & pose )

at the start of a job this is called, e.g., by the AbrelaxMover it generates a pose with appropriate foldtree and initializes dofs, adds constraints, etc.

--------------------— Job Setup ---------------------------------------—

References accept_claims(), add_chainbreak_variants(), add_constraints(), broking(), build_fold_tree(), build_fold_tree_from_claimer(), bUseJobPose_, claimer(), claimers_, core::pose::Pose::clear(), core::pose::Pose::conformation(), current_pose_, core::kinematics::FoldTree::cutpoint(), core::io::raw_data::DisulfideFile::disulfides(), core::pose::Pose::dump_pdb(), core::pose::Pose::empty(), core::conformation::Conformation::fix_disulfides(), core::pose::Pose::fold_tree(), fold_tree_, generate_final_claims(), generate_round1(), generate_sequence_claims(), generate_symmetry_claims(), core::scoring::get_score_function(), initialize_cuts(), initialize_dofs(), initialize_sequence(), core::scoring::dssp::Dssp::insert_ss_into_pose(), core::conformation::symmetry::is_symmetric(), core::pose::symmetry::make_asymmetric_pose(), core::kinematics::FoldTree::num_cutpoint(), repack_scorefxn_, resolve_symmetry_claims(), sequence_claims_, sequence_number_resolver_, core::pose::Pose::size(), start_pose_cuts_, tr(), and use_fold_tree_from_claimer_.

◆ apply_filter()

void protocols::topology_broker::TopologyBroker::apply_filter	(	core::pose::Pose const &	pose,
		abinitio::StageID	stage_id,
		core::Real	progress
	)		const

apply filter (TopologyClaimer::passes_filter() ) and raise exception EXCN_FILTER_FAILED if failed

References claimer(), claimers_, and tr().

Referenced by protocols::abinitio::FragmentSampler::apply(), and protocols::abinitio::FragmentSampler::mover().

◆ begin()

TopologyClaimers::const_iterator protocols::topology_broker::TopologyBroker::begin ( ) const

inline

References claimers_.

◆ broking()

bool protocols::topology_broker::TopologyBroker::broking	(	claims::DofClaims const &	all_claims,
		claims::DofClaims &	pre_accepted
	)

private

run thru list of claims, ask all claimers if this claims is acceptable — > returns accepted claims in pre_accepted throws EXCN_ExclusiveClaimDeclined if the call to the owners TopologyClaimer::accept_declined_claim( declined_claim ) returns false

References claimers_, and tr().

Referenced by apply().

◆ build_fold_tree()

void protocols::topology_broker::TopologyBroker::build_fold_tree	(	claims::DofClaims &	claims,
		core::Size	nres
	)

private

creates a fold-tree from the Jump- and CutClaims throws EXCN_InvalidFoldTree at failure

References claimer(), claimers_, final_fold_tree_, fold_tree_, sequence_number_resolver_, start_pose_cuts_, and tr().

Referenced by apply().

◆ build_fold_tree_from_claimer()

void protocols::topology_broker::TopologyBroker::build_fold_tree_from_claimer	(	core::pose::Pose &	pose,
		core::kinematics::FoldTree &	fold_tree
	)

private

References claimer(), claimers_, fold_tree_, and tr().

Referenced by apply().

◆ check_chainbreak_variants()

bool protocols::topology_broker::TopologyBroker::check_chainbreak_variants ( core::pose::Pose & pose ) const

check that each chainbreak residue has a chainbreak variant

References core::pose::Pose::annotated_sequence(), protocols::jd2::current_output_name(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), core::pose::Pose::residue(), to_be_closed_cuts_, and tr().

◆ claimer()

const TopologyClaimerOP& protocols::topology_broker::TopologyBroker::claimer ( core::Size i ) const

inline

Returns the ith topology claimer if it exists.

References claimers_.

Referenced by add_constraints(), adjust_relax_movemap(), apply(), apply_filter(), build_fold_tree(), build_fold_tree_from_claimer(), generate_final_claims(), generate_round1(), generate_sequence_claims(), generate_symmetry_claims(), initialize_dofs(), loop_frags(), mover(), and relay_message().

◆ current_pose()

core::pose::Pose const& protocols::topology_broker::TopologyBroker::current_pose ( ) const

inline

References current_pose_.

Referenced by protocols::topology_broker::MembraneTopologyClaimer::generate_claims().

◆ does_final_fold_tree_exist()

bool protocols::topology_broker::TopologyBroker::does_final_fold_tree_exist ( ) const

inline

References final_fold_tree_.

◆ end()

TopologyClaimers::const_iterator protocols::topology_broker::TopologyBroker::end ( ) const

inline

References claimers_.

◆ final_fold_tree()

core::kinematics::FoldTree& protocols::topology_broker::TopologyBroker::final_fold_tree ( ) const

inline

access for hacky claimers

References final_fold_tree_.

Referenced by protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane().

◆ generate_final_claims()

void protocols::topology_broker::TopologyBroker::generate_final_claims ( claims::DofClaims & all_claims )

private

second round claims are collected

References claimer(), claimers_, and tr().

Referenced by apply().

◆ generate_round1()

void protocols::topology_broker::TopologyBroker::generate_round1 ( claims::DofClaims & all_claims )

private

first round claims are collected

References claimer(), claimers_, and tr().

Referenced by apply().

◆ generate_sequence_claims()

void protocols::topology_broker::TopologyBroker::generate_sequence_claims ( claims::DofClaims & all_claims )

private

first round claims are collected

References claimer(), claimers_, and tr().

Referenced by apply(), and has_sequence_claimer().

◆ generate_symmetry_claims()

void protocols::topology_broker::TopologyBroker::generate_symmetry_claims ( claims::SymmetryClaims & all_claims )

private

collects symmetry claims

References claimer(), and claimers_.

Referenced by apply().

◆ get_self_ptr() [1/2]

TopologyBrokerOP protocols::topology_broker::TopologyBroker::get_self_ptr ( )

inline

◆ get_self_ptr() [2/2]

TopologyBrokerCOP protocols::topology_broker::TopologyBroker::get_self_ptr ( ) const

inline

self pointers

◆ get_self_weak_ptr() [1/2]

TopologyBrokerAP protocols::topology_broker::TopologyBroker::get_self_weak_ptr ( )

inline

◆ get_self_weak_ptr() [2/2]

TopologyBrokerCAP protocols::topology_broker::TopologyBroker::get_self_weak_ptr ( ) const

inline

Referenced by add().

◆ has_chainbreaks_to_close()

bool protocols::topology_broker::TopologyBroker::has_chainbreaks_to_close ( ) const

do we need to close loops ( unphysical chainbreaks have been introduced? )

References to_be_closed_cuts_.

◆ has_sequence_claimer()

bool protocols::topology_broker::TopologyBroker::has_sequence_claimer ( )

References generate_sequence_claims().

Referenced by protocols::topology_broker::add_cmdline_claims().

◆ initialize_cuts()

void protocols::topology_broker::TopologyBroker::initialize_cuts	(	claims::DofClaims &	claims,
		core::pose::Pose &	new_pose
	)

private

creates the list "to_be_closed_cuts_" from current fold-tree and CutClaims

References core::kinematics::FoldTree::cutpoint(), core::kinematics::FoldTree::cutpoint_map(), core::pose::Pose::fold_tree(), core::chemical::ResidueTypeBase::name(), core::conformation::Residue::name3(), core::pose::Pose::num_jump(), core::pose::Pose::residue(), sequence_number_resolver_, to_be_closed_cuts_, tr(), and core::conformation::Residue::type().

Referenced by apply().

◆ initialize_dofs()

void protocols::topology_broker::TopologyBroker::initialize_dofs	(	claims::DofClaims &	claims,
		core::pose::Pose &	new_pose
	)

private

initialize dofs

References claimer(), claimers_, protocols::topology_broker::claims::DofClaim::EXCLUSIVE, core::pose::Pose::fold_tree(), core::kinematics::FoldTree::jump_nr(), core::pose::Pose::num_jump(), sequence_number_resolver_, core::pose::Pose::size(), and tr().

Referenced by apply().

◆ initialize_sequence()

void protocols::topology_broker::TopologyBroker::initialize_sequence	(	claims::DofClaims &	claims,
		core::pose::Pose &	new_pose
	)

private

create new pose from SeqClaims

References core::chemical::CENTROID, protocols::topology_broker::compare_sequence_claim_priority(), core::conformation::Residue::is_protein(), core::pose::make_pose_from_sequence(), core::pose::Pose::residue(), sequence_claims_, sequence_number_resolver_, core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::pose::Pose::size(), and tr().

Referenced by apply().

◆ loop_frags()

core::fragment::FragSetCOP protocols::topology_broker::TopologyBroker::loop_frags ( core::kinematics::MoveMap & movemap ) const

the SlidingWindowLoopClosure needs pure fragments, because it changes the the residue number in the ShortLoopClosure part thus extra hook for this — > only some Claimers will answer

References claimer(), and claimers_.

◆ make_sequence_symmetric()

void protocols::topology_broker::TopologyBroker::make_sequence_symmetric	(	claims::DofClaims	pre_accepted,
		core::pose::Pose &	pose
	)

private

◆ mover()

moves::MoverOP protocols::topology_broker::TopologyBroker::mover	(	core::pose::Pose const &	pose,
		abinitio::StageID	stage_id,
		core::scoring::ScoreFunction const &	scorefxn,
		core::Real	progress
	)		const

return a set of Movers ( RandomMover, i.e. container of movers )

-------------------------------— Consulting -------------------------------------------------— the following interface is for the Mover to consult the Broker during the course of a simulation usually these calls a relayed to the Claimers only some will answer, others will ignore it. e.g., ConstraintClaimer will not add a Mover, JumpClaimer and RigidChunkClaimer will add chainbreaks a basic FragmentClaimer will not

References claimer(), claimers_, and tr().

Referenced by protocols::abinitio::FragmentSampler::mover().

◆ num_claimers()

core::Size protocols::topology_broker::TopologyBroker::num_claimers ( ) const

inline

Returns the number of claimers associated with the broker.

References claimers_.

◆ operator=()

TopologyBroker & protocols::topology_broker::TopologyBroker::operator= ( TopologyBroker const & src )

References claimers_, current_claims_, current_pose_, final_fold_tree_, fold_tree_, nres_, repack_scorefxn_, start_pose_cuts_, to_be_closed_cuts_, and use_fold_tree_from_claimer_.

◆ relay_message()

void protocols::topology_broker::TopologyBroker::relay_message ( ClaimerMessage & msg ) const

References claimer(), claimers_, and protocols::topology_broker::ClaimerMessage::matches().

Referenced by protocols::topology_broker::CoordConstraintClaimer::generate_claims().

◆ resolve_sequence_label()

claims::SequenceClaim & protocols::topology_broker::TopologyBroker::resolve_sequence_label ( std::string const & label ) const

get the sequence claim that is consistent with the label, throws EXCN_Unknown_SequenceLabel if not found

References sequence_claims_.

Referenced by protocols::topology_broker::BasicJumpClaimer::generate_claims(), protocols::topology_broker::FragmentClaimer::generate_claims(), protocols::topology_broker::StartStructClaimer::generate_claims(), protocols::topology_broker::MetalloClaimer::generate_claims(), and protocols::topology_broker::FragmentClaimer::get_sequence_region().

◆ resolve_symmetry_claims()

SymmetryClaimerOP protocols::topology_broker::TopologyBroker::resolve_symmetry_claims ( claims::SymmetryClaims & symm_claims )

private

checks whether only one sequence claim is there, otherwise crashes.

References tr().

Referenced by apply().

◆ sequence_number_resolver()

const SequenceNumberResolver& protocols::topology_broker::TopologyBroker::sequence_number_resolver ( ) const

inline

References sequence_number_resolver_.

Referenced by protocols::topology_broker::RigidChunkClaimer::allow_claim(), protocols::topology_broker::BasicJumpClaimer::generate_claims(), protocols::topology_broker::FragmentClaimer::generate_claims(), protocols::topology_broker::FragmentJumpClaimer::generate_claims(), protocols::topology_broker::MetalloClaimer::generate_claims(), and protocols::topology_broker::FragmentClaimer::get_sequence_region().

◆ switch_to_fullatom()

void protocols::topology_broker::TopologyBroker::switch_to_fullatom ( core::pose::Pose & pose )

switch to fullatom — some Claimers might help by providing template based side-chain information

References add_constraints(), core::pose::Pose::annotated_sequence(), protocols::minimization_packing::PackRotamersMover::apply(), claimers_, core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), core::pack::task::TaskFactory::create_packer_task(), core::conformation::Conformation::detect_bonds(), core::conformation::Conformation::detect_disulfides(), core::io::raw_data::DisulfideFile::disulfides(), core::conformation::Conformation::fix_disulfides(), core::chemical::FULL_ATOM_t, core::pose::Pose::is_fullatom(), core::conformation::symmetry::is_symmetric(), core::pose::symmetry::make_symmetric_movemap(), repack_scorefxn_, core::optimization::AtomTreeMinimizer::run(), core::optimization::symmetry::SymAtomTreeMinimizer::run(), core::pose::Pose::size(), core::util::switch_to_residue_type_set(), and tr().

◆ use_job_pose() [1/2]

bool protocols::topology_broker::TopologyBroker::use_job_pose ( ) const

inline

Returns true if we are using the input pose from the job (i.e. new_decoy(pose)), false otherwise.

References bUseJobPose_.

◆ use_job_pose() [2/2]

void protocols::topology_broker::TopologyBroker::use_job_pose ( bool setting )

inline

use the input pose from the job (i.e., call new_decoy( pose ) )

References bUseJobPose_.

Referenced by protocols::topology_broker::add_claims_from_stream().

Member Data Documentation

◆ bUseJobPose_

bool protocols::topology_broker::TopologyBroker::bUseJobPose_

private

we restart from the input pose... call steal( pose ) for all claimers

Referenced by apply(), and use_job_pose().

◆ claimers_

TopologyClaimers protocols::topology_broker::TopologyBroker::claimers_

private

vector of Claimers — RigidChunkClaimer, FragmentClaimer, ConstraintClaimer, etc.

Referenced by add(), add_constraints(), adjust_relax_movemap(), apply(), apply_filter(), begin(), broking(), build_fold_tree(), build_fold_tree_from_claimer(), claimer(), end(), generate_final_claims(), generate_round1(), generate_sequence_claims(), generate_symmetry_claims(), initialize_dofs(), loop_frags(), mover(), num_claimers(), operator=(), relay_message(), and switch_to_fullatom().

◆ current_claims_

claims::DofClaims protocols::topology_broker::TopologyBroker::current_claims_

private

list of dof-claims currently active

Referenced by operator=(), and TopologyBroker().

◆ current_pose_

core::pose::PoseOP protocols::topology_broker::TopologyBroker::current_pose_

private

Referenced by apply(), current_pose(), operator=(), and TopologyBroker().

◆ final_fold_tree_

core::kinematics::FoldTreeOP protocols::topology_broker::TopologyBroker::final_fold_tree_

mutableprivate

current final-fold-tree — after removal to_bel_closed_cuts_

mutable here is hack to make wrong MembraneTopologyClaimer work — don't want to clean up that guy right now...

Referenced by build_fold_tree(), does_final_fold_tree_exist(), final_fold_tree(), operator=(), and TopologyBroker().

◆ fold_tree_

core::kinematics::FoldTreeOP protocols::topology_broker::TopologyBroker::fold_tree_

private

the current fold-tree

Referenced by apply(), build_fold_tree(), build_fold_tree_from_claimer(), operator=(), and TopologyBroker().

◆ nres_

core::Size protocols::topology_broker::TopologyBroker::nres_

private

current pose has nres total_residues

Referenced by operator=(), and TopologyBroker().

◆ repack_scorefxn_

core::scoring::ScoreFunctionOP protocols::topology_broker::TopologyBroker::repack_scorefxn_

private

Scorefunction used in switch_to_fullatom.

Referenced by apply(), operator=(), switch_to_fullatom(), and TopologyBroker().

◆ sequence_claims_

claims::SequenceClaims protocols::topology_broker::TopologyBroker::sequence_claims_

private

Referenced by apply(), initialize_sequence(), and resolve_sequence_label().

◆ sequence_number_resolver_

SequenceNumberResolverOP protocols::topology_broker::TopologyBroker::sequence_number_resolver_

private

Referenced by apply(), build_fold_tree(), initialize_cuts(), initialize_dofs(), initialize_sequence(), sequence_number_resolver(), and TopologyBroker().

◆ start_pose_cuts_

utility::vector1< core::Size > protocols::topology_broker::TopologyBroker::start_pose_cuts_

private

these cuts are not physical and should be closed ( i.e., chainbreak energy, loop-closing )

Referenced by apply(), build_fold_tree(), operator=(), and TopologyBroker().

◆ to_be_closed_cuts_

utility::vector1< core::Size > protocols::topology_broker::TopologyBroker::to_be_closed_cuts_

private

these cuts are not physical and should be closed ( i.e., chainbreak energy, loop-closing )

Referenced by add_chainbreak_variants(), check_chainbreak_variants(), has_chainbreaks_to_close(), initialize_cuts(), operator=(), and TopologyBroker().

◆ use_fold_tree_from_claimer_

bool protocols::topology_broker::TopologyBroker::use_fold_tree_from_claimer_

private

Referenced by apply(), operator=(), and TopologyBroker().

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

src/protocols/topology_broker/TopologyBroker.hh
src/protocols/topology_broker/TopologyBroker.cc

Public Types

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Member Typedef Documentation

◆ const_iterator

◆ StageID

◆ TopologyClaimers

Constructor & Destructor Documentation

◆ TopologyBroker() [1/2]

◆ ~TopologyBroker()

◆ TopologyBroker() [2/2]

Member Function Documentation

◆ accept_claims()

◆ add()

◆ add_chainbreak_variants()

◆ add_constraints()

◆ adjust_relax_movemap()

◆ apply()

◆ apply_filter()

◆ begin()

◆ broking()

◆ build_fold_tree()

◆ build_fold_tree_from_claimer()

◆ check_chainbreak_variants()

◆ claimer()

◆ current_pose()

◆ does_final_fold_tree_exist()

◆ end()

◆ final_fold_tree()

◆ generate_final_claims()

◆ generate_round1()

◆ generate_sequence_claims()

◆ generate_symmetry_claims()

◆ get_self_ptr() [1/2]

◆ get_self_ptr() [2/2]

◆ get_self_weak_ptr() [1/2]

◆ get_self_weak_ptr() [2/2]

◆ has_chainbreaks_to_close()

◆ has_sequence_claimer()

◆ initialize_cuts()

◆ initialize_dofs()

◆ initialize_sequence()

◆ loop_frags()

◆ make_sequence_symmetric()

◆ mover()

◆ num_claimers()

◆ operator=()

◆ relay_message()

◆ resolve_sequence_label()

◆ resolve_symmetry_claims()

◆ sequence_number_resolver()

◆ switch_to_fullatom()

◆ use_job_pose() [1/2]

◆ use_job_pose() [2/2]

Member Data Documentation

◆ bUseJobPose_

◆ claimers_

◆ current_claims_

◆ current_pose_

◆ final_fold_tree_

◆ fold_tree_

◆ nres_

◆ repack_scorefxn_

◆ sequence_claims_

◆ sequence_number_resolver_

◆ start_pose_cuts_

◆ to_be_closed_cuts_

◆ use_fold_tree_from_claimer_