#include <TopologyBroker.hh>

Inheritance diagram for protocols::topology_broker::TopologyBroker:

Collaboration diagram for protocols::topology_broker::TopologyBroker:

Public Types
typedef TopologyClaimers::const_iterator	const_iterator

Public Member Functions
	TopologyBroker ()
	constructor More...

virtual	~TopologyBroker ()

	TopologyBroker (TopologyBroker const &)

TopologyBroker const &	operator= (TopologyBroker const &)

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=NULL) 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...

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

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...

core::Size	resolve_residue (std::string const &chain_label, core::Size pos) 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 (DofClaims &all_claims)
	first round claims are collected More...

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

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

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

bool	broking (DofClaims const &all_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 (DofClaims &claims, Size nres)
	creates a fold-tree from the Jump- and CutClaims throws EXCN_InvalidFoldTree at failure More...

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

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

void	initialize_dofs (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...

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

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

SequenceClaims	sequence_claims_

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

core::pose::PoseOP	current_pose_

Member Typedef Documentation

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

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

private

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

private

Constructor & Destructor Documentation

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

constructor

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

virtual

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

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

Member Function Documentation

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

private

notify owner of accepted claims

Referenced by apply().

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

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

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

References claimers_.

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

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

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

private

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

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

Referenced by apply(), and switch_to_fullatom().

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 claimers_.

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(), bUseJobPose_, claimers_, core::pose::Pose::clear(), core::pose::Pose::conformation(), current_pose_, core::kinematics::FoldTree::cutpoint(), core::io::raw_data::DisulfideFile::disulfides(), core::conformation::Conformation::fix_disulfides(), core::pose::Pose::fold_tree(), fold_tree_, generate_final_claims(), generate_round1(), generate_sequence_claims(), core::scoring::getScoreFunction(), 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_, sequence_claims_, start_pose_cuts_, core::pose::Pose::total_residue(), and tr().

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 claimers_, and tr().

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

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

inline

References claimers_.

bool protocols::topology_broker::TopologyBroker::broking	(	DofClaims const &	all_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().

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

private

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

References claimers_, protocols::topology_broker::DofClaim::CUT, final_fold_tree_, fold_tree_, protocols::topology_broker::DofClaim::JUMP, protocols::topology_broker::DofClaim::ROOT, start_pose_cuts_, and tr().

Referenced by apply().

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().

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

inline

Returns the ith topology claimer if it exists.

References claimers_.

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

inline

References current_pose_.

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

inline

References claimers_.

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().

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

private

second round claims are collected

References claimers_, and tr().

Referenced by apply().

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

private

first round claims are collected

References claimers_, and tr().

Referenced by apply().

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

private

first round claims are collected

References claimers_, and tr().

Referenced by apply(), and has_sequence_claimer().

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_.

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

References generate_sequence_claims().

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

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

private

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

References protocols::topology_broker::DofClaim::CUT, core::kinematics::FoldTree::cutpoint(), core::kinematics::FoldTree::cutpoint_map(), core::pose::Pose::fold_tree(), core::pose::Pose::num_jump(), to_be_closed_cuts_, and tr().

Referenced by apply().

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

private

initialize dofs

References protocols::topology_broker::DofClaim::BB, claimers_, protocols::topology_broker::DofClaim::EXCLUSIVE, core::pose::Pose::fold_tree(), protocols::topology_broker::DofClaim::JUMP, core::kinematics::FoldTree::jump_nr(), core::pose::Pose::num_jump(), core::pose::Pose::total_residue(), and tr().

Referenced by apply().

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

private

create new pose from SeqClaims

References protocols::topology_broker::DofClaim::SEQUENCE, sequence_claims_, and tr().

Referenced by apply().

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 claimers_.

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 protocols::moves::MoverContainer::add_mover(), claimers_, and tr().

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

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

inline

Returns the number of claimers associated with the broker.

References claimers_.

TopologyBroker const & 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_, and to_be_closed_cuts_.

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

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

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

core::Size protocols::topology_broker::TopologyBroker::resolve_residue	(	std::string const &	chain_label,
		core::Size	pos
	)		const

References protocols::topology_broker::SequenceClaim::offset(), and resolve_sequence_label().

Referenced by protocols::topology_broker::MetalloClaimer::initialize_residues().

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::FragmentClaimer::get_sequence_region(), and resolve_residue().

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::simple_moves::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::chemical::FA_STANDARD, core::conformation::Conformation::fix_disulfides(), core::pose::Pose::is_fullatom(), core::conformation::symmetry::is_symmetric(), core::pose::symmetry::make_symmetric_movemap(), repack_scorefxn_, core::optimization::symmetry::SymAtomTreeMinimizer::run(), core::optimization::AtomTreeMinimizer::run(), core::util::switch_to_residue_type_set(), core::pose::Pose::total_residue(), and tr().

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().

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_.

Member Data Documentation

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().

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(), claimer(), end(), generate_final_claims(), generate_round1(), generate_sequence_claims(), initialize_dofs(), loop_frags(), mover(), num_claimers(), operator=(), relay_message(), and switch_to_fullatom().

DofClaims protocols::topology_broker::TopologyBroker::current_claims_

private

list of dof-claims currently active

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

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

private

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

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(), final_fold_tree(), operator=(), and TopologyBroker().

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

private

the current fold-tree

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

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

private

current pose has nres total_residues

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

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().

SequenceClaims protocols::topology_broker::TopologyBroker::sequence_claims_

private

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

utility::vector1< 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().

utility::vector1< 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().

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

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation