#include <TopologyClaimer.hh>

Public Member Functions
virtual	~TopologyClaimer ()
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...

	TopologyClaimer ()

	TopologyClaimer (weights::AbinitioMoverWeightOP weight)
	construct with weight-set ( how important is mover for different abinitio stages ? ) More...

virtual TopologyClaimerOP	clone () const =0
	clone it! More...

virtual std::string	type () const =0
	name of Claimer More...

virtual bool	claimer_builds_own_fold_tree ()

virtual core::kinematics::FoldTreeOP	get_fold_tree (core::pose::Pose &)
	in case a claimer has its own fold_tree. get_fold_tree() is called by the broker More...

virtual void	build_fold_tree (core::pose::Pose &, core::kinematics::FoldTree &)

virtual void	set_pose_from_broker (core::pose::Pose &)

virtual void	read (std::istream &)
	read definition of Claimer from setup file, i.e., a CLAIMER <type> ... END_CLAIMER block More...

virtual void	pre_process (core::pose::Pose &)

virtual void	generate_sequence_claims (claims::DofClaims &)
	generate claims that affect the sequence of the pose More...

virtual void	generate_symmetry_claims (claims::SymmetryClaims &)
	generate claims that affect the sequence of the pose More...

virtual void	generate_claims (claims::DofClaims &)
	generate first round of DOF claims More...

virtual void	finalize_claims (claims::DofClaims &)
	is called after all round1 claims have been approved or retracted – additional claims can be issued in this round More...

virtual bool	allow_claim (claims::DofClaim const &)
	allow a claim from a foreign Claimer More...

virtual void	initialize_dofs (core::pose::Pose &, claims::DofClaims const &init_claims, claims::DofClaims &failed_to_init)
	initialize sequence ( for approved sequence claims given as init_claim ) Claimer searches init_claims for claims owned by *this More...

virtual void	switch_to_fullatom (core::pose::Pose &, utility::vector1< bool >) const
	has this Claimer some side chain conformations to add? starts with bNeedToRepack true for all residues... if you have a sidechain —> copy it to pose and set needtoRepack false for this residue More...

virtual void	manipulate_cut_bias (utility::vector1< core::Real > &)
	multiply your bias to this – if its zero don't change that, i.e., multiply only this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues. Fragments can add their loop-fraction More...

virtual bool	accept_declined_claim (claims::DofClaim const &)
	notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false – if you can't live without this claim being accepted. ( e.g., RigidChunks ... ) More...

virtual void	claim_accepted (claims::DofClaimOP my_claim)
	this claim of yours was accepted.... I so far haven't done anything with this... might go away. More...

virtual void	add_constraints (core::pose::Pose &) const
	add constraints to pose... might make this stage dependent as with movers... More...

virtual core::fragment::FragSetCOP	loop_frags (core::kinematics::MoveMap &) const
	return fragments that can be used for loop-sampling... unfortunately some loop-samplers need fragments, rather then fragmovers (e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. ) overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling More...

virtual bool	passes_filter (core::pose::Pose const &, abinitio::StageID, core::Real, std::ostringstream &)
	claimers can add movers to the RandomMover (Container). add your moves, make it dependent on stage if you want to. So far this is called only by abinitio... if you don't want to do anything special — don't overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_ More...

virtual void	add_mover (moves::RandomMover &, core::pose::Pose const &, abinitio::StageID, core::scoring::ScoreFunction const &, core::Real)
	claimers can add movers to the RandomMover (Container). add your moves, make it dependent on stage if you want to. So far this is called only by abinitio... if you don't want to do anything special — don't overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_ More...

void	set_mover_weight (weights::AbinitioMoverWeightOP wset)

weights::AbinitioMoverWeight &	mover_weight ()

void	read_mover_weight (std::istream &is)
	read mover weight from Stream. - so far recognizes: LargeStage, SmallStage, SmoothStage, AllStage More...

virtual void	adjust_relax_movemap (core::kinematics::MoveMap &) const

void	set_broker (TopologyBrokerCAP ptr)
	don't use this — it is called by TopologyBroker add_claim only More...

TopologyBroker const &	broker () const
	return the broker we are collaborating with More...

virtual void	new_decoy ()
	a new decoy — random choices to be made ? make them here More...

virtual void	new_decoy (core::pose::Pose const &)
	an input pose is given, i.e., a starting structure for resampling don't make random choices, base choices on given pose More...

std::string const &	label () const

void	set_label (std::string const &str)

virtual void	receive_message (ClaimerMessage &)

virtual core::pose::PoseOP	get_pose_from_claimer ()

Protected Member Functions
virtual moves::MoverOP	get_mover (core::pose::Pose const &) const
	what is your mover ... called by add_mover — overload this or add_mover if you have movers too supply More...

virtual bool	read_tag (std::string tag, std::istream &is)

virtual void	set_defaults ()

virtual void	init_after_reading ()

Private Member Functions
void	unknown_tag (std::string tag, std::istream &is) const

Private Attributes
claims::DofClaims	current_claims_
	currently accepted claims... dunno haven't used that yet. More...

weights::AbinitioMoverWeightOP	abinitio_mover_weight_
	weight set .. how often shall this claimer's mover be sampled during different stages ? More...

TopologyBrokerCAP	broker_
	oh, our master. (use broker() to get this ). More...

std::string	label_
	a user defined string, can be used to send messages from claimer to claimer More...

Detailed Description

Constructor & Destructor Documentation

virtual protocols::topology_broker::TopologyClaimer::~TopologyClaimer ( )

inlinevirtual

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

protocols::topology_broker::TopologyClaimer::TopologyClaimer ( )

inline

References weights.

protocols::topology_broker::TopologyClaimer::TopologyClaimer ( weights::AbinitioMoverWeightOP weight )

inline

construct with weight-set ( how important is mover for different abinitio stages ? )

References abinitio_mover_weight_.

Member Function Documentation

virtual bool protocols::topology_broker::TopologyClaimer::accept_declined_claim ( claims::DofClaim const & )

inlinevirtual

notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false – if you can't live without this claim being accepted. ( e.g., RigidChunks ... )

Reimplemented in protocols::topology_broker::RigidChunkClaimer, protocols::topology_broker::DensityScoringClaimer, and protocols::topology_broker::FragmentClaimer.

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

inlinevirtual

add constraints to pose... might make this stage dependent as with movers...

Reimplemented in protocols::topology_broker::MetalloClaimer, protocols::topology_broker::DensityScoringClaimer, protocols::topology_broker::ConstraintClaimer, and protocols::topology_broker::CoordConstraintClaimer.

void protocols::topology_broker::TopologyClaimer::add_mover	(	moves::RandomMover &	random_mover,
		core::pose::Pose const &	pose,
		abinitio::StageID	stageID,
		core::scoring::ScoreFunction const &	,
		core::Real	progress
	)

virtual

claimers can add movers to the RandomMover (Container). add your moves, make it dependent on stage if you want to. So far this is called only by abinitio... if you don't want to do anything special — don't overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_

References protocols::moves::MoverContainer::add_mover().

virtual void protocols::topology_broker::TopologyClaimer::adjust_relax_movemap ( core::kinematics::MoveMap & ) const

inlinevirtual

Reimplemented in protocols::topology_broker::RigidChunkClaimer.

virtual bool protocols::topology_broker::TopologyClaimer::allow_claim ( claims::DofClaim const & )

inlinevirtual

allow a claim from a foreign Claimer

Reimplemented in protocols::topology_broker::FibrilModelingClaimer, and protocols::topology_broker::RigidChunkClaimer.

TopologyBroker const& protocols::topology_broker::TopologyClaimer::broker ( ) const

inline

return the broker we are collaborating with

References broker_, and runtime_assert.

virtual void protocols::topology_broker::TopologyClaimer::build_fold_tree	(	core::pose::Pose &	,
		core::kinematics::FoldTree &
	)

inlinevirtual

Reimplemented in protocols::topology_broker::TMHTopologySamplerClaimer, and protocols::topology_broker::MembraneTopologyClaimer.

virtual void protocols::topology_broker::TopologyClaimer::claim_accepted ( claims::DofClaimOP my_claim )

inlinevirtual

this claim of yours was accepted.... I so far haven't done anything with this... might go away.

References current_claims_.

virtual bool protocols::topology_broker::TopologyClaimer::claimer_builds_own_fold_tree ( )

inlinevirtual

Reimplemented in protocols::topology_broker::TMHTopologySamplerClaimer, and protocols::topology_broker::MembraneTopologyClaimer.

virtual TopologyClaimerOP protocols::topology_broker::TopologyClaimer::clone ( ) const

pure virtual

clone it!

virtual void protocols::topology_broker::TopologyClaimer::finalize_claims ( claims::DofClaims & )

inlinevirtual

is called after all round1 claims have been approved or retracted – additional claims can be issued in this round

Reimplemented in protocols::topology_broker::RigidChunkClaimer.

virtual void protocols::topology_broker::TopologyClaimer::generate_claims ( claims::DofClaims & )

inlinevirtual

generate first round of DOF claims

virtual void protocols::topology_broker::TopologyClaimer::generate_sequence_claims ( claims::DofClaims & )

inlinevirtual

generate claims that affect the sequence of the pose

Reimplemented in protocols::topology_broker::MetalloClaimer, protocols::topology_broker::DensityScoringClaimer, and protocols::topology_broker::SequenceClaimer.

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

virtual void protocols::topology_broker::TopologyClaimer::generate_symmetry_claims ( claims::SymmetryClaims & )

inlinevirtual

generate claims that affect the sequence of the pose

Reimplemented in protocols::topology_broker::SymmetryClaimer.

virtual core::kinematics::FoldTreeOP protocols::topology_broker::TopologyClaimer::get_fold_tree ( core::pose::Pose & )

inlinevirtual

in case a claimer has its own fold_tree. get_fold_tree() is called by the broker

Reimplemented in protocols::topology_broker::TMHTopologySamplerClaimer, and protocols::topology_broker::MembraneTopologyClaimer.

virtual moves::MoverOP protocols::topology_broker::TopologyClaimer::get_mover ( core::pose::Pose const & ) const

inlineprotectedvirtual

what is your mover ... called by add_mover — overload this or add_mover if you have movers too supply

Reimplemented in protocols::topology_broker::FragmentClaimer, protocols::topology_broker::StartStructClaimer, and protocols::topology_broker::LoopFragmentClaimer.

virtual core::pose::PoseOP protocols::topology_broker::TopologyClaimer::get_pose_from_claimer ( )

inlinevirtual

Reimplemented in protocols::topology_broker::TMHTopologySamplerClaimer.

virtual void protocols::topology_broker::TopologyClaimer::init_after_reading ( )

inlineprotectedvirtual

void protocols::topology_broker::TopologyClaimer::initialize_dofs	(	core::pose::Pose &	,
		claims::DofClaims const &	init_claims,
		claims::DofClaims &	failed_to_init
	)

virtual

initialize sequence ( for approved sequence claims given as init_claim ) Claimer searches init_claims for claims owned by *this

initialize dofs – e.g., torsions, jumps – Claimer searches init_claims for claims owned by *this

References tr, and type.

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

std::string const& protocols::topology_broker::TopologyClaimer::label ( ) const

inline

References label_.

virtual core::fragment::FragSetCOP protocols::topology_broker::TopologyClaimer::loop_frags ( core::kinematics::MoveMap & ) const

inlinevirtual

return fragments that can be used for loop-sampling... unfortunately some loop-samplers need fragments, rather then fragmovers (e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. ) overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling

Reimplemented in protocols::topology_broker::LoopFragmentClaimer.

virtual void protocols::topology_broker::TopologyClaimer::manipulate_cut_bias ( utility::vector1< core::Real > & )

inlinevirtual

multiply your bias to this – if its zero don't change that, i.e., multiply only this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues. Fragments can add their loop-fraction

Reimplemented in protocols::topology_broker::RigidChunkClaimer, and protocols::topology_broker::CutBiasClaimer.

weights::AbinitioMoverWeight& protocols::topology_broker::TopologyClaimer::mover_weight ( )

inline

References abinitio_mover_weight_.

virtual void protocols::topology_broker::TopologyClaimer::new_decoy ( )

inlinevirtual

a new decoy — random choices to be made ? make them here

Reimplemented in protocols::topology_broker::StartStructClaimer, protocols::topology_broker::CoordConstraintClaimer, protocols::topology_broker::ConstraintClaimer, protocols::topology_broker::FragmentJumpClaimer, protocols::topology_broker::RigidChunkClaimer, and protocols::topology_broker::DisulfJumpClaimer.

virtual void protocols::topology_broker::TopologyClaimer::new_decoy ( core::pose::Pose const & )

inlinevirtual

an input pose is given, i.e., a starting structure for resampling don't make random choices, base choices on given pose

Reimplemented in protocols::topology_broker::StartStructClaimer, protocols::topology_broker::CoordConstraintClaimer, protocols::topology_broker::FragmentJumpClaimer, protocols::topology_broker::RigidChunkClaimer, and protocols::topology_broker::DisulfJumpClaimer.

References new_decoy().

Referenced by new_decoy().

virtual bool protocols::topology_broker::TopologyClaimer::passes_filter	(	core::pose::Pose const &	,
		abinitio::StageID	,
		core::Real	,
		std::ostringstream &
	)

inlinevirtual

claimers can add movers to the RandomMover (Container). add your moves, make it dependent on stage if you want to. So far this is called only by abinitio... if you don't want to do anything special — don't overload this method! default: adds mover given by virtual call get_mover() with stage-dependent weight given by abinitio_mover_weight_

virtual void protocols::topology_broker::TopologyClaimer::pre_process ( core::pose::Pose & )

inlinevirtual

Reimplemented in protocols::topology_broker::TMHTopologySamplerClaimer, and protocols::topology_broker::MembraneTopologyClaimer.

void protocols::topology_broker::TopologyClaimer::read ( std::istream & is )

virtual

read definition of Claimer from setup file, i.e., a CLAIMER <type> ... END_CLAIMER block

Reimplemented in protocols::topology_broker::CutBiasClaimer.

References getline(), tag, tr, and type.

Referenced by protocols::topology_broker::operator>>().

void protocols::topology_broker::TopologyClaimer::read_mover_weight ( std::istream & is )

read mover weight from Stream. - so far recognizes: LargeStage, SmallStage, SmoothStage, AllStage

References type, and weight.

Referenced by protocols::topology_broker::TemplateFragmentClaimer::read_tag(), protocols::topology_broker::DisulfJumpClaimer::read_tag(), and protocols::topology_broker::TemplateJumpClaimer::read_tag().

bool protocols::topology_broker::TopologyClaimer::read_tag	(	std::string	tag,
		std::istream &	is
	)

protectedvirtual

References tr.

virtual void protocols::topology_broker::TopologyClaimer::receive_message ( ClaimerMessage & )

inlinevirtual

Reimplemented in protocols::topology_broker::RigidChunkClaimer.

void protocols::topology_broker::TopologyClaimer::set_broker ( TopologyBrokerCAP ptr )

inline

don't use this — it is called by TopologyBroker add_claim only

References broker_.

void protocols::topology_broker::TopologyClaimer::set_defaults ( )

protectedvirtual

Referenced by protocols::topology_broker::CoordConstraintClaimer::set_defaults(), protocols::topology_broker::RigidChunkClaimer::set_defaults(), and protocols::topology_broker::MetalloClaimer::set_defaults().

void protocols::topology_broker::TopologyClaimer::set_label ( std::string const & str )

inline

References label_, and protocols::kinmatch::str().

Referenced by protocols::topology_broker::FragmentClaimer::FragmentClaimer(), protocols::topology_broker::MetalloClaimer::init_after_reading(), protocols::topology_broker::LoopFragmentClaimer::LoopFragmentClaimer(), and protocols::topology_broker::SequenceClaimer::SequenceClaimer().

void protocols::topology_broker::TopologyClaimer::set_mover_weight ( weights::AbinitioMoverWeightOP wset )

inline

References abinitio_mover_weight_.

virtual void protocols::topology_broker::TopologyClaimer::set_pose_from_broker ( core::pose::Pose & )

inlinevirtual

Reimplemented in protocols::topology_broker::TMHTopologySamplerClaimer, and protocols::topology_broker::MembraneTopologyClaimer.

virtual void protocols::topology_broker::TopologyClaimer::switch_to_fullatom	(	core::pose::Pose &	,
		utility::vector1< bool >
	)		const

inlinevirtual

has this Claimer some side chain conformations to add? starts with bNeedToRepack true for all residues... if you have a sidechain —> copy it to pose and set needtoRepack false for this residue

Reimplemented in protocols::topology_broker::RigidChunkClaimer.

virtual std::string protocols::topology_broker::TopologyClaimer::type ( ) const

pure virtual

name of Claimer

Referenced by protocols::topology_broker::claims::CutClaim::show(), protocols::topology_broker::claims::BBClaim::show(), and protocols::topology_broker::claims::JumpClaim::show().

void protocols::topology_broker::TopologyClaimer::unknown_tag	(	std::string	tag,
		std::istream &	is
	)		const

private

References getline().

Member Data Documentation

weights::AbinitioMoverWeightOP protocols::topology_broker::TopologyClaimer::abinitio_mover_weight_

private

weight set .. how often shall this claimer's mover be sampled during different stages ?

Referenced by mover_weight(), set_mover_weight(), and TopologyClaimer().

TopologyBrokerCAP protocols::topology_broker::TopologyClaimer::broker_

private

oh, our master. (use broker() to get this ).

Referenced by broker(), and set_broker().

claims::DofClaims protocols::topology_broker::TopologyClaimer::current_claims_

private

currently accepted claims... dunno haven't used that yet.

Referenced by claim_accepted().

std::string protocols::topology_broker::TopologyClaimer::label_

private

a user defined string, can be used to send messages from claimer to claimer

Referenced by label(), and set_label().

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

src/protocols/topology_broker/TopologyClaimer.hh
src/protocols/topology_broker/TopologyClaimer.cc

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation