#include <TopologyClaimer.hh>

Inheritance diagram for protocols::topology_broker::TopologyClaimer:

Collaboration diagram for protocols::topology_broker::TopologyClaimer:

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

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

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

virtual void	finalize_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 (DofClaim const &)
	allow a claim from a foreign Claimer More...

virtual void	initialize_residues (core::pose::Pose &, SequenceClaimOP init_claim, 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	initialize_dofs (core::pose::Pose &, DofClaims const &init_claims, DofClaims &failed_to_init)
	initialize dofs – e.g., torsions, jumps – 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 (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 (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 &)

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
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

Definition at line 63 of file TopologyClaimer.hh.

Constructor & Destructor Documentation

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

virtual

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

Definition at line 49 of file TopologyClaimer.cc.

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

inline

Definition at line 67 of file TopologyClaimer.hh.

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

inline

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

Definition at line 70 of file TopologyClaimer.hh.

References abinitio_mover_weight_.

Member Function Documentation

virtual bool protocols::topology_broker::TopologyClaimer::accept_declined_claim ( 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.

Definition at line 113 of file TopologyClaimer.hh.

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.

Definition at line 121 of file TopologyClaimer.hh.

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_

Reimplemented in protocols::topology_broker::PcsEnergyController, protocols::topology_broker::PseudocontactShiftEnergyController, protocols::topology_broker::FibrilModelingClaimer, protocols::topology_broker::MembraneTopologyClaimer, protocols::topology_broker::AsymFoldandDockClaimer, and protocols::topology_broker::FoldandDockClaimer.

Definition at line 73 of file TopologyClaimer.cc.

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.

Definition at line 162 of file TopologyClaimer.hh.

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

inlinevirtual

allow a claim from a foreign Claimer

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

Definition at line 94 of file TopologyClaimer.hh.

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

inline

return the broker we are collaborating with

Definition at line 170 of file TopologyClaimer.hh.

References broker_.

Referenced by protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), protocols::topology_broker::CoordConstraintClaimer::generate_claims(), protocols::topology_broker::FragmentClaimer::get_sequence_region(), and protocols::topology_broker::MetalloClaimer::initialize_residues().

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

inlinevirtual

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

Definition at line 116 of file TopologyClaimer.hh.

References current_claims_.

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

pure virtual

clone it!

virtual void protocols::topology_broker::TopologyClaimer::finalize_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.

Definition at line 91 of file TopologyClaimer.hh.

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

inlinevirtual

generate first round of DOF claims

Definition at line 88 of file TopologyClaimer.hh.

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

inlinevirtual

generate claims that affect the sequence of the pose

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

Definition at line 85 of file TopologyClaimer.hh.

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

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

Definition at line 195 of file TopologyClaimer.hh.

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

inlineprotectedvirtual

Definition at line 201 of file TopologyClaimer.hh.

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

virtual

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

Definition at line 53 of file TopologyClaimer.cc.

References tr().

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

void protocols::topology_broker::TopologyClaimer::initialize_residues	(	core::pose::Pose &	,
		SequenceClaimOP	init_claim,
		DofClaims &	failed_to_init
	)

virtual

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

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

Definition at line 67 of file TopologyClaimer.cc.

References tr().

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

inline

Definition at line 182 of file TopologyClaimer.hh.

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.

Definition at line 126 of file TopologyClaimer.hh.

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.

Definition at line 109 of file TopologyClaimer.hh.

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

inline

Definition at line 155 of file TopologyClaimer.hh.

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::DisulfJumpClaimer, protocols::topology_broker::StartStructClaimer, protocols::topology_broker::CoordConstraintClaimer, protocols::topology_broker::ConstraintClaimer, protocols::topology_broker::JumpClaimer, and protocols::topology_broker::RigidChunkClaimer.

Definition at line 176 of file TopologyClaimer.hh.

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::DisulfJumpClaimer, protocols::topology_broker::StartStructClaimer, protocols::topology_broker::CoordConstraintClaimer, protocols::topology_broker::JumpClaimer, and protocols::topology_broker::RigidChunkClaimer.

Definition at line 180 of file TopologyClaimer.hh.

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_

Definition at line 132 of file TopologyClaimer.hh.

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.

Definition at line 108 of file TopologyClaimer.cc.

References tr().

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

Definition at line 86 of file TopologyClaimer.cc.

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

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

protectedvirtual

Definition at line 122 of file TopologyClaimer.cc.

Referenced by protocols::topology_broker::PcsEnergyController::read_tag(), protocols::topology_broker::ConstraintClaimer::read_tag(), protocols::topology_broker::FibrilModelingClaimer::read_tag(), protocols::topology_broker::CoordConstraintClaimer::read_tag(), protocols::topology_broker::SequenceClaimer::read_tag(), protocols::topology_broker::FragmentClaimer::read_tag(), and protocols::topology_broker::RigidChunkClaimer::read_tag().

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

inlinevirtual

Reimplemented in protocols::topology_broker::RigidChunkClaimer.

Definition at line 190 of file TopologyClaimer.hh.

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

inline

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

Definition at line 165 of file TopologyClaimer.hh.

References broker_.

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

protectedvirtual

Reimplemented in protocols::topology_broker::MetalloClaimer, protocols::topology_broker::RigidChunkClaimer, protocols::topology_broker::CoordConstraintClaimer, protocols::topology_broker::DensityScoringClaimer, protocols::topology_broker::PcsEnergyController, and protocols::topology_broker::PseudocontactShiftEnergyController.

Definition at line 129 of file TopologyClaimer.cc.

Referenced by protocols::topology_broker::DensityScoringClaimer::set_defaults(), 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

Definition at line 186 of file TopologyClaimer.hh.

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

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

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

inline

Definition at line 151 of file TopologyClaimer.hh.

References abinitio_mover_weight_.

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.

Definition at line 104 of file TopologyClaimer.hh.

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

pure virtual

name of Claimer

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

private

Definition at line 103 of file TopologyClaimer.cc.

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 ?

Definition at line 211 of file TopologyClaimer.hh.

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

TopologyBrokerCAP protocols::topology_broker::TopologyClaimer::broker_

private

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

Definition at line 214 of file TopologyClaimer.hh.

Referenced by broker(), and set_broker().

DofClaims protocols::topology_broker::TopologyClaimer::current_claims_

private

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

Definition at line 208 of file TopologyClaimer.hh.

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

Definition at line 217 of file TopologyClaimer.hh.

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