#include <DensityScoringClaimer.hh>

Inheritance diagram for protocols::topology_broker::DensityScoringClaimer:

Collaboration diagram for protocols::topology_broker::DensityScoringClaimer:

Public Member Functions
	DensityScoringClaimer ()

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

virtual void	initialize_residues (core::pose::Pose &, SequenceClaimOP init_claim, DofClaims &failed_to_init)
	mainly calls parent function... but is also used to figure out what residue number we are jumping to. More...

virtual void	generate_claims (protocols::topology_broker::DofClaims &dc)
	is called after all round1 claims have been approved or retracted – additional claims can be issued in this round if this Sequence has been moved from position 1 — needs to issue a fixed CUT in the fold-tree More...

virtual void	initialize_dofs (core::pose::Pose &pose, DofClaims const &, DofClaims &failed_to_init)
	initialize dofs – e.g., torsions, jumps – Claimer searches init_claims for claims owned by *this More...

virtual std::string	type () const
	type() is specifying the output name of the TopologyClaimer More...

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

virtual bool	accept_declined_claim (DofClaim const &was_declined)
	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...

Public Member Functions inherited from protocols::topology_broker::SequenceClaimer
	SequenceClaimer ()

	SequenceClaimer (std::string const &sequence, std::string const &rsd_type_set_identifier, std::string label)

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

core::Size	offset ()

void	set_sequence (std::string const &str)

Public Member Functions inherited from protocols::topology_broker::TopologyClaimer
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 void	read (std::istream &)
	read definition of Claimer from setup file, i.e., a CLAIMER <type> ... END_CLAIMER block 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	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 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 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 &)

Static Public Member Functions
static std::string	_static_type_name ()

Static Public Member Functions inherited from protocols::topology_broker::SequenceClaimer
static std::string	_static_type_name ()

Protected Member Functions
virtual void	set_defaults ()

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

virtual void	init_after_reading ()

Private Attributes
core::Size	anchor_residue_

std::string	anchor_chain_

core::Size	resolved_anchor_residue_

core::Size	vrt_id_

Detailed Description

Definition at line 62 of file DensityScoringClaimer.hh.

Constructor & Destructor Documentation

protocols::topology_broker::DensityScoringClaimer::DensityScoringClaimer ( )

Definition at line 60 of file DensityScoringClaimer.cc.

Member Function Documentation

static std::string protocols::topology_broker::DensityScoringClaimer::_static_type_name ( )

inlinestatic

Definition at line 83 of file DensityScoringClaimer.hh.

Referenced by type().

bool protocols::topology_broker::DensityScoringClaimer::accept_declined_claim ( DofClaim const & )

virtual

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 from protocols::topology_broker::TopologyClaimer.

Definition at line 110 of file DensityScoringClaimer.cc.

References tr().

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

virtual

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

Reimplemented from protocols::topology_broker::TopologyClaimer.

Definition at line 89 of file DensityScoringClaimer.cc.

TopologyClaimerOP protocols::topology_broker::DensityScoringClaimer::clone ( ) const

virtual

clone it!

Reimplemented from protocols::topology_broker::SequenceClaimer.

Definition at line 84 of file DensityScoringClaimer.cc.

void protocols::topology_broker::DensityScoringClaimer::generate_claims ( protocols::topology_broker::DofClaims & new_claims)

virtual

is called after all round1 claims have been approved or retracted – additional claims can be issued in this round if this Sequence has been moved from position 1 — needs to issue a fixed CUT in the fold-tree

Reimplemented from protocols::topology_broker::SequenceClaimer.

Definition at line 72 of file DensityScoringClaimer.cc.

References protocols::topology_broker::DofClaim::EXCLUSIVE, and protocols::topology_broker::SequenceClaimer::generate_claims().

void protocols::topology_broker::DensityScoringClaimer::init_after_reading ( )

protectedvirtual

Reimplemented from protocols::topology_broker::SequenceClaimer.

Definition at line 116 of file DensityScoringClaimer.cc.

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

inlinevirtual

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

Reimplemented from protocols::topology_broker::SequenceClaimer.

Definition at line 73 of file DensityScoringClaimer.hh.

References protocols::topology_broker::SequenceClaimer::initialize_dofs().

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