#include <SequenceClaimer.hh>

Public Member Functions
	SequenceClaimer ()

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

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

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

virtual void	generate_claims (claims::DofClaims &)
	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 std::string	type () const
	type() is specifying the output name of the TopologyClaimer More...

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 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_symmetry_claims (claims::SymmetryClaims &)
	generate claims that affect the sequence of the pose 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 ()

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

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

virtual void	init_after_reading ()

void	make_sequence_claim ()

void	set_sequence (std::string const &str)

void	set_priority (core::Real pr)

Protected Member Functions inherited from protocols::topology_broker::TopologyClaimer
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 void	set_defaults ()

Private Types
typedef TopologyClaimer	Parent

Private Member Functions
void	read_fasta_file (std::string file)

Private Attributes
std::string	rsd_type_set_

core::Real	priority_

std::string	input_sequence_

claims::SequenceClaimOP	sequence_claim_

Member Typedef Documentation

typedef TopologyClaimer protocols::topology_broker::SequenceClaimer::Parent

private

Constructor & Destructor Documentation

protocols::topology_broker::SequenceClaimer::SequenceClaimer ( )

References CENTROID, and chemical.

Referenced by clone().

protocols::topology_broker::SequenceClaimer::SequenceClaimer	(	std::string const &	sequence,
		std::string const &	label,
		std::string const &	rsd_type_set_identifier = `core::chemical::CENTROID`
	)

References protocols::topology_broker::TopologyClaimer::set_label().

Member Function Documentation

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

inlinestatic

Referenced by type().

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

virtual

clone it!

Implements protocols::topology_broker::TopologyClaimer.

Reimplemented in protocols::topology_broker::MetalloClaimer.

References SequenceClaimer().

void protocols::topology_broker::SequenceClaimer::generate_claims ( claims::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::TopologyClaimer.

Reimplemented in protocols::topology_broker::MetalloClaimer.

References protocols::topology_broker::TopologyClaimer::label(), and sequence_claim_.

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

void protocols::topology_broker::SequenceClaimer::generate_sequence_claims ( claims::DofClaims & )

virtual

generate claims that affect the sequence of the pose

Reimplemented from protocols::topology_broker::TopologyClaimer.

Reimplemented in protocols::topology_broker::MetalloClaimer.

References make_sequence_claim(), and sequence_claim_.

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

void protocols::topology_broker::SequenceClaimer::init_after_reading ( )