#include <FragmentClaimer.hh>

Inheritance diagram for protocols::topology_broker::FragmentClaimer:

Collaboration diagram for protocols::topology_broker::FragmentClaimer:

Public Member Functions
	FragmentClaimer ()

	FragmentClaimer (simple_moves::FragmentMoverOP, std::string mover_tag, weights::AbinitioMoverWeightOP weight)

	FragmentClaimer (simple_moves::FragmentMoverOP)

	FragmentClaimer (FragmentClaimer const &src)

	~FragmentClaimer ()

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

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

virtual void	initialize_dofs (core::pose::Pose &, DofClaims const &init_claims, DofClaims &failed_to_init)
	is called after all round1 claims have been approved or retracted – additional claims can be issued in this round 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...

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

void	set_mover (simple_moves::FragmentMoverOP mover)

void	set_mover_tag (std::string const &str)

void	set_bInitDofs (bool set)

std::string const &	mover_tag () const

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...

void	get_sequence_region (std::set< core::Size > &start_region) const

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	generate_sequence_claims (DofClaims &)
	generate claims that affect the sequence of the pose 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	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 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 &)

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

Protected Member Functions
simple_moves::FragmentMover const &	mover () const

simple_moves::FragmentMoverOP	get_frag_mover_ptr ()

void	set_claim_right (DofClaim::ClaimRight setting)

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

virtual void	init_after_reading ()

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

Protected Attributes
core::kinematics::MoveMapOP	movemap_

Private Types
typedef TopologyClaimer	Parent

Private Attributes
simple_moves::FragmentMoverOP	mover_

std::string	mover_tag_

bool	bInitDofs_

DofClaim::ClaimRight	claim_right_

loops::Loops	region_
	regions that can be used for fragment insertions More...

utility::vector1< std::string >	active_sequence_labels_
	if non-empty this claimer operates only on the sequences with these labels... create std::set< Size > with residue numbers by get_sequence_region(); More...

Detailed Description

Definition at line 48 of file FragmentClaimer.hh.

Member Typedef Documentation

typedef TopologyClaimer protocols::topology_broker::FragmentClaimer::Parent

private

Definition at line 49 of file FragmentClaimer.hh.

Constructor & Destructor Documentation

protocols::topology_broker::FragmentClaimer::FragmentClaimer ( )

Definition at line 61 of file FragmentClaimer.cc.

References movemap_.

Referenced by clone().

protocols::topology_broker::FragmentClaimer::FragmentClaimer	(	simple_moves::FragmentMoverOP	mover,
		std::string	mover_tag,
		weights::AbinitioMoverWeightOP	weight
	)

Definition at line 70 of file FragmentClaimer.cc.

References movemap_.

protocols::topology_broker::FragmentClaimer::FragmentClaimer ( simple_moves::FragmentMoverOP mover)

Definition at line 80 of file FragmentClaimer.cc.

References movemap_, mover_, and mover_tag_.

protocols::topology_broker::FragmentClaimer::FragmentClaimer ( FragmentClaimer const & src)

SHALLOW COPY to duplicate the pre-9/7/2009 behavior provided by the compiler.

Definition at line 90 of file FragmentClaimer.cc.

References bInitDofs_, claim_right_, movemap_, mover_, mover_tag_, and region_.

protocols::topology_broker::FragmentClaimer::~FragmentClaimer ( )

Definition at line 102 of file FragmentClaimer.cc.

Member Function Documentation

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

inlinestatic

Definition at line 76 of file FragmentClaimer.hh.

Referenced by type().

bool protocols::topology_broker::FragmentClaimer::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 158 of file FragmentClaimer.cc.

References movemap_, protocols::topology_broker::DofClaim::toggle(), and tr().

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

inlinevirtual

clone it!

Implements protocols::topology_broker::TopologyClaimer.

Reimplemented in protocols::topology_broker::DisulfJumpClaimer, protocols::topology_broker::StartStructClaimer, protocols::topology_broker::JumpClaimer, protocols::topology_broker::MetalloClaimer, protocols::topology_broker::TemplateJumpClaimer, and protocols::topology_broker::TemplateFragmentClaimer.

Definition at line 58 of file FragmentClaimer.hh.

References FragmentClaimer().

void protocols::topology_broker::FragmentClaimer::generate_claims ( DofClaims & )

virtual

generate first round of DOF claims

Reimplemented from protocols::topology_broker::TopologyClaimer.

Reimplemented in protocols::topology_broker::DisulfJumpClaimer, protocols::topology_broker::MetalloClaimer, and protocols::topology_broker::JumpClaimer.

Definition at line 117 of file FragmentClaimer.cc.

References core::id::BB, claim_right_, for(), movemap_, mover_, region_, protocols::loops::Loops::size(), protocols::loops::start, protocols::loops::Loops::switch_movemap(), and tr().

simple_moves::FragmentMoverOP protocols::topology_broker::FragmentClaimer::get_frag_mover_ptr ( )

protected

Definition at line 174 of file FragmentClaimer.cc.

References mover_.

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

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

virtual

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

Reimplemented from protocols::topology_broker::TopologyClaimer.

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

Definition at line 260 of file FragmentClaimer.cc.

References mover_.

void protocols::topology_broker::FragmentClaimer::get_sequence_region ( std::set< core::Size > & start_region) const

Definition at line 104 of file FragmentClaimer.cc.

References active_sequence_labels_, protocols::topology_broker::TopologyClaimer::broker(), protocols::topology_broker::SequenceClaim::last_residue(), protocols::topology_broker::SequenceClaim::offset(), protocols::topology_broker::TopologyBroker::resolve_sequence_label(), and tr().

Referenced by protocols::topology_broker::StartStructClaimer::generate_init_frags(), and protocols::topology_broker::JumpClaimer::init_jumps().

void protocols::topology_broker::FragmentClaimer::init_after_reading ( )

protectedvirtual

Reimplemented from protocols::topology_broker::TopologyClaimer.

Reimplemented in protocols::topology_broker::MetalloClaimer, protocols::topology_broker::TemplateJumpClaimer, and protocols::topology_broker::TemplateFragmentClaimer.

Definition at line 254 of file FragmentClaimer.cc.

References active_sequence_labels_.

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