#include <FragmentClaimer.hh>

Public Member Functions
	FragmentClaimer ()

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

	FragmentClaimer (simple_moves::FragmentMoverOP, std::string mover_tag, weights::AbinitioMoverWeightOP weight, std::string label, core::fragment::FragSetOP fags)

	FragmentClaimer (simple_moves::FragmentMoverOP)

	FragmentClaimer (FragmentClaimer const &src)

	~FragmentClaimer ()

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

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

virtual void	initialize_dofs (core::pose::Pose &, claims::DofClaims const &init_claims, 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 (claims::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 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	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	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 (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
simple_moves::FragmentMover const &	mover () const

simple_moves::FragmentMoverOP	get_frag_mover_ptr ()

core::fragment::FragSetCOP	fragments ()

void	set_fragments (core::fragment::FragSetOP)

void	set_claim_right (claims::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_

claims::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...

Member Typedef Documentation

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

private

Constructor & Destructor Documentation

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

References movemap_.

Referenced by clone().

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

References fragments(), movemap_, and runtime_assert.

protocols::topology_broker::FragmentClaimer::FragmentClaimer	(	simple_moves::FragmentMoverOP	mover,
		std::string	mover_tag,
		weights::AbinitioMoverWeightOP	weight,
		std::string	label,
		core::fragment::FragSetOP	fags
	)

References fragments(), movemap_, runtime_assert, set_fragments(), and protocols::topology_broker::TopologyClaimer::set_label().

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

References fragments(), movemap_, mover_, mover_tag_, and runtime_assert.

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

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

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

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

Member Function Documentation

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

inlinestatic

Referenced by type().

bool protocols::topology_broker::FragmentClaimer::accept_declined_claim ( claims::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.

References movemap_, protocols::topology_broker::claims::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::StartStructClaimer, protocols::topology_broker::FragmentJumpClaimer, protocols::topology_broker::MetalloClaimer, protocols::topology_broker::TemplateJumpClaimer, protocols::topology_broker::TemplateFragmentClaimer, and protocols::topology_broker::DisulfJumpClaimer.

References FragmentClaimer().

core::fragment::FragSetCOP protocols::topology_broker::FragmentClaimer::fragments ( )

protected

References mover_.

Referenced by FragmentClaimer(), generate_claims(), and initialize_dofs().

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

virtual

generate first round of DOF claims

Reimplemented from protocols::topology_broker::TopologyClaimer.

Reimplemented in protocols::topology_broker::StartStructClaimer, protocols::topology_broker::MetalloClaimer, protocols::topology_broker::FragmentJumpClaimer, and protocols::topology_broker::DisulfJumpClaimer.

References core::id::BB, protocols::topology_broker::TopologyClaimer::broker(), claim_right_, for(), fragments(), protocols::topology_broker::TopologyClaimer::label(), length, protocols::topology_broker::claims::SequenceClaim::length(), movemap_, mover_, mover_tag_, protocols::topology_broker::SequenceNumberResolver::offset(), region_, protocols::topology_broker::TopologyBroker::resolve_sequence_label(), protocols::topology_broker::TopologyBroker::sequence_number_resolver(), core::kinematics::MoveMap::set_bb(), set_fragments(), core::kinematics::MoveMap::set_jump(), protocols::loops::Loops::size(), protocols::loops::start, protocols::loops::Loops::switch_movemap(), tr, and utility_exit_with_message.

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

protected

References mover_.

Referenced by protocols::topology_broker::FragmentJumpClaimer::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.

References mover_.

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

References active_sequence_labels_, protocols::topology_broker::TopologyClaimer::broker(), protocols::topology_broker::SequenceNumberResolver::find_global_pose_number(), protocols::topology_broker::claims::SequenceClaim::length(), protocols::topology_broker::TopologyBroker::resolve_sequence_label(), protocols::topology_broker::TopologyBroker::sequence_number_resolver(), and tr.

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

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

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

virtual

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

Reimplemented from protocols::topology_broker::TopologyClaimer.

Reimplemented in protocols::topology_broker::MetalloClaimer, protocols::topology_broker::FragmentJumpClaimer, protocols::topology_broker::StartStructClaimer, and protocols::topology_broker::DisulfJumpClaimer.

References bInitDofs_, core::pose::Pose::fold_tree(), fragments(), protocols::topology_broker::TopologyClaimer::label(), movemap_, mover_, core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_jump(), core::kinematics::simple_visualize_fold_tree_and_movemap(), tr, and type().

Referenced by protocols::topology_broker::DisulfJumpClaimer::initialize_dofs(), protocols::topology_broker::StartStructClaimer::initialize_dofs(), and protocols::topology_broker::FragmentJumpClaimer::initialize_dofs().

simple_moves::FragmentMover const& protocols::topology_broker::FragmentClaimer::mover ( ) const

inlineprotected

References mover_.

Referenced by protocols::topology_broker::StartStructClaimer::generate_init_frags(), protocols::topology_broker::StartStructClaimer::initialize_dofs(), protocols::topology_broker::LoopFragmentClaimer::loop_frags(), protocols::topology_broker::DisulfJumpClaimer::new_decoy(), and set_mover().

std::string const& protocols::topology_broker::FragmentClaimer::mover_tag ( ) const

inline

References mover_tag_.

Referenced by protocols::topology_broker::FragmentJumpClaimer::generate_claims(), protocols::topology_broker::FragmentJumpClaimer::init_jumps(), and protocols::topology_broker::DisulfJumpClaimer::new_decoy().

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

protectedvirtual

Reimplemented from protocols::topology_broker::TopologyClaimer.

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

References active_sequence_labels_, file, protocols::loops::PoseNumberedLoopFileReader::hijack_loop_reading_code_set_loop_line_begin_token(), protocols::topology_broker::TopologyClaimer::label(), loops, protocols::loops::PoseNumberedLoopFileReader::read_pose_numbered_loops_file(), protocols::topology_broker::TopologyClaimer::read_tag(), region_, tr, type(), and utility_exit_with_message.

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

void protocols::topology_broker::FragmentClaimer::set_bInitDofs ( bool set )

inline

References bInitDofs_.

Referenced by protocols::topology_broker::DisulfJumpClaimer::DisulfJumpClaimer(), protocols::topology_broker::FragmentJumpClaimer::FragmentJumpClaimer(), and protocols::topology_broker::StartStructClaimer::StartStructClaimer().

void protocols::topology_broker::FragmentClaimer::set_claim_right ( claims::DofClaim::ClaimRight setting )

inlineprotected

References claim_right_.

Referenced by protocols::topology_broker::StartStructClaimer::StartStructClaimer().

void protocols::topology_broker::FragmentClaimer::set_fragments ( core::fragment::FragSetOP frags )

protected

References mover_.

Referenced by FragmentClaimer(), generate_claims(), and protocols::topology_broker::StartStructClaimer::generate_init_frags().

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

References mover(), and mover_.

Referenced by protocols::topology_broker::FragmentJumpClaimer::generate_claims(), protocols::topology_broker::StartStructClaimer::generate_init_frags(), protocols::topology_broker::FragmentJumpClaimer::initialize_dofs(), protocols::topology_broker::DisulfJumpClaimer::new_decoy(), and protocols::topology_broker::TemplateFragmentClaimer::read_config_file().

void protocols::topology_broker::FragmentClaimer::set_mover_tag ( std::string const & str )

References mover_, mover_tag_, and protocols::kinmatch::str().

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

inlinevirtual

type() is specifying the output name of the TopologyClaimer

Implements protocols::topology_broker::TopologyClaimer.

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

References _static_type_name().

Referenced by initialize_dofs(), and read_tag().

Member Data Documentation

utility::vector1< std::string > protocols::topology_broker::FragmentClaimer::active_sequence_labels_

private

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

Referenced by get_sequence_region(), init_after_reading(), and read_tag().

bool protocols::topology_broker::FragmentClaimer::bInitDofs_

private

Referenced by FragmentClaimer(), initialize_dofs(), and set_bInitDofs().

claims::DofClaim::ClaimRight protocols::topology_broker::FragmentClaimer::claim_right_

private

Referenced by FragmentClaimer(), generate_claims(), and set_claim_right().

core::kinematics::MoveMapOP protocols::topology_broker::FragmentClaimer::movemap_

protected

Referenced by accept_declined_claim(), FragmentClaimer(), generate_claims(), protocols::topology_broker::DisulfJumpClaimer::generate_claims(), protocols::topology_broker::FragmentJumpClaimer::generate_claims(), protocols::topology_broker::FragmentJumpClaimer::init_jumps(), initialize_dofs(), and protocols::topology_broker::DisulfJumpClaimer::new_decoy().

simple_moves::FragmentMoverOP protocols::topology_broker::FragmentClaimer::mover_

private

Referenced by FragmentClaimer(), fragments(), generate_claims(), get_frag_mover_ptr(), get_mover(), initialize_dofs(), mover(), set_fragments(), set_mover(), and set_mover_tag().

std::string protocols::topology_broker::FragmentClaimer::mover_tag_

private

Referenced by FragmentClaimer(), generate_claims(), mover_tag(), and set_mover_tag().

loops::Loops protocols::topology_broker::FragmentClaimer::region_

private

regions that can be used for fragment insertions

Referenced by FragmentClaimer(), generate_claims(), and read_tag().

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

src/protocols/topology_broker/FragmentClaimer.hh
src/protocols/topology_broker/FragmentClaimer.cc

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Private Types

Private Attributes

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation