#include <FibrilModelingClaimer.hh>

Inheritance diagram for protocols::topology_broker::FibrilModelingClaimer:

Collaboration diagram for protocols::topology_broker::FibrilModelingClaimer:

Public Member Functions
	FibrilModelingClaimer ()

	FibrilModelingClaimer (core::pose::Pose const &input_pose, loops::Loops rigid, int shift=0)

	FibrilModelingClaimer (core::pose::Pose const &input_pose, loops::Loops rigid, loops::Loops input_rigid)

void	make_fibril (core::pose::Pose &pose)

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

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

virtual void	add_mover (moves::RandomMover &random_mover, core::pose::Pose const &pose, abinitio::StageID stageID, core::scoring::ScoreFunction const &scorefxn, core::Real progress)
	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	initialize_dofs (core::pose::Pose &, DofClaims const &init_claims, DofClaims &)
	initialize dofs – e.g., torsions, jumps – Claimer searches init_claims for claims owned by *this More...

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

virtual bool	allow_claim (DofClaim const &)
	has to decline foreign BB claims for slave regions 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 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 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 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...

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

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 ()

virtual void	init_after_reading ()

Private Types
typedef TopologyClaimer	Parent

Private Attributes
core::pose::Pose	input_pose_
	monomer pose More...

loops::Loops	rigid_core_
	regions that can be used for rigid core More...

loops::Loops	input_rigid_core_

bool	bAlign_
	align to the monomer before create symmetry More...

int	sequence_shift_

core::conformation::symmetry::SymmetryInfoOP	symminfo_
	symmetry information More...

Member Typedef Documentation

typedef TopologyClaimer protocols::topology_broker::FibrilModelingClaimer::Parent

private

Constructor & Destructor Documentation

protocols::topology_broker::FibrilModelingClaimer::FibrilModelingClaimer ( )

Referenced by clone().

protocols::topology_broker::FibrilModelingClaimer::FibrilModelingClaimer	(	core::pose::Pose const &	input_pose,
		loops::Loops	rigid,
		int	shift = `0`
	)

References bAlign_, input_rigid_core_, protocols::loops::Loops::make_sequence_shift(), rigid_core_, and sequence_shift_.

protocols::topology_broker::FibrilModelingClaimer::FibrilModelingClaimer	(	core::pose::Pose const &	input_pose,
		loops::Loops	rigid,
		loops::Loops	input_rigid
	)

References bAlign_, input_rigid_core_, rigid_core_, and sequence_shift_.

Member Function Documentation

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

inlinestatic

Referenced by type().

void protocols::topology_broker::FibrilModelingClaimer::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 from protocols::topology_broker::TopologyClaimer.

References protocols::moves::MoverContainer::add_mover().

bool protocols::topology_broker::FibrilModelingClaimer::allow_claim ( DofClaim const & foreign_claim)

virtual

has to decline foreign BB claims for slave regions

Reimplemented from protocols::topology_broker::TopologyClaimer.

References protocols::topology_broker::DofClaim::BB, core::conformation::symmetry::is_symmetric(), protocols::topology_broker::DofClaim::owner(), protocols::topology_broker::DofClaim::pos(), symminfo_, and protocols::topology_broker::DofClaim::type().

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

inlinevirtual

clone it!

Implements protocols::topology_broker::TopologyClaimer.

References FibrilModelingClaimer().

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

virtual

generate first round of DOF claims

Reimplemented from protocols::topology_broker::TopologyClaimer.

References core::pose::Pose::conformation(), core::kinematics::FoldTree::cutpoints(), core::conformation::Conformation::fold_tree(), protocols::topology_broker::DofClaim::INIT, and input_pose_.

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