#include <SymmetryClaimer.hh>

Inheritance diagram for protocols::topology_broker::SymmetryClaimer:

[legend]

Public Member Functions
	SymmetryClaimer ()

	~SymmetryClaimer () override=default

	SymmetryClaimer (SymmetryClaimer const &src)

SymmetryClaimerOP	shared_from_this ()

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

std::string	type () const override
	name of Claimer More...

void	generate_symmetry_claims (claims::SymmetryClaims &) override
	generate claims that affect the sequence of the pose More...

virtual void	symmetry_duplicate (claims::DofClaims &, core::pose::Pose &)

Public Member Functions inherited from protocols::topology_broker::TopologyClaimer
	~TopologyClaimer () override=default
	Automatically generated virtual destructor for class deriving directly from VirtualBase. More...

	TopologyClaimer ()

	TopologyClaimer (weights::AbinitioMoverWeightOP weight)
	construct with weight-set ( how important is mover for different abinitio stages ? ) More...

TopologyClaimerCOP	get_self_ptr () const
	self pointers More...

TopologyClaimerOP	get_self_ptr ()

TopologyClaimerCAP	get_self_weak_ptr () const

TopologyClaimerAP	get_self_weak_ptr ()

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_claims (claims::DofClaims &)
	generate first round of DOF claims 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
bool	read_tag (std::string tag, std::istream &) override

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::conformation::symmetry::SymmDataOP	symm_data_

core::Size	asymmetric_res_

Member Typedef Documentation

◆ Parent

typedef TopologyClaimer protocols::topology_broker::SymmetryClaimer::Parent

private

Constructor & Destructor Documentation

◆ SymmetryClaimer() [1/2]

protocols::topology_broker::SymmetryClaimer::SymmetryClaimer ( )

◆ ~SymmetryClaimer()

protocols::topology_broker::SymmetryClaimer::~SymmetryClaimer ( )

overridedefault

◆ SymmetryClaimer() [2/2]

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

Member Function Documentation

◆ _static_type_name()

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

inlinestatic

Referenced by type().

◆ clone()

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

inlineoverridevirtual

clone it!

Implements protocols::topology_broker::TopologyClaimer.

◆ generate_symmetry_claims()

void protocols::topology_broker::SymmetryClaimer::generate_symmetry_claims ( claims::SymmetryClaims & )

overridevirtual

generate claims that affect the sequence of the pose

Reimplemented from protocols::topology_broker::TopologyClaimer.

References protocols::topology_broker::TopologyClaimer::get_self_weak_ptr(), protocols::topology_broker::claims::DofClaim::INIT, and symm_data_.

◆ read_tag()

bool protocols::topology_broker::SymmetryClaimer::read_tag	(	std::string	tag,
		std::istream &	in
	)

overrideprotectedvirtual

Reimplemented from protocols::topology_broker::TopologyClaimer.

References core::conformation::membrane::in, protocols::topology_broker::TopologyClaimer::read_tag(), symm_data_, and tr().

◆ shared_from_this()

SymmetryClaimerOP protocols::topology_broker::SymmetryClaimer::shared_from_this ( )

inline

◆ symmetry_duplicate()

void protocols::topology_broker::SymmetryClaimer::symmetry_duplicate	(	claims::DofClaims &	pre_accepted,
		core::pose::Pose &	pose
	)

virtual

References core::pose::Pose::annotated_sequence(), core::pose::Pose::append_residue_by_jump(), asymmetric_res_, core::chemical::CENTROID, core::conformation::ResidueFactory::create_residue(), core::conformation::symmetry::VirtualCoordinate::get_origin(), protocols::topology_broker::TopologyClaimer::get_self_weak_ptr(), core::conformation::symmetry::VirtualCoordinate::get_x(), core::conformation::symmetry::VirtualCoordinate::get_y(), core::pose::make_pose_from_sequence(), core::pose::Pose::size(), symm_data_, and core::pose::virtual_type_for_pose().

◆ type()

std::string protocols::topology_broker::SymmetryClaimer::type ( ) const

inlineoverridevirtual

name of Claimer

Implements protocols::topology_broker::TopologyClaimer.

References _static_type_name().

Member Data Documentation

◆ asymmetric_res_

core::Size protocols::topology_broker::SymmetryClaimer::asymmetric_res_

private

Referenced by symmetry_duplicate().

◆ symm_data_

core::conformation::symmetry::SymmDataOP protocols::topology_broker::SymmetryClaimer::symm_data_

private

Referenced by generate_symmetry_claims(), read_tag(), and symmetry_duplicate().

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

src/protocols/topology_broker/SymmetryClaimer.hh
src/protocols/topology_broker/SymmetryClaimer.cc

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Types

Private Attributes

Member Typedef Documentation

◆ Parent

Constructor & Destructor Documentation

◆ SymmetryClaimer() [1/2]

◆ ~SymmetryClaimer()

◆ SymmetryClaimer() [2/2]

Member Function Documentation

◆ _static_type_name()

◆ clone()

◆ generate_symmetry_claims()

◆ read_tag()

◆ shared_from_this()

◆ symmetry_duplicate()

◆ type()

Member Data Documentation

◆ asymmetric_res_

◆ symm_data_