Claimer that works with the old system of BaseJumpSetup it supports only JumpFrames of type [ BBTorsion ] UpJump DownJump [ BBTorsion ] the class JumpSample is still used to transport the information jumps and jump_atoms, but cuts are ignored all functionality of JumpSample is not used anymore. More...

#include <FragmentJumpClaimer.hh>

Inheritance diagram for protocols::topology_broker::FragmentJumpClaimer:

[legend]

Public Member Functions
	FragmentJumpClaimer ()

	FragmentJumpClaimer (jumping::BaseJumpSetupOP jump_def, std::string const &mover_tag="JumpMove", weights::AbinitioMoverWeightOP weight=nullptr)

	FragmentJumpClaimer (FragmentJumpClaimer const &src)

	~FragmentJumpClaimer () override

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

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

void	new_decoy (core::pose::Pose const &) override
	an input pose is given, i.e., a starting structure for resampling don't make random choices, base choices on given pose More...

void	new_decoy () override
	a new decoy — random choices to be made ? make them here More...

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

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

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

Public Member Functions inherited from protocols::topology_broker::FragmentClaimer
	FragmentClaimer ()

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

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

	FragmentClaimer (simple_moves::FragmentMoverOP)

	FragmentClaimer (FragmentClaimer const &src)

	~FragmentClaimer () override

FragmentClaimerOP	shared_from_this ()

bool	accept_declined_claim (claims::DofClaim const &was_declined) override
	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...

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

moves::MoverOP	get_mover (core::pose::Pose const &) const override
	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
	~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_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...

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 ()

Static Public Member Functions inherited from protocols::topology_broker::FragmentClaimer
static std::string	_static_type_name ()

Protected Member Functions
void	set_jump_def (jumping::BaseJumpSetupOP jump_def)

virtual void	generate_claims (claims::DofClaims &, std::string, std::string)

jumping::BaseJumpSetupOP	jump_def ()

void	set_keep_jumps_from_input_pose (bool setting)

void	init_jumps ()

Protected Member Functions inherited from protocols::topology_broker::FragmentClaimer
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)

void	init_after_reading () override

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

Private Types
typedef FragmentClaimer	Parent

Private Attributes
jumping::BaseJumpSetupOP	jump_def_

jumping::JumpSample	current_jumps_

simple_moves::ClassicFragmentMoverOP	init_mover_

bool	bKeepJumpsFromInputPose_

core::pose::Pose	input_pose_

bool	discard_jumps_

Additional Inherited Members
Protected Attributes inherited from protocols::topology_broker::FragmentClaimer
core::kinematics::MoveMapOP	movemap_

Detailed Description

Claimer that works with the old system of BaseJumpSetup it supports only JumpFrames of type [ BBTorsion ] UpJump DownJump [ BBTorsion ] the class JumpSample is still used to transport the information jumps and jump_atoms, but cuts are ignored all functionality of JumpSample is not used anymore.

Member Typedef Documentation

typedef FragmentClaimer protocols::topology_broker::FragmentJumpClaimer::Parent

private

Constructor & Destructor Documentation

protocols::topology_broker::FragmentJumpClaimer::FragmentJumpClaimer ( )

References protocols::topology_broker::FragmentClaimer::set_bInitDofs().

protocols::topology_broker::FragmentJumpClaimer::FragmentJumpClaimer	(	jumping::BaseJumpSetupOP	jump_def,
		std::string const &	mover_tag = `"JumpMove"`,
		weights::AbinitioMoverWeightOP	weight = `nullptr`
	)

References protocols::topology_broker::FragmentClaimer::set_bInitDofs().

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

References bKeepJumpsFromInputPose_, current_jumps_, init_mover_, and jump_def_.

protocols::topology_broker::FragmentJumpClaimer::~FragmentJumpClaimer ( )

overridedefault

Member Function Documentation

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

inlinestatic

Referenced by type().

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

overridevirtual

clone it!

Reimplemented from protocols::topology_broker::FragmentClaimer.

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

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

overridevirtual

generate first round of DOF claims

Reimplemented from protocols::topology_broker::FragmentClaimer.

Reimplemented in protocols::topology_broker::MetalloClaimer.

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

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

void protocols::topology_broker::FragmentJumpClaimer::generate_claims	(	claims::DofClaims &	new_claims,
		std::string	uplabel,
		std::string	downlabel
	)

protectedvirtual

void protocols::topology_broker::FragmentJumpClaimer::init_jumps ( )

protected

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