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 <DisulfJumpClaimer.hh>

Public Member Functions
	DisulfJumpClaimer ()

	~DisulfJumpClaimer ()

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

void	generate_jump_frags (protocols::jumping::DisulfPairingLibrary const &lib, core::fragment::FrameList &all_frames) const

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

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

virtual std::string	type () const
	type() is specifying the output name of the TopologyClaimer 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	read_tag (std::string tag, std::istream &is)

Public Member Functions inherited from protocols::topology_broker::FragmentClaimer
	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 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...

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 (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 &)

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 ()

Private Types
typedef FragmentClaimer	Parent

Private Attributes
utility::vector1 < claims::JumpClaimOP >	local_disulf_data_

utility::vector1 < protocols::jumping::DisulfPairing >	all_jump_pairings_

core::fragment::FrameList	all_frames_

bool	bKeepJumpsFromInputPose_

Additional Inherited Members
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)

virtual void	init_after_reading ()

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

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::DisulfJumpClaimer::Parent

private

Constructor & Destructor Documentation

protocols::topology_broker::DisulfJumpClaimer::DisulfJumpClaimer ( )

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

Referenced by clone().

protocols::topology_broker::DisulfJumpClaimer::~DisulfJumpClaimer ( )

Member Function Documentation

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

inlinestatic

Referenced by type().

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

virtual

clone it!

Reimplemented from protocols::topology_broker::FragmentClaimer.

References DisulfJumpClaimer().

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

virtual

generate first round of DOF claims

Reimplemented from protocols::topology_broker::FragmentClaimer.

References all_jump_pairings_, utility::pointer::owning_ptr< T >::get(), protocols::topology_broker::claims::DofClaim::INIT, local_disulf_data_, protocols::topology_broker::FragmentClaimer::movemap_, protocols::jumping::DisulfPairing::pos1, protocols::jumping::DisulfPairing::pos2, protocols::jumping::DisulfPairing::seq_sep, core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_jump(), and protocols::jumping::DisulfPairing::ss_type.

void protocols::topology_broker::DisulfJumpClaimer::generate_jump_frags	(	protocols::jumping::DisulfPairingLibrary const &	lib,
		core::fragment::FrameList &	all_frames
	)		const

References all_jump_pairings_, protocols::jumping::DisulfPairingLibrary::create_jump_fragments(), frame(), local_disulf_data_, and runtime_assert.

Referenced by new_decoy().

void protocols::topology_broker::DisulfJumpClaimer::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::FragmentClaimer.

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

void protocols::topology_broker::DisulfJumpClaimer::new_decoy ( core::pose::Pose const & )

virtual

an input pose is given, i.e., a starting structure for resampling don't make random choices, base choices on given pose

Reimplemented from protocols::topology_broker::TopologyClaimer.

References new_decoy().

void protocols::topology_broker::DisulfJumpClaimer::new_decoy ( )

virtual

a new decoy — random choices to be made ? make them here

Reimplemented from protocols::topology_broker::TopologyClaimer.

References all_frames_, protocols::simple_moves::ClassicFragmentMover::enable_end_bias_check(), generate_jump_frags(), protocols::jumping::StandardDisulfPairingLibrary::get_instance(), protocols::topology_broker::FragmentClaimer::movemap_, protocols::topology_broker::FragmentClaimer::mover(), protocols::topology_broker::FragmentClaimer::mover_tag(), protocols::simple_moves::ClassicFragmentMover::set_check_ss(), protocols::topology_broker::FragmentClaimer::set_mover(), and protocols::moves::Mover::type().

Referenced by new_decoy().

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

virtual

Reimplemented from protocols::topology_broker::FragmentClaimer.

References bKeepJumpsFromInputPose_, local_disulf_data_, protocols::topology_broker::TopologyClaimer::read_mover_weight(), protocols::topology_broker::FragmentClaimer::read_tag(), ss1, and ss2.

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

inlinevirtual

type() is specifying the output name of the TopologyClaimer

Reimplemented from protocols::topology_broker::FragmentClaimer.

References _static_type_name().

Member Data Documentation

core::fragment::FrameList protocols::topology_broker::DisulfJumpClaimer::all_frames_

private

Referenced by new_decoy().

utility::vector1< protocols::jumping::DisulfPairing > protocols::topology_broker::DisulfJumpClaimer::all_jump_pairings_

private

Referenced by generate_claims(), and generate_jump_frags().

bool protocols::topology_broker::DisulfJumpClaimer::bKeepJumpsFromInputPose_

private

Referenced by read_tag().

utility::vector1< claims::JumpClaimOP > protocols::topology_broker::DisulfJumpClaimer::local_disulf_data_

private

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

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

symlinks/rosetta/src/protocols/topology_broker/DisulfJumpClaimer.hh
symlinks/rosetta/src/protocols/topology_broker/DisulfJumpClaimer.cc

Public Member Functions

Static Public Member Functions

Private Types

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation