defines a rigid part of structure... imagine a loop-relax application core structure is fixed via jumps and loops can move the rigid chunk takes a definition of rigid regions in form of an instance of Loops (just taken as bunch of start-end residue numbers — here defining the rigid residues and not the loops). the rigid chunk to keep its integrity will need jumps, the claimer will reuse jumps if somebody else claims them, or submit in finalize_claims his own jumps, if not enough jumps are present. in "bExclusive_ mode" the RigidChunk will reclaim any jump claim that is useful and wihin the rigid region. (i.e., foreign claim is dissallowed but own claim with same residues is issued — in this way the claimer uses e.g., beta-sheet jumps, where they are suggested the input pose is used to initialize the rigid region ( via copying of internal coordinates ) e.g., a hole in the structure shouldn't pose a problem, since we basically copy the atom-tree. More...

#include <RigidChunkClaimer.hh>

Inheritance diagram for protocols::topology_broker::RigidChunkClaimer:

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Collaboration diagram for protocols::topology_broker::RigidChunkClaimer:

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Classes
class	CM_SuggestFixResidue

class	JumpCalculator
	helper class – computes if we have all jupms needed to rigidify the chosen chunk and generate more jumps if needed. More...

Public Member Functions
	RigidChunkClaimer ()

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

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

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

virtual void	generate_claims (DofClaims &)
	generate DofClaims for BB More...

virtual bool	allow_claim (DofClaim const &)
	has to decline foreign BB claims for rigid regions, reclaim jumps where appropriate More...

virtual void	finalize_claims (DofClaims &)
	issue jump-claims for jumps yet missing to keep rigid regions fixed More...

virtual void	initialize_dofs (core::pose::Pose &, DofClaims const &init_claims, DofClaims &failed_to_init)
	initialize BB residues and rigid-internal jumps from starting structure — copying atom-tree dofs More...

virtual void	switch_to_fullatom (core::pose::Pose &, utility::vector1< bool > bNeedToRepack) const
	rigid-chunk can probably provide some side-chain info from full-length model More...

virtual bool	accept_declined_claim (DofClaim const &was_declined)
	will fail if a BB torsion claim of the rigid region has been declined More...

virtual void	manipulate_cut_bias (utility::vector1< core::Real > &cut_bias)
	multiply your bias to this – if its zero don't change that, i.e., multiply only More...

virtual void	adjust_relax_movemap (core::kinematics::MoveMap &) const
	disallow torsion moves in relax if bRigidInRelax More...

virtual void	receive_message (ClaimerMessage &cm)

bool	use_loops_from_threading_job () const
	Returns true if we are using loop definitions from ThreadingJob. More...

void	use_loops_from_threading_job (bool setting)
	Sets whether we should use loop definitions from ThreadingJob. 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	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	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...

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...

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)

Static Public Member Functions
static std::string	_static_type_name ()

Protected Member Functions
void	select_parts ()
	select sub-regions from rigid_core_, if skip-rate is specified More...

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

virtual void	set_defaults ()

virtual void	init_after_reading ()

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...

Private Types
typedef TopologyClaimer	Parent

typedef utility::pointer::owning_ptr < JumpCalculator >	JumpCalculatorOP

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

core::pose::Pose	centroid_input_pose_
	starting pose in centroid mode More...

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

loops::Loops	current_rigid_core_
	if skip-rate is given (in loop-definitions) current_rigid_core_ will contain the current "choice" of regions... set in generate_claims() More...

DofClaims	current_jumps_
	jumps used this round — since generate_claims() More...

bool	bExclusive_
	flag used to specify if the rigid regions should really be treated exclusivity — i.e., are they really rigid ? More...

bool	bAllowAdjacentJumps_
	jump residues that are just next to rigid region are probably leading to impossibl fold-trees (not always – but most of the time) if false we don't allow such jumps More...

bool	bUseInputPose_
	use the pose in new_decoy( pose ) More...

bool	bUseThreadingJobLoops_
	use loop-definition from ThreadingJob More...

core::Size	min_loop_size_
	min_loop_size for Threading-loops More...

core::Real	random_grow_loops_by_
	same effect as OptionKeys::loops::random_grow_loops_by ]() for looprelax More...

bool	bRigidInRelax_
	keep this chunk rigid in relax — adjust movemap to keep BB-Torsions fixed... More...

JumpCalculatorOP	current_jump_calculator_

Detailed Description

defines a rigid part of structure... imagine a loop-relax application core structure is fixed via jumps and loops can move the rigid chunk takes a definition of rigid regions in form of an instance of Loops (just taken as bunch of start-end residue numbers — here defining the rigid residues and not the loops). the rigid chunk to keep its integrity will need jumps, the claimer will reuse jumps if somebody else claims them, or submit in finalize_claims his own jumps, if not enough jumps are present. in "bExclusive_ mode" the RigidChunk will reclaim any jump claim that is useful and wihin the rigid region. (i.e., foreign claim is dissallowed but own claim with same residues is issued — in this way the claimer uses e.g., beta-sheet jumps, where they are suggested the input pose is used to initialize the rigid region ( via copying of internal coordinates ) e.g., a hole in the structure shouldn't pose a problem, since we basically copy the atom-tree.

Definition at line 44 of file RigidChunkClaimer.hh.

Member Typedef Documentation

typedef utility::pointer::owning_ptr< JumpCalculator > protocols::topology_broker::RigidChunkClaimer::JumpCalculatorOP

private

Definition at line 202 of file RigidChunkClaimer.hh.

typedef TopologyClaimer protocols::topology_broker::RigidChunkClaimer::Parent

private

Definition at line 45 of file RigidChunkClaimer.hh.

Constructor & Destructor Documentation

protocols::topology_broker::RigidChunkClaimer::RigidChunkClaimer ( )

Definition at line 84 of file RigidChunkClaimer.cc.

Referenced by clone().

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

Definition at line 90 of file RigidChunkClaimer.cc.

References core::chemical::CENTROID, centroid_input_pose_, core::pose::Pose::is_fullatom(), core::util::switch_to_residue_type_set(), and core::pose::Pose::total_residue().

Member Function Documentation

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

inlinestatic

Definition at line 69 of file RigidChunkClaimer.hh.

Referenced by type().

bool protocols::topology_broker::RigidChunkClaimer::accept_declined_claim ( DofClaim const & was_declined)

virtual

will fail if a BB torsion claim of the rigid region has been declined

Reimplemented from protocols::topology_broker::TopologyClaimer.

Definition at line 299 of file RigidChunkClaimer.cc.

References tr().

void protocols::topology_broker::RigidChunkClaimer::adjust_relax_movemap ( core::kinematics::MoveMap & mm) const

virtual

disallow torsion moves in relax if bRigidInRelax

Reimplemented from protocols::topology_broker::TopologyClaimer.

Definition at line 456 of file RigidChunkClaimer.cc.

References core::id::BB, bRigidInRelax_, rigid_core_, and protocols::loops::Loops::switch_movemap().

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

virtual

has to decline foreign BB claims for rigid regions, reclaim jumps where appropriate

Reimplemented from protocols::topology_broker::TopologyClaimer.

Definition at line 263 of file RigidChunkClaimer.cc.

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

inlinevirtual

clone it!

Implements protocols::topology_broker::TopologyClaimer.

Definition at line 60 of file RigidChunkClaimer.hh.

References RigidChunkClaimer().

void protocols::topology_broker::RigidChunkClaimer::finalize_claims ( DofClaims & new_claims)

virtual

issue jump-claims for jumps yet missing to keep rigid regions fixed

Reimplemented from protocols::topology_broker::TopologyClaimer.

Definition at line 304 of file RigidChunkClaimer.cc.

References current_jump_calculator_, and current_jumps_.

void protocols::topology_broker::RigidChunkClaimer::generate_claims ( DofClaims & new_claims)

virtual

generate DofClaims for BB

generate exclusive backbone claims for each residue of the rigid-chunk jumps are not exclusive and are added later in final_claims — want to reuse other jumps if possible

Reimplemented from protocols::topology_broker::TopologyClaimer.

Definition at line 220 of file RigidChunkClaimer.cc.

References protocols::loops::Loops::begin(), current_rigid_core_, protocols::loops::Loops::end(), protocols::topology_broker::DofClaim::EXCLUSIVE, and tr().

void protocols::topology_broker::RigidChunkClaimer::init_after_reading ( )

protectedvirtual

Reimplemented from protocols::topology_broker::TopologyClaimer.

Definition at line 186 of file RigidChunkClaimer.cc.

References core::chemical::CENTROID, centroid_input_pose_, input_pose_, core::pose::Pose::is_fullatom(), rigid_core_, core::pose::Pose::sequence(), core::util::switch_to_residue_type_set(), core::pose::Pose::total_residue(), tr(), and type().

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

virtual

initialize BB residues and rigid-internal jumps from starting structure — copying atom-tree dofs

Reimplemented from protocols::topology_broker::TopologyClaimer.

Definition at line 462 of file RigidChunkClaimer.cc.

References core::conformation::Residue::atom(), protocols::loops::Loops::begin(), centroid_input_pose_, protocols::topology_broker::copy_internal_coords(), current_rigid_core_, protocols::loops::Loops::end(), input_pose_, core::pose::Pose::is_fullatom(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), tr(), and core::conformation::Atom::xyz().

void protocols::topology_broker::RigidChunkClaimer::manipulate_cut_bias ( utility::vector1< core::Real > & cut_bias)

virtual

multiply your bias to this – if its zero don't change that, i.e., multiply only

Reimplemented from protocols::topology_broker::TopologyClaimer.

Definition at line 514 of file RigidChunkClaimer.cc.

References current_rigid_core_, and protocols::loops::Loops::transfer_to_residue_vector().

void protocols::topology_broker::RigidChunkClaimer::new_decoy ( )

virtual

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

Reimplemented from protocols::topology_broker::TopologyClaimer.

Definition at line 235 of file RigidChunkClaimer.cc.

References bAllowAdjacentJumps_, current_jump_calculator_, current_jumps_, current_rigid_core_, and select_parts().

Referenced by new_decoy().

void protocols::topology_broker::RigidChunkClaimer::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.

Definition at line 241 of file RigidChunkClaimer.cc.

References bUseInputPose_, bUseThreadingJobLoops_, core::chemical::CENTROID, centroid_input_pose_, protocols::topology_broker::generate_rigid_from_alignment(), input_pose_, core::pose::Pose::is_fullatom(), min_loop_size_, new_decoy(), rigid_core_, core::util::switch_to_residue_type_set(), core::pose::Pose::total_residue(), and tr().

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

protectedvirtual

void protocols::topology_broker::RigidChunkClaimer::receive_message ( ClaimerMessage & cm)

virtual

Reimplemented from protocols::topology_broker::TopologyClaimer.

Definition at line 112 of file RigidChunkClaimer.cc.

References protocols::loops::Loops::begin(), current_rigid_core_, protocols::topology_broker::RigidChunkClaimer::CM_SuggestFixResidue::good_fix_pos_, protocols::topology_broker::ClaimerMessage::received_by_me(), and protocols::loops::Loops::size().

void protocols::topology_broker::RigidChunkClaimer::select_parts ( )

protected

select sub-regions from rigid_core_, if skip-rate is specified

Definition at line 192 of file RigidChunkClaimer.cc.

References protocols::loops::Loops::begin(), protocols::loops::Loops::clear(), current_rigid_core_, protocols::loops::Loops::end(), protocols::loops::Loops::grow_all_loops(), protocols::loops::Loops::invert(), protocols::loops::Loops::push_back(), random_grow_loops_by_, protocols::RG(), rigid_core_, protocols::loops::Loops::size(), and tr().

Referenced by new_decoy().

void protocols::topology_broker::RigidChunkClaimer::set_defaults ( )

protectedvirtual

Reimplemented from protocols::topology_broker::TopologyClaimer.

Definition at line 103 of file RigidChunkClaimer.cc.

References bUseInputPose_, bUseThreadingJobLoops_, min_loop_size_, random_grow_loops_by_, and protocols::topology_broker::TopologyClaimer::set_defaults().

void protocols::topology_broker::RigidChunkClaimer::switch_to_fullatom	(	core::pose::Pose &	pose,
		utility::vector1< bool >	bNeedToRepack
	)		const

virtual

rigid-chunk can probably provide some side-chain info from full-length model

Reimplemented from protocols::topology_broker::TopologyClaimer.

Definition at line 519 of file RigidChunkClaimer.cc.

References core::pose::add_variant_type_to_pose_residue(), core::conformation::Residue::atom(), protocols::loops::Loops::begin(), current_rigid_core_, core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, protocols::loops::Loops::end(), core::conformation::Residue::has_variant_type(), input_pose_, core::conformation::Residue::natoms(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), tr(), and core::conformation::Atom::xyz().

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

inlinevirtual

type() is specifying the output name of the TopologyClaimer

Implements protocols::topology_broker::TopologyClaimer.

Definition at line 65 of file RigidChunkClaimer.hh.

References _static_type_name().

Referenced by init_after_reading(), and read_tag().

bool protocols::topology_broker::RigidChunkClaimer::use_loops_from_threading_job ( ) const

inline

Returns true if we are using loop definitions from ThreadingJob.

Definition at line 107 of file RigidChunkClaimer.hh.

References bUseThreadingJobLoops_.

void protocols::topology_broker::RigidChunkClaimer::use_loops_from_threading_job ( bool setting)

inline

Sets whether we should use loop definitions from ThreadingJob.

Definition at line 112 of file RigidChunkClaimer.hh.

References bUseThreadingJobLoops_.

Member Data Documentation

bool protocols::topology_broker::RigidChunkClaimer::bAllowAdjacentJumps_

private

jump residues that are just next to rigid region are probably leading to impossibl fold-trees (not always – but most of the time) if false we don't allow such jumps

Definition at line 150 of file RigidChunkClaimer.hh.

Referenced by protocols::topology_broker::RigidChunkClaimer::JumpCalculator::good_jump(), protocols::topology_broker::RigidChunkClaimer::JumpCalculator::irrelevant_jump(), and new_decoy().

bool protocols::topology_broker::RigidChunkClaimer::bExclusive_

private

flag used to specify if the rigid regions should really be treated exclusivity — i.e., are they really rigid ?

changing this flag to false, will allow everything to move, but together with coordinate constraints this might yield a pose that is easier sampled ?

Definition at line 146 of file RigidChunkClaimer.hh.

Referenced by allow_claim(), and read_tag().

bool protocols::topology_broker::RigidChunkClaimer::bRigidInRelax_

private

keep this chunk rigid in relax — adjust movemap to keep BB-Torsions fixed...

Definition at line 165 of file RigidChunkClaimer.hh.