defines a rigid part of structure... imagine a loop-relax application core structure is fixed via jumps and loops can move @detail 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:

[legend]

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)

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

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

void	new_decoy () override
	a new decoy — random choices to be made ? make them here 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	generate_claims (claims::DofClaims &) override
	generate DofClaims for BB More...

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

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

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

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

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

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

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

void	receive_message (ClaimerMessage &cm) override

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
	~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	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...

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 core::pose::PoseOP	get_pose_from_claimer ()

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...

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

void	set_defaults () override

void	init_after_reading () 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...

Private Types
typedef TopologyClaimer	Parent

typedef utility::pointer::shared_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...

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

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

bool	bAllowAdjacentJumps_ = false
	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_ = true
	use the pose in new_decoy( pose ) More...

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

core::Size	min_loop_size_ = 0
	min_loop_size for Threading-loops More...

core::Real	random_grow_loops_by_ = 0.0
	same effect as OptionKeys::loops::random_grow_loops_by ]() for looprelax More...

bool	bRigidInRelax_ = false
	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 @detail 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.

Member Typedef Documentation

◆ JumpCalculatorOP

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

private

◆ Parent

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

private

Constructor & Destructor Documentation

◆ RigidChunkClaimer() [1/2]

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

default

◆ RigidChunkClaimer() [2/2]

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

References centroid_input_pose_, core::chemical::CENTROID_t, core::pose::Pose::is_fullatom(), core::pose::Pose::size(), and core::util::switch_to_residue_type_set().

Member Function Documentation

◆ _static_type_name()

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

inlinestatic

Referenced by type().

◆ accept_declined_claim()

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

overridevirtual

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

Reimplemented from protocols::topology_broker::TopologyClaimer.

References tr().

◆ adjust_relax_movemap()

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

overridevirtual

disallow torsion moves in relax if bRigidInRelax

Reimplemented from protocols::topology_broker::TopologyClaimer.

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

◆ allow_claim()

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

overridevirtual

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

Reimplemented from protocols::topology_broker::TopologyClaimer.

◆ clone()

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

inlineoverridevirtual

clone it!

Implements protocols::topology_broker::TopologyClaimer.

◆ finalize_claims()

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

overridevirtual

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

Reimplemented from protocols::topology_broker::TopologyClaimer.

References current_jump_calculator_, current_jumps_, and protocols::topology_broker::TopologyClaimer::label().

◆ generate_claims()

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

overridevirtual

generate DofClaims for BB

@detail 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.

References current_rigid_core_, protocols::topology_broker::claims::DofClaim::EXCLUSIVE, protocols::topology_broker::TopologyClaimer::get_self_weak_ptr(), protocols::topology_broker::TopologyClaimer::label(), protocols::loops::Loops::push_back(), and tr().

◆ init_after_reading()

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

overrideprotectedvirtual

Reimplemented from protocols::topology_broker::TopologyClaimer.

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

◆ initialize_dofs()

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

overridevirtual

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

Reimplemented from protocols::topology_broker::TopologyClaimer.

References core::conformation::Residue::atom(), centroid_input_pose_, protocols::topology_broker::copy_internal_coords(), current_rigid_core_, input_pose_, core::pose::Pose::is_fullatom(), protocols::mean_field::max(), core::pose::Pose::residue(), core::pose::Pose::size(), tr(), and core::conformation::Atom::xyz().

◆ manipulate_cut_bias()

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

overridevirtual

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

Reimplemented from protocols::topology_broker::TopologyClaimer.

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

◆ new_decoy() [1/2]

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

overridevirtual

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

Reimplemented from protocols::topology_broker::TopologyClaimer.

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

Referenced by new_decoy().

◆ new_decoy() [2/2]

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

overridevirtual

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 bUseInputPose_, bUseThreadingJobLoops_, centroid_input_pose_, core::chemical::CENTROID_t, protocols::topology_broker::generate_rigid_from_alignment(), protocols::jd2::JobDistributor::get_instance(), input_pose_, core::pose::Pose::is_fullatom(), min_loop_size_, new_decoy(), rigid_core_, core::pose::Pose::size(), core::util::switch_to_residue_type_set(), and tr().

◆ read_tag()

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

overrideprotectedvirtual

◆ receive_message()

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

overridevirtual

Reimplemented from protocols::topology_broker::TopologyClaimer.

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

◆ select_parts()

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

protected

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

References protocols::loops::Loops::clear(), current_rigid_core_, protocols::loops::Loops::grow_all_loops(), protocols::loops::Loops::invert(), protocols::loops::Loops::push_back(), random_grow_loops_by_, core::scoring::rg, rigid_core_, protocols::loops::Loops::size(), and tr().

Referenced by new_decoy().

◆ set_defaults()

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

overrideprotectedvirtual

Reimplemented from protocols::topology_broker::TopologyClaimer.

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

◆ switch_to_fullatom()

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

overridevirtual

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

Reimplemented from protocols::topology_broker::TopologyClaimer.

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

◆ type()

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

inlineoverridevirtual

type() is specifying the output name of the TopologyClaimer

Implements protocols::topology_broker::TopologyClaimer.

References _static_type_name().

Referenced by init_after_reading(), and read_tag().

◆ use_loops_from_threading_job() [1/2]

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

inline

Returns true if we are using loop definitions from ThreadingJob.

References bUseThreadingJobLoops_.

◆ use_loops_from_threading_job() [2/2]

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

inline

Sets whether we should use loop definitions from ThreadingJob.

References bUseThreadingJobLoops_.

Member Data Documentation

◆ bAllowAdjacentJumps_

bool protocols::topology_broker::RigidChunkClaimer::bAllowAdjacentJumps_ = false

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

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

◆ bExclusive_

bool protocols::topology_broker::RigidChunkClaimer::bExclusive_ = true

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 ?

Referenced by allow_claim(), and read_tag().

◆ bRigidInRelax_

bool protocols::topology_broker::RigidChunkClaimer::bRigidInRelax_ = false

private

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

Referenced by adjust_relax_movemap(), and read_tag().

◆ bUseInputPose_

bool protocols::topology_broker::RigidChunkClaimer::bUseInputPose_ = true

private

use the pose in new_decoy( pose )

Referenced by new_decoy(), read_tag(), and set_defaults().

◆ bUseThreadingJobLoops_

bool protocols::topology_broker::RigidChunkClaimer::bUseThreadingJobLoops_ = false

private

use loop-definition from ThreadingJob

Referenced by new_decoy(), read_tag(), set_defaults(), and use_loops_from_threading_job().

◆ centroid_input_pose_

core::pose::Pose protocols::topology_broker::RigidChunkClaimer::centroid_input_pose_

private

starting pose in centroid mode

Referenced by init_after_reading(), initialize_dofs(), new_decoy(), and RigidChunkClaimer().

◆ current_jump_calculator_

JumpCalculatorOP protocols::topology_broker::RigidChunkClaimer::current_jump_calculator_

private

Referenced by allow_claim(), finalize_claims(), and new_decoy().

◆ current_jumps_

claims::DofClaims protocols::topology_broker::RigidChunkClaimer::current_jumps_

private

jumps used this round — since generate_claims()

Referenced by allow_claim(), finalize_claims(), and new_decoy().

◆ current_rigid_core_

loops::Loops protocols::topology_broker::RigidChunkClaimer::current_rigid_core_

private

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

Referenced by allow_claim(), generate_claims(), initialize_dofs(), manipulate_cut_bias(), new_decoy(), receive_message(), select_parts(), and switch_to_fullatom().

◆ input_pose_

core::pose::Pose protocols::topology_broker::RigidChunkClaimer::input_pose_

private

starting pose

Referenced by init_after_reading(), initialize_dofs(), new_decoy(), read_tag(), and switch_to_fullatom().

◆ min_loop_size_

core::Size protocols::topology_broker::RigidChunkClaimer::min_loop_size_ = 0

private

min_loop_size for Threading-loops

Referenced by new_decoy(), read_tag(), and set_defaults().

◆ random_grow_loops_by_

core::Real protocols::topology_broker::RigidChunkClaimer::random_grow_loops_by_ = 0.0

private

same effect as OptionKeys::loops::random_grow_loops_by ]() for looprelax

Referenced by read_tag(), select_parts(), and set_defaults().

◆ rigid_core_

loops::Loops protocols::topology_broker::RigidChunkClaimer::rigid_core_

private

regions that can be used for rigid core

Referenced by adjust_relax_movemap(), init_after_reading(), new_decoy(), read_tag(), and select_parts().

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

src/protocols/topology_broker/RigidChunkClaimer.hh
src/protocols/topology_broker/RigidChunkClaimer.cc

Classes

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Types

Private Attributes

Detailed Description

Member Typedef Documentation

◆ JumpCalculatorOP

◆ Parent

Constructor & Destructor Documentation

◆ RigidChunkClaimer() [1/2]

◆ RigidChunkClaimer() [2/2]

Member Function Documentation

◆ _static_type_name()

◆ accept_declined_claim()

◆ adjust_relax_movemap()

◆ allow_claim()

◆ clone()

◆ finalize_claims()

◆ generate_claims()

◆ init_after_reading()

◆ initialize_dofs()

◆ manipulate_cut_bias()

◆ new_decoy() [1/2]

◆ new_decoy() [2/2]

◆ read_tag()

◆ receive_message()

◆ select_parts()

◆ set_defaults()

◆ switch_to_fullatom()

◆ type()

◆ use_loops_from_threading_job() [1/2]

◆ use_loops_from_threading_job() [2/2]

Member Data Documentation

◆ bAllowAdjacentJumps_

◆ bExclusive_

◆ bRigidInRelax_

◆ bUseInputPose_

◆ bUseThreadingJobLoops_

◆ centroid_input_pose_

◆ current_jump_calculator_

◆ current_jumps_

◆ current_rigid_core_

◆ input_pose_

◆ min_loop_size_

◆ random_grow_loops_by_

◆ rigid_core_