#include <ConstraintClaimer.hh>

Inheritance diagram for protocols::topology_broker::ConstraintClaimer:

[legend]

Public Member Functions
	ConstraintClaimer ()

	ConstraintClaimer (std::string const &cst_file, std::string const &tag="")

	ConstraintClaimer (bool CmdFlag, bool centroid=true, bool fullatom=false)

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

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

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

void	add_constraints (core::pose::Pose &) const override
	add constraints to pose... might make this stage dependent as with movers... More...

core::Real	filter_weight () const

std::string const &	filter_name () const

core::Size	combine_ratio () const

core::Real	drop_random_rate () const

std::string const &	tag () const

void	set_cst_file (std::string const &)

void	set_fullatom (bool setting)

void	set_centroid (bool setting)

void	set_skip_redundant (core::Size setting)

void	set_combine_ratio (core::Size setting)

void	set_filter_weight (core::Real weight)

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	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 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 (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 ()

Private Types
typedef TopologyClaimer	Parent

Private Attributes
std::string	filename_

std::string	fa_filename_

std::string	cst_filename_

std::string	tag_

core::scoring::constraints::ConstraintSetOP	constraints_

core::scoring::constraints::ConstraintSetOP	fa_constraints_

core::pose::Pose	constraint_ref_pose_

std::string	sequence_

utility::vector1< bool >	combine_exclude_res_

bool	bCentroid_
	true if constraints are active in centroid mode More...

bool	bFullatom_
	true if constraints are active in full-atom mode if true use fa_constraints if available... normal constraints otherwise More...

bool	bCmdFlag_
	use constraints defined via command line More...

core::Size	combine_ratio_
	combine constraints randomly into Ambiguous Constraints More...

core::Real	drop_random_rate_
	drop restraints with this rate randomly – default 0 – no dropping More...

bool	skip_redundant_
	at most one constraint per residue pair ( does not look at bounds... ) More...

core::Size	skip_redundant_width_
	how many residues left and right do we exclude other "redundant" constraints... More...

core::Real	filter_weight_
	which weight should this constraint set have when used as a filter More...

std::string	filter_name_

Additional Inherited Members
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 ()

Member Typedef Documentation

◆ Parent

typedef TopologyClaimer protocols::topology_broker::ConstraintClaimer::Parent

private

Constructor & Destructor Documentation

◆ ConstraintClaimer() [1/3]

protocols::topology_broker::ConstraintClaimer::ConstraintClaimer ( )

◆ ConstraintClaimer() [2/3]

protocols::topology_broker::ConstraintClaimer::ConstraintClaimer	(	std::string const &	cst_file,
		std::string const &	tag = `""`
	)

◆ ConstraintClaimer() [3/3]

protocols::topology_broker::ConstraintClaimer::ConstraintClaimer	(	bool	CmdFlag,
		bool	centroid = `true`,
		bool	fullatom = `false`
	)

Member Function Documentation

◆ _static_type_name()

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

inlinestatic

Referenced by protocols::topology_broker::add_claims_from_stream(), and type().

◆ add_constraints()

void protocols::topology_broker::ConstraintClaimer::add_constraints ( core::pose::Pose & ) const

overridevirtual

add constraints to pose... might make this stage dependent as with movers...

Reimplemented from protocols::topology_broker::TopologyClaimer.

References core::pose::Pose::add_constraints(), core::pose::Pose::annotated_sequence(), bCentroid_, bCmdFlag_, bFullatom_, core::scoring::constraints::choose_effective_sequence_separation(), core::scoring::constraints::combine_constraints(), combine_exclude_res_, combine_ratio_, constraint_ref_pose_, core::pose::Pose::constraint_set(), constraints_, core::scoring::constraints::drop_constraints(), drop_random_rate_, core::pose::Pose::dump_pdb(), filename_, core::pose::Pose::fold_tree(), protocols::loops::PoseNumberedLoopFileReader::hijack_loop_reading_code_set_loop_line_begin_token(), core::pose::Pose::is_fullatom(), protocols::loops::PoseNumberedLoopFileReader::read_pose_numbered_loops_file(), sequence_, core::pose::Pose::size(), skip_redundant_, core::scoring::constraints::skip_redundant_constraints(), skip_redundant_width_, tag_, tr(), and protocols::loops::Loops::transfer_to_residue_vector().

◆ clone()

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

inlineoverridevirtual

clone it!

Implements protocols::topology_broker::TopologyClaimer.

◆ combine_ratio()

core::Size protocols::topology_broker::ConstraintClaimer::combine_ratio ( ) const

inline

References combine_ratio_.

◆ drop_random_rate()

core::Real protocols::topology_broker::ConstraintClaimer::drop_random_rate ( ) const

inline

References drop_random_rate_.

◆ filter_name()

std::string const& protocols::topology_broker::ConstraintClaimer::filter_name ( ) const

inline

References filter_name_.

◆ filter_weight()

core::Real protocols::topology_broker::ConstraintClaimer::filter_weight ( ) const

inline

References filter_weight_.

◆ generate_claims()

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

overridevirtual

generate first round of DOF claims

Reimplemented from protocols::topology_broker::TopologyClaimer.

◆ new_decoy()

void protocols::topology_broker::ConstraintClaimer::new_decoy ( )

overridevirtual

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

Reimplemented from protocols::topology_broker::TopologyClaimer.

References bCentroid_, bCmdFlag_, bFullatom_, core::chemical::combine(), combine_ratio_, constraints_, filename_, core::scoring::constraints::get_cst_fa_file_option(), core::scoring::constraints::get_cst_file_option(), skip_redundant_, skip_redundant_width_, and tr().

◆ read_tag()

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

overridevirtual

Reimplemented from protocols::topology_broker::TopologyClaimer.

References bCentroid_, bCmdFlag_, bFullatom_, combine_ratio_, drop_random_rate_, filename_, filter_name_, filter_weight_, protocols::topology_broker::TopologyClaimer::read_tag(), skip_redundant_, skip_redundant_width_, and tag().

◆ set_centroid()

void protocols::topology_broker::ConstraintClaimer::set_centroid ( bool setting )

References bCentroid_, constraints_, and fa_constraints_.

◆ set_combine_ratio()

void protocols::topology_broker::ConstraintClaimer::set_combine_ratio ( core::Size setting )

References combine_ratio_, constraints_, and fa_constraints_.

◆ set_cst_file()

void protocols::topology_broker::ConstraintClaimer::set_cst_file ( std::string const & file )

References constraints_, fa_constraints_, and filename_.

◆ set_filter_weight()

void protocols::topology_broker::ConstraintClaimer::set_filter_weight ( core::Real weight )

References filter_weight_.

◆ set_fullatom()

void protocols::topology_broker::ConstraintClaimer::set_fullatom ( bool setting )

References bFullatom_, constraints_, and fa_constraints_.

◆ set_skip_redundant()

void protocols::topology_broker::ConstraintClaimer::set_skip_redundant ( core::Size setting )

References constraints_, fa_constraints_, skip_redundant_, and skip_redundant_width_.

◆ tag()

std::string const& protocols::topology_broker::ConstraintClaimer::tag ( ) const

inline

References tag_.

Referenced by read_tag().

◆ type()

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

inlineoverridevirtual

type() is specifying the output name of the TopologyClaimer

Implements protocols::topology_broker::TopologyClaimer.

References _static_type_name().

Member Data Documentation

◆ bCentroid_

bool protocols::topology_broker::ConstraintClaimer::bCentroid_

private

true if constraints are active in centroid mode

Referenced by add_constraints(), new_decoy(), read_tag(), and set_centroid().

◆ bCmdFlag_

bool protocols::topology_broker::ConstraintClaimer::bCmdFlag_

private

use constraints defined via command line

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

◆ bFullatom_

bool protocols::topology_broker::ConstraintClaimer::bFullatom_

private

true if constraints are active in full-atom mode if true use fa_constraints if available... normal constraints otherwise

Referenced by add_constraints(), new_decoy(), read_tag(), and set_fullatom().

◆ combine_exclude_res_

utility::vector1< bool > protocols::topology_broker::ConstraintClaimer::combine_exclude_res_

mutableprivate

Referenced by add_constraints().

◆ combine_ratio_

core::Size protocols::topology_broker::ConstraintClaimer::combine_ratio_

private

combine constraints randomly into Ambiguous Constraints

Referenced by add_constraints(), combine_ratio(), new_decoy(), read_tag(), and set_combine_ratio().

◆ constraint_ref_pose_

core::pose::Pose protocols::topology_broker::ConstraintClaimer::constraint_ref_pose_

mutableprivate

Referenced by add_constraints().

◆ constraints_

core::scoring::constraints::ConstraintSetOP protocols::topology_broker::ConstraintClaimer::constraints_

mutableprivate

Referenced by add_constraints(), new_decoy(), set_centroid(), set_combine_ratio(), set_cst_file(), set_fullatom(), and set_skip_redundant().

◆ cst_filename_

std::string protocols::topology_broker::ConstraintClaimer::cst_filename_

private

◆ drop_random_rate_

core::Real protocols::topology_broker::ConstraintClaimer::drop_random_rate_

private

drop restraints with this rate randomly – default 0 – no dropping

Referenced by add_constraints(), drop_random_rate(), and read_tag().

◆ fa_constraints_

core::scoring::constraints::ConstraintSetOP protocols::topology_broker::ConstraintClaimer::fa_constraints_

mutableprivate

Referenced by set_centroid(), set_combine_ratio(), set_cst_file(), set_fullatom(), and set_skip_redundant().

◆ fa_filename_

std::string protocols::topology_broker::ConstraintClaimer::fa_filename_

private

◆ filename_

std::string protocols::topology_broker::ConstraintClaimer::filename_

private

Referenced by add_constraints(), new_decoy(), read_tag(), and set_cst_file().

◆ filter_name_

std::string protocols::topology_broker::ConstraintClaimer::filter_name_

private

Referenced by filter_name(), and read_tag().

◆ filter_weight_

core::Real protocols::topology_broker::ConstraintClaimer::filter_weight_

private

which weight should this constraint set have when used as a filter

Referenced by filter_weight(), read_tag(), and set_filter_weight().

◆ sequence_

std::string protocols::topology_broker::ConstraintClaimer::sequence_

mutableprivate

Referenced by add_constraints().

◆ skip_redundant_

bool protocols::topology_broker::ConstraintClaimer::skip_redundant_

private

at most one constraint per residue pair ( does not look at bounds... )

Referenced by add_constraints(), new_decoy(), read_tag(), and set_skip_redundant().

◆ skip_redundant_width_

core::Size protocols::topology_broker::ConstraintClaimer::skip_redundant_width_

private

how many residues left and right do we exclude other "redundant" constraints...

Referenced by add_constraints(), new_decoy(), read_tag(), and set_skip_redundant().

◆ tag_

std::string protocols::topology_broker::ConstraintClaimer::tag_

private

Referenced by add_constraints(), and tag().

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

src/protocols/topology_broker/ConstraintClaimer.hh
src/protocols/topology_broker/ConstraintClaimer.cc

Public Member Functions

Static Public Member Functions

Private Types

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ Parent

Constructor & Destructor Documentation

◆ ConstraintClaimer() [1/3]

◆ ConstraintClaimer() [2/3]

◆ ConstraintClaimer() [3/3]

Member Function Documentation

◆ _static_type_name()

◆ add_constraints()

◆ clone()

◆ combine_ratio()

◆ drop_random_rate()

◆ filter_name()

◆ filter_weight()

◆ generate_claims()

◆ new_decoy()

◆ read_tag()

◆ set_centroid()

◆ set_combine_ratio()

◆ set_cst_file()

◆ set_filter_weight()

◆ set_fullatom()

◆ set_skip_redundant()

◆ tag()

◆ type()

Member Data Documentation

◆ bCentroid_

◆ bCmdFlag_

◆ bFullatom_

◆ combine_exclude_res_

◆ combine_ratio_

◆ constraint_ref_pose_

◆ constraints_

◆ cst_filename_

◆ drop_random_rate_

◆ fa_constraints_

◆ fa_filename_

◆ filename_

◆ filter_name_

◆ filter_weight_

◆ sequence_

◆ skip_redundant_

◆ skip_redundant_width_

◆ tag_