#include <ConstraintClaimer.hh>

Inheritance diagram for protocols::topology_broker::ConstraintClaimer:

Collaboration diagram for protocols::topology_broker::ConstraintClaimer:

Public Member Functions
	ConstraintClaimer ()

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

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

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

virtual void	generate_claims (DofClaims &)
	generate first round of DOF claims 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 bool	read_tag (std::string tag, std::istream &)

virtual void	add_constraints (core::pose::Pose &) const
	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)

void	set_drop_random_rate (core::Real setting)

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	finalize_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 (DofClaim const &)
	allow a claim from a foreign Claimer 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	initialize_dofs (core::pose::Pose &, DofClaims const &init_claims, DofClaims &failed_to_init)
	initialize dofs – e.g., torsions, jumps – 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 (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 (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 &)

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 ()

Detailed Description

Definition at line 56 of file ConstraintClaimer.hh.

Member Typedef Documentation

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

private

Definition at line 57 of file ConstraintClaimer.hh.

Constructor & Destructor Documentation

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

Definition at line 66 of file ConstraintClaimer.cc.

Referenced by clone().

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

Definition at line 81 of file ConstraintClaimer.cc.

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

Definition at line 96 of file ConstraintClaimer.cc.

Member Function Documentation

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

inlinestatic

Definition at line 74 of file ConstraintClaimer.hh.

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

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

virtual

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

Reimplemented from protocols::topology_broker::TopologyClaimer.

Definition at line 147 of file ConstraintClaimer.cc.

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(), core::scoring::constraints::ConstraintIO::get_instance(), protocols::loops::PoseNumberedLoopFileReader::hijack_loop_reading_code_set_loop_line_begin_token(), core::pose::Pose::is_fullatom(), core::scoring::constraints::ConstraintIO::read_constraints(), protocols::loops::PoseNumberedLoopFileReader::read_pose_numbered_loops_file(), sequence_, skip_redundant_, core::scoring::constraints::skip_redundant_constraints(), skip_redundant_width_, tag_, core::pose::Pose::total_residue(), tr(), and protocols::loops::Loops::transfer_to_residue_vector().

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

inlinevirtual

clone it!

Implements protocols::topology_broker::TopologyClaimer.

Definition at line 63 of file ConstraintClaimer.hh.

References ConstraintClaimer().

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

inline

Definition at line 88 of file ConstraintClaimer.hh.

References combine_ratio_.

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

inline

Definition at line 89 of file ConstraintClaimer.hh.

References drop_random_rate_.

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

inline

Definition at line 87 of file ConstraintClaimer.hh.

References filter_name_.

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

inline

Definition at line 86 of file ConstraintClaimer.hh.

References filter_weight_.

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

virtual

generate first round of DOF claims

Reimplemented from protocols::topology_broker::TopologyClaimer.

Definition at line 113 of file ConstraintClaimer.cc.

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

virtual

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

Reimplemented from protocols::topology_broker::TopologyClaimer.

Definition at line 116 of file ConstraintClaimer.cc.

References bCentroid_, bCmdFlag_, bFullatom_, 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().

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

virtual

Reimplemented from protocols::topology_broker::TopologyClaimer.

Definition at line 214 of file ConstraintClaimer.cc.

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

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

Definition at line 253 of file ConstraintClaimer.cc.

References bCentroid_, constraints_, and fa_constraints_.

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

Definition at line 266 of file ConstraintClaimer.cc.

References combine_ratio_, constraints_, and fa_constraints_.

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

Definition at line 241 of file ConstraintClaimer.cc.

References constraints_, fa_constraints_, and filename_.

void protocols::topology_broker::ConstraintClaimer::set_drop_random_rate ( core::Real setting)

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

Definition at line 272 of file ConstraintClaimer.cc.

References filter_weight_.

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

Definition at line 247 of file ConstraintClaimer.cc.

References bFullatom_, constraints_, and fa_constraints_.

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

Definition at line 259 of file ConstraintClaimer.cc.

References constraints_, fa_constraints_, skip_redundant_, and skip_redundant_width_.

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

inline

Definition at line 90 of file ConstraintClaimer.hh.

References tag_.

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

inlinevirtual

type() is specifying the output name of the TopologyClaimer

Implements protocols::topology_broker::TopologyClaimer.

Definition at line 70 of file ConstraintClaimer.hh.

References _static_type_name().

Member Data Documentation

bool protocols::topology_broker::ConstraintClaimer::bCentroid_

private

true if constraints are active in centroid mode

Definition at line 110 of file ConstraintClaimer.hh.

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

bool protocols::topology_broker::ConstraintClaimer::bCmdFlag_

private

use constraints defined via command line

Definition at line 117 of file ConstraintClaimer.hh.

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

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

Definition at line 114 of file ConstraintClaimer.hh.

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

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

mutableprivate

Definition at line 108 of file ConstraintClaimer.hh.

Referenced by add_constraints().

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

private

combine constraints randomly into Ambiguous Constraints

Definition at line 121 of file ConstraintClaimer.hh.

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

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

mutableprivate

Definition at line 106 of file ConstraintClaimer.hh.

Referenced by add_constraints().

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

mutableprivate

Definition at line 103 of file ConstraintClaimer.hh.

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

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

private

Definition at line 101 of file ConstraintClaimer.hh.

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

private

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

Definition at line 124 of file ConstraintClaimer.hh.

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

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

mutableprivate

Definition at line 104 of file ConstraintClaimer.hh.

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

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

private

Definition at line 100 of file ConstraintClaimer.hh.

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

private

Definition at line 100 of file ConstraintClaimer.hh.

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

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

private

Definition at line 134 of file ConstraintClaimer.hh.

Referenced by filter_name(), and read_tag().

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

private

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

Definition at line 133 of file ConstraintClaimer.hh.

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

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

mutableprivate

Definition at line 107 of file ConstraintClaimer.hh.

Referenced by add_constraints().

bool protocols::topology_broker::ConstraintClaimer::skip_redundant_

private

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

Definition at line 127 of file ConstraintClaimer.hh.

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

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

private

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

Definition at line 130 of file ConstraintClaimer.hh.

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

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

private

Definition at line 102 of file ConstraintClaimer.hh.

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

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation