#include <CoordConstraintClaimer.hh>

Public Member Functions
	CoordConstraintClaimer ()

	~CoordConstraintClaimer ()

	CoordConstraintClaimer (std::string pdb_file)

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

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

void	superimpose (core::pose::Pose const &) const
	superimpose xyz coords in constraints_ with pose 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 (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...

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 ()

Protected Member Functions
virtual bool	read_tag (std::string tag, std::istream &)
	virtual functions for IO More...

virtual void	set_defaults ()
	read setup file More...

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

Private Member Functions
void	read_cst_pose ()

void	set_cst_root ()

void	generate_constraints (core::pose::Pose const &cst_pose) const

void	read_constraints_from_file (core::pose::Pose const &cst_pose) const

Private Attributes
std::string	filename_

std::string	cst_filename_

loops::Loops	rigid_

core::scoring::constraints::ConstraintSetOP	constraints_

std::string	sequence_

core::scoring::func::FuncOP	cst_func_

Size	root_

std::string	root_from_label_

bool	bRegenerateFromInputPose_

bool	bUseXYZ_in_cstfile_

core::pose::PoseOP	cst_pose_

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

bool	bFullatom_
	true if constraints are active in full-atom mode More...

bool	bLocal_
	tmp for backwards compatibility More...

core::Real	perturb_
	add 0..perturb_ random number to xyz-coords. More...

bool	bSuperimpose_
	superimpose xyz coordinates with pose in add_constraints() More...

loops::Loops	superimpose_regions_
	superimpose on these residues More...

Member Typedef Documentation

typedef TopologyClaimer protocols::topology_broker::CoordConstraintClaimer::Parent

private

Constructor & Destructor Documentation

protocols::topology_broker::CoordConstraintClaimer::CoordConstraintClaimer ( )

Referenced by clone().

protocols::topology_broker::CoordConstraintClaimer::~CoordConstraintClaimer ( )

protocols::topology_broker::CoordConstraintClaimer::CoordConstraintClaimer ( std::string pdb_file )

Member Function Documentation

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

inlinestatic

Referenced by type().

void protocols::topology_broker::CoordConstraintClaimer::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.

References core::pose::Pose::add_constraints(), core::pose::Pose::annotated_sequence(), bCentroid_, bFullatom_, bSuperimpose_, bUseXYZ_in_cstfile_, constraints_, cst_pose_, core::pose::Pose::dump_pdb(), fullatom, core::scoring::constraints::ConstraintSet::get_all_constraints(), core::pose::Pose::is_fullatom(), protocols::topology_broker::TopologyClaimer::label(), core::scoring::constraints::ConstraintSet::remapped_clone(), runtime_assert, sequence_, core::scoring::constraints::ConstraintSet::show_definition(), core::scoring::constraints::ConstraintSet::steal_def_clone(), superimpose(), and tr.

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

inlinevirtual

clone it!

Implements protocols::topology_broker::TopologyClaimer.

References CoordConstraintClaimer().

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

virtual

generate first round of DOF claims

Reimplemented from protocols::topology_broker::TopologyClaimer.

References bLocal_, protocols::topology_broker::TopologyClaimer::broker(), bUseXYZ_in_cstfile_, constraints_, cst_pose_, protocols::topology_broker::RigidChunkClaimer::CM_SuggestFixResidue::good_fix_pos_, protocols::topology_broker::TopologyClaimer::label(), protocols::topology_broker::claims::DofClaim::NEED_TO_KNOW, read_constraints_from_file(), protocols::topology_broker::ClaimerMessage::received(), protocols::topology_broker::TopologyBroker::relay_message(), root_, root_from_label_, runtime_assert, set_cst_root(), and tr.

void protocols::topology_broker::CoordConstraintClaimer::generate_constraints ( core::pose::Pose const & cst_pose ) const

private

void protocols::topology_broker::CoordConstraintClaimer::init_after_reading ( )

protectedvirtual

Reimplemented from protocols::topology_broker::TopologyClaimer.

References cst_filename_, cst_func_, cst_pose_, generate_constraints(), read_constraints_from_file(), sequence_, and type().

void protocols::topology_broker::CoordConstraintClaimer::new_decoy ( )

virtual

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

Reimplemented from protocols::topology_broker::TopologyClaimer.

References bUseXYZ_in_cstfile_, constraints_, cst_pose_, and generate_constraints().

Referenced by new_decoy().

void protocols::topology_broker::CoordConstraintClaimer::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 bRegenerateFromInputPose_, bSuperimpose_, cst_pose_, new_decoy(), and sequence_.

void protocols::topology_broker::CoordConstraintClaimer::read_constraints_from_file ( core::pose::Pose const & cst_pose ) const

private

References constraints_, cst_filename_, core::scoring::constraints::ConstraintIO::get_instance(), core::scoring::constraints::ConstraintIO::read_constraints(), core::scoring::constraints::ConstraintSet::show_definition(), and tr.

Referenced by generate_claims(), and init_after_reading().

void protocols::topology_broker::CoordConstraintClaimer::read_cst_pose ( )

private

References core::chemical::CENTROID, cst_pose_, filename_, core::chemical::ChemicalManager::get_instance(), core::import_pose::pose_from_pdb(), residue_type_set, and sequence_.

Referenced by read_tag().

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

protectedvirtual

void protocols::topology_broker::CoordConstraintClaimer::set_cst_root ( )

private

References core::scoring::constraints::ConstraintSet::add_constraint(), constraints_, cst_pose_, utility::pointer::owning_ptr< T >::get(), core::scoring::constraints::ConstraintSet::get_all_constraints(), core::pose::named_stub_id_to_stub_id(), root_, and runtime_assert.

Referenced by generate_claims().

void protocols::topology_broker::CoordConstraintClaimer::set_defaults ( )

protectedvirtual

read setup file

Reimplemented from protocols::topology_broker::TopologyClaimer.

References bSuperimpose_, bUseXYZ_in_cstfile_, protocols::loops::Loops::clear(), cst_filename_, filename_, perturb_, root_, root_from_label_, protocols::topology_broker::TopologyClaimer::set_defaults(), and superimpose_regions_.

void protocols::topology_broker::CoordConstraintClaimer::superimpose ( core::pose::Pose const & pose ) const

superimpose xyz coords in constraints_ with pose

References core::scoring::constraints::ConstraintSet::add_constraint(), constraints_, protocols::toolbox::fit_centered_coords(), utility::pointer::owning_ptr< T >::get(), core::scoring::constraints::ConstraintSet::get_all_constraints(), protocols::loops::Loops::is_loop_residue(), protocols::topology_broker::TopologyClaimer::label(), protocols::toolbox::reset_x(), runtime_assert, core::scoring::constraints::ConstraintSet::show_definition(), protocols::loops::Loops::size(), superimpose_regions_, tr, weights, and core::pose::Pose::xyz().

Referenced by add_constraints().

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

inlinevirtual

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().

Member Data Documentation

bool protocols::topology_broker::CoordConstraintClaimer::bCentroid_

private

true if constraints are active in centroid mode

Referenced by add_constraints(), and read_tag().

bool protocols::topology_broker::CoordConstraintClaimer::bFullatom_

private

true if constraints are active in full-atom mode

Referenced by add_constraints(), and read_tag().

bool protocols::topology_broker::CoordConstraintClaimer::bLocal_

private

tmp for backwards compatibility

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

bool protocols::topology_broker::CoordConstraintClaimer::bRegenerateFromInputPose_

private

Referenced by new_decoy(), and read_tag().

bool protocols::topology_broker::CoordConstraintClaimer::bSuperimpose_

private

superimpose xyz coordinates with pose in add_constraints()

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

bool protocols::topology_broker::CoordConstraintClaimer::bUseXYZ_in_cstfile_

private

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

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

mutableprivate

Referenced by add_constraints(), generate_claims(), generate_constraints(), new_decoy(), read_constraints_from_file(), set_cst_root(), and superimpose().

std::string protocols::topology_broker::CoordConstraintClaimer::cst_filename_

private

Referenced by init_after_reading(), read_constraints_from_file(), read_tag(), and set_defaults().

core::scoring::func::FuncOP protocols::topology_broker::CoordConstraintClaimer::cst_func_

private

Referenced by generate_constraints(), init_after_reading(), and read_tag().

core::pose::PoseOP protocols::topology_broker::CoordConstraintClaimer::cst_pose_

private

Referenced by add_constraints(), generate_claims(), init_after_reading(), new_decoy(), read_cst_pose(), and set_cst_root().

std::string protocols::topology_broker::CoordConstraintClaimer::filename_

private

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

core::Real protocols::topology_broker::CoordConstraintClaimer::perturb_

private

add 0..perturb_ random number to xyz-coords.

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

loops::Loops protocols::topology_broker::CoordConstraintClaimer::rigid_

private

Referenced by generate_constraints(), and read_tag().

Size protocols::topology_broker::CoordConstraintClaimer::root_

private

Referenced by generate_claims(), generate_constraints(), read_tag(), set_cst_root(), and set_defaults().

std::string protocols::topology_broker::CoordConstraintClaimer::root_from_label_

private

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

std::string protocols::topology_broker::CoordConstraintClaimer::sequence_

mutableprivate

Referenced by add_constraints(), init_after_reading(), new_decoy(), and read_cst_pose().

loops::Loops protocols::topology_broker::CoordConstraintClaimer::superimpose_regions_

private

superimpose on these residues

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

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

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

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Types

Private Member Functions

Private Attributes

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation