#include <MembraneTopologyClaimer.hh>

Inheritance diagram for protocols::topology_broker::MembraneTopologyClaimer:

[legend]

Public Member Functions
	MembraneTopologyClaimer ()

	MembraneTopologyClaimer (core::pose::Pose const &input_pose)

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

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

bool	claimer_builds_own_fold_tree () override

void	set_pose_from_broker (core::pose::Pose &pose) override

void	pre_process (core::pose::Pose &pose) override

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

void	build_fold_tree (core::pose::Pose &pose, core::kinematics::FoldTree &fold_tree_in) override

core::kinematics::FoldTreeOP	get_fold_tree (core::pose::Pose &pose) override
	in case a claimer has its own fold_tree. get_fold_tree() is called by the broker More...

void	add_mover (moves::RandomMover &random_mover, core::pose::Pose const &pose, abinitio::StageID stageID, core::scoring::ScoreFunction const &scorefxn, core::Real progress) override
	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	initialize_dofs (core::pose::Pose &, claims::DofClaims const &init_claims, claims::DofClaims &) override
	initialize sequence ( for approved sequence claims given as init_claim ) Claimer searches init_claims for claims owned by *this More...

void	addVirtualResAsRootMembrane (core::pose::Pose &pose)

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 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	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 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...

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 ()
	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...

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

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

virtual void	set_defaults ()

virtual void	init_after_reading ()

Member Typedef Documentation

◆ Parent

typedef TopologyClaimer protocols::topology_broker::MembraneTopologyClaimer::Parent

private

Constructor & Destructor Documentation

◆ MembraneTopologyClaimer() [1/2]

protocols::topology_broker::MembraneTopologyClaimer::MembraneTopologyClaimer ( )

default

◆ MembraneTopologyClaimer() [2/2]

protocols::topology_broker::MembraneTopologyClaimer::MembraneTopologyClaimer ( core::pose::Pose const & input_pose )

Member Function Documentation

◆ _static_type_name()

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

inlinestatic

Referenced by type().

◆ add_mover()

void protocols::topology_broker::MembraneTopologyClaimer::add_mover	(	moves::RandomMover &	random_mover,
		core::pose::Pose const &	pose,
		abinitio::StageID	stageID,
		core::scoring::ScoreFunction const &	,
		core::Real	progress
	)

overridevirtual

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_

Reimplemented from protocols::topology_broker::TopologyClaimer.

References protocols::moves::MoverContainer::add_mover(), and core::pose::symmetry::is_symmetric().

◆ addVirtualResAsRootMembrane()

void protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane ( core::pose::Pose & pose )

Adds a virtual residue to a pose as the root. Jump is to a residue in the middle of a transmembrane segment.

References core::pose::Pose::append_residue_by_jump(), core::conformation::Residue::atom(), core::conformation::Residue::atom_name(), core::kinematics::FoldTree::begin(), protocols::topology_broker::TopologyClaimer::broker(), core::conformation::ResidueFactory::create_residue(), protocols::topology_broker::TopologyBroker::final_fold_tree(), core::pose::Pose::fold_tree(), core::conformation::Residue::is_virtual_residue(), core::scoring::MembraneTopology_from_pose(), core::conformation::Residue::name(), core::conformation::Residue::name3(), core::kinematics::FoldTree::reorder(), core::pose::Pose::residue(), core::pose::Pose::residue_type_set_for_pose(), core::scoring::rg, core::kinematics::FoldTree::root(), core::pose::Pose::size(), core::scoring::MembraneTopology::span_begin(), core::scoring::MembraneTopology::span_end(), core::scoring::MembraneTopology::tmhelix(), and protocols::topology_broker::TR().

Referenced by initialize_dofs(), and pre_process().

◆ build_fold_tree()

void protocols::topology_broker::MembraneTopologyClaimer::build_fold_tree	(	core::pose::Pose &	pose,
		core::kinematics::FoldTree &	fold_tree_in
	)

overridevirtual

Reimplemented from protocols::topology_broker::TopologyClaimer.

References core::pose::Pose::fold_tree().

◆ claimer_builds_own_fold_tree()

bool protocols::topology_broker::MembraneTopologyClaimer::claimer_builds_own_fold_tree ( )

overridevirtual

Reimplemented from protocols::topology_broker::TopologyClaimer.

◆ clone()

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

inlineoverridevirtual

clone it!

Implements protocols::topology_broker::TopologyClaimer.

◆ generate_claims()

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

overridevirtual

generate first round of DOF claims

Reimplemented from protocols::topology_broker::TopologyClaimer.

References protocols::topology_broker::TopologyClaimer::broker(), protocols::topology_broker::claims::DofClaim::CAN_INIT, protocols::topology_broker::TopologyBroker::current_pose(), core::pose::Pose::fold_tree(), protocols::topology_broker::TopologyClaimer::get_self_weak_ptr(), core::conformation::Residue::is_virtual_residue(), core::kinematics::FoldTree::jump_edge(), core::conformation::Residue::name3(), core::kinematics::FoldTree::num_jump(), core::pose::Pose::residue(), core::kinematics::FoldTree::root(), core::kinematics::FoldTree::show(), core::kinematics::Edge::start(), core::kinematics::Edge::stop(), and protocols::topology_broker::TR().

◆ get_fold_tree()

core::kinematics::FoldTreeOP protocols::topology_broker::MembraneTopologyClaimer::get_fold_tree ( core::pose::Pose & )

overridevirtual

in case a claimer has its own fold_tree. get_fold_tree() is called by the broker

Reimplemented from protocols::topology_broker::TopologyClaimer.

References core::pose::Pose::fold_tree().

◆ initialize_dofs()

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

overridevirtual

initialize sequence ( for approved sequence claims given as init_claim ) Claimer searches init_claims for claims owned by *this

initialize dofs – e.g., torsions, jumps – Claimer searches init_claims for claims owned by *this

Reimplemented from protocols::topology_broker::TopologyClaimer.

References addVirtualResAsRootMembrane(), core::pose::Pose::data(), core::scoring::MembraneTopology::initialize(), core::pose::symmetry::is_symmetric(), and core::pose::datacache::CacheableDataType::MEMBRANE_TOPOLOGY.

◆ pre_process()

void protocols::topology_broker::MembraneTopologyClaimer::pre_process ( core::pose::Pose & pose )

overridevirtual

Reimplemented from protocols::topology_broker::TopologyClaimer.

References addVirtualResAsRootMembrane(), core::pose::Pose::data(), core::scoring::MembraneTopology::initialize(), core::pose::symmetry::is_symmetric(), and core::pose::datacache::CacheableDataType::MEMBRANE_TOPOLOGY.

◆ set_pose_from_broker()

void protocols::topology_broker::MembraneTopologyClaimer::set_pose_from_broker ( core::pose::Pose & pose )

overridevirtual

Reimplemented from protocols::topology_broker::TopologyClaimer.

References input_pose_.

◆ type()

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

inlineoverridevirtual

type() is specifying the output name of the TopologyClaimer

Implements protocols::topology_broker::TopologyClaimer.

References _static_type_name().

Member Data Documentation

◆ input_pose_

core::pose::Pose protocols::topology_broker::MembraneTopologyClaimer::input_pose_

private

starting pose

Referenced by set_pose_from_broker().

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

src/protocols/topology_broker/MembraneTopologyClaimer.hh
src/protocols/topology_broker/MembraneTopologyClaimer.cc

Public Member Functions

Static Public Member Functions

Private Types

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ Parent

Constructor & Destructor Documentation

◆ MembraneTopologyClaimer() [1/2]

◆ MembraneTopologyClaimer() [2/2]

Member Function Documentation

◆ _static_type_name()

◆ add_mover()

◆ addVirtualResAsRootMembrane()

◆ build_fold_tree()

◆ claimer_builds_own_fold_tree()

◆ clone()

◆ generate_claims()

◆ get_fold_tree()

◆ initialize_dofs()

◆ pre_process()

◆ set_pose_from_broker()

◆ type()

Member Data Documentation

◆ input_pose_