#include <TMHTopologySamplerClaimer.hh>

Inheritance diagram for protocols::topology_broker::TMHTopologySamplerClaimer:

[legend]

Public Member Functions
	TMHTopologySamplerClaimer ()

	TMHTopologySamplerClaimer (topology_broker::TopologyBrokerOP broker)
	constructor: supply mover classes for Fragment Moves More...

	~TMHTopologySamplerClaimer () override
	destructor More...

TopologyClaimerOP	clone () const override
	TMHTopologySamplerClaimer has virtual functions... use this to obtain a new instance. More...

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

void	set_pose_from_broker (core::pose::Pose &pose) override
	get the pose from the boker and set it as this object's pose More...

void	pre_process (core::pose::Pose &pose) override
	read in the pose's spans via the MembraneTopology store din the pose, determine jumps, TMHs, loops, etc. More...

bool	claimer_builds_own_fold_tree () override
	the broker checks if the claimer builds its own fold tree to figure out if needs to build one itself More...

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...

core::pose::PoseOP	get_pose_from_claimer () override

void	generate_claims (claims::DofClaims &dof_claims) override
	generate DofClaims More...

void	initialize_dofs (core::pose::Pose &pose, claims::DofClaims const &init_dofs, claims::DofClaims &failed_to_init) override
	make move_map and add the DoF claims from generate_claims() to the movemap. Now we can move certain parts with certain DOFs. More...

void	add_mover (moves::RandomMover &, core::pose::Pose const &, abinitio::StageID, core::scoring::ScoreFunction const &, core::Real) 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	build_fold_tree (core::pose::Pose &pose, core::kinematics::FoldTree &fold_tree) override
	this claimer builds its own radial fold tree based on read-in spanfile More...

bool	read_tag (std::string tag, std::istream &is) override
	read tag from topology broker file (setup.tpb) 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 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 &)

Static Public Member Functions
static std::string	_static_type_name ()

static void	register_options ()
	register cmd-line options in option system ( call before core::init ) More...

Protected Member Functions
void	set_defaults () override
	called by constructor — calls all set_default_XXX methods More...

void	set_pose_torsions (core::pose::Pose &pose)
	Make extended chain an idealized helix. More...

void	move_spans (core::pose::Pose &pose)
	move helices closer together More...

core::Vector	output_membrane_vector (core::pose::Pose &pose)
	output membrane center and normal as virtual atoms More...

utility::vector1< core::Vector >	pre_compute_grid_points (core::pose::Pose &pose)
	pre-compute grid points where you want to move the helices More...

core::scoring::MembraneTopologyOP	get_membrane_topology (core::pose::Pose &pose)
	get membrane topology information More...

core::scoring::MembraneEmbed	get_membrane_embed (core::pose::Pose &pose)
	get membrane embedding information More...

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	init_after_reading ()

Private Types
typedef TopologyClaimer	Parent

Private Attributes
core::Real	rotation_mag_

core::Real	translation_mag_

core::Real	rb_mover_stage1_weight_

core::pose::Pose	current_pose_

core::Size	nres_

core::Size	njumps_

ObjexxFCL::FArray2D< core::Size >	jump_array_

ObjexxFCL::FArray1D< core::Size >	cuts_

core::Size	topology_root_res_

core::Size	tmhelix_

Member Typedef Documentation

◆ Parent

typedef TopologyClaimer protocols::topology_broker::TMHTopologySamplerClaimer::Parent

private

Constructor & Destructor Documentation

◆ TMHTopologySamplerClaimer() [1/2]

protocols::topology_broker::TMHTopologySamplerClaimer::TMHTopologySamplerClaimer ( )

References set_defaults().

◆ TMHTopologySamplerClaimer() [2/2]

protocols::topology_broker::TMHTopologySamplerClaimer::TMHTopologySamplerClaimer ( topology_broker::TopologyBrokerOP broker )

constructor: supply mover classes for Fragment Moves

References set_defaults().

◆ ~TMHTopologySamplerClaimer()

protocols::topology_broker::TMHTopologySamplerClaimer::~TMHTopologySamplerClaimer ( )

overridedefault

destructor

Member Function Documentation

◆ _static_type_name()

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

inlinestatic

Referenced by type().

◆ add_mover()

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

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 tr().

◆ build_fold_tree()

void protocols::topology_broker::TMHTopologySamplerClaimer::build_fold_tree	(	core::pose::Pose &	pose,
		core::kinematics::FoldTree &	fold_tree
	)

overridevirtual

this claimer builds its own radial fold tree based on read-in spanfile

Reimplemented from protocols::topology_broker::TopologyClaimer.

References core::pose::Pose::annotated_sequence(), core::kinematics::FoldTree::begin(), core::kinematics::FoldTree::empty(), core::kinematics::FoldTree::end(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::num_jump(), core::kinematics::FoldTree::set_jump_atoms(), core::pose::Pose::size(), tr(), and core::kinematics::FoldTree::tree_from_jumps_and_cuts().

◆ claimer_builds_own_fold_tree()

bool protocols::topology_broker::TMHTopologySamplerClaimer::claimer_builds_own_fold_tree ( )

overridevirtual

the broker checks if the claimer builds its own fold tree to figure out if needs to build one itself

Reimplemented from protocols::topology_broker::TopologyClaimer.

◆ clone()

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

inlineoverridevirtual

TMHTopologySamplerClaimer has virtual functions... use this to obtain a new instance.

Implements protocols::topology_broker::TopologyClaimer.

◆ generate_claims()

void protocols::topology_broker::TMHTopologySamplerClaimer::generate_claims ( claims::DofClaims & dof_claims )

overridevirtual

generate DofClaims

generate DoF Claims to be read in by broker

Reimplemented from protocols::topology_broker::TopologyClaimer.

References protocols::topology_broker::claims::DofClaim::CAN_INIT, and protocols::topology_broker::TopologyClaimer::label().

◆ get_fold_tree()

core::kinematics::FoldTreeOP protocols::topology_broker::TMHTopologySamplerClaimer::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().

◆ get_membrane_embed()

core::scoring::MembraneEmbed protocols::topology_broker::TMHTopologySamplerClaimer::get_membrane_embed ( core::pose::Pose & pose )

protected

get membrane embedding information

References core::scoring::MembranePotential::compute_membrane_embedding(), and core::scoring::nonconst_MembraneEmbed_from_pose().

◆ get_membrane_topology()

core::scoring::MembraneTopologyOP protocols::topology_broker::TMHTopologySamplerClaimer::get_membrane_topology ( core::pose::Pose & pose )

protected

get membrane topology information

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::MEMBRANE_TOPOLOGY.

◆ get_pose_from_claimer()

core::pose::PoseOP protocols::topology_broker::TMHTopologySamplerClaimer::get_pose_from_claimer ( )

overridevirtual

Reimplemented from protocols::topology_broker::TopologyClaimer.

◆ initialize_dofs()

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

overridevirtual

make move_map and add the DoF claims from generate_claims() to the movemap. Now we can move certain parts with certain DOFs.

Reimplemented from protocols::topology_broker::TopologyClaimer.

References tr().

◆ move_spans()

void protocols::topology_broker::TMHTopologySamplerClaimer::move_spans ( core::pose::Pose & pose )

protected

move helices closer together

References protocols::rigid::RigidBodyDeterministicSpinMover::apply(), protocols::rigid::RigidBodyTransMover::apply(), core::pose::Pose::dump_pdb(), core::pose::Pose::fold_tree(), core::conformation::Residue::is_virtual_residue(), core::kinematics::FoldTree::jump_edge(), core::conformation::Residue::name3(), core::pose::Pose::num_jump(), core::pose::Pose::residue(), core::scoring::rg, core::conformation::Residue::seqpos(), core::kinematics::Edge::start(), protocols::rigid::RigidBodyTransMover::step_size(), core::kinematics::Edge::stop(), tr(), protocols::rigid::RigidBodyTransMover::trans_axis(), and core::conformation::Residue::xyz().

◆ output_membrane_vector()

core::Vector protocols::topology_broker::TMHTopologySamplerClaimer::output_membrane_vector ( core::pose::Pose & pose )

protected

output membrane center and normal as virtual atoms

References core::pose::Pose::append_residue_by_jump(), core::scoring::MembraneEmbed::center(), core::conformation::ResidueFactory::create_residue(), core::pose::Pose::fold_tree(), core::scoring::MembraneEmbed::normal(), core::pose::Pose::residue(), core::pose::Pose::residue_type_set_for_pose(), core::kinematics::FoldTree::root(), and core::conformation::Residue::seqpos().

◆ pre_compute_grid_points()

utility::vector1< core::Vector > protocols::topology_broker::TMHTopologySamplerClaimer::pre_compute_grid_points ( core::pose::Pose & pose )

protected

pre-compute grid points where you want to move the helices

References core::conformation::membrane::center, and tr().

◆ pre_process()

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

overridevirtual

read in the pose's spans via the MembraneTopology store din the pose, determine jumps, TMHs, loops, etc.

read in the pose's spans via the MembraneTopology stored in the pose, determine jumps, TMHs, loops, etc.

Reimplemented from protocols::topology_broker::TopologyClaimer.

References core::conformation::Residue::atom_name(), core::kinematics::FoldTree::begin(), core::pose::Pose::fold_tree(), core::pose::Pose::residue(), core::pose::residue_center_of_mass(), core::scoring::rg, core::kinematics::FoldTree::root(), core::pose::Pose::size(), and tr().

◆ read_tag()

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

overridevirtual

read tag from topology broker file (setup.tpb)

Reimplemented from protocols::topology_broker::TopologyClaimer.

◆ register_options()

void protocols::topology_broker::TMHTopologySamplerClaimer::register_options ( )

static

register cmd-line options in option system ( call before core::init )

◆ set_defaults()

void protocols::topology_broker::TMHTopologySamplerClaimer::set_defaults ( )

overrideprotectedvirtual

called by constructor — calls all set_default_XXX methods

Reimplemented from protocols::topology_broker::TopologyClaimer.

Referenced by TMHTopologySamplerClaimer().

◆ set_pose_from_broker()

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

overridevirtual

get the pose from the boker and set it as this object's pose

Reimplemented from protocols::topology_broker::TopologyClaimer.

◆ set_pose_torsions()

void protocols::topology_broker::TMHTopologySamplerClaimer::set_pose_torsions ( core::pose::Pose & pose )

protected

Make extended chain an idealized helix.

References core::conformation::Residue::is_virtual_residue(), core::conformation::Residue::name3(), core::pose::Pose::residue(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), and core::pose::Pose::size().

◆ type()

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

inlineoverridevirtual

type() is specifying the output name of the TopologyClaimer

Implements protocols::topology_broker::TopologyClaimer.

References _static_type_name().

Member Data Documentation

◆ current_pose_

core::pose::Pose protocols::topology_broker::TMHTopologySamplerClaimer::current_pose_

private

◆ cuts_

ObjexxFCL::FArray1D< core::Size > protocols::topology_broker::TMHTopologySamplerClaimer::cuts_

private

◆ jump_array_

ObjexxFCL::FArray2D< core::Size > protocols::topology_broker::TMHTopologySamplerClaimer::jump_array_

private

◆ njumps_

core::Size protocols::topology_broker::TMHTopologySamplerClaimer::njumps_

private

◆ nres_

core::Size protocols::topology_broker::TMHTopologySamplerClaimer::nres_

private

◆ rb_mover_stage1_weight_

core::Real protocols::topology_broker::TMHTopologySamplerClaimer::rb_mover_stage1_weight_

private

◆ rotation_mag_

core::Real protocols::topology_broker::TMHTopologySamplerClaimer::rotation_mag_

private

◆ tmhelix_

core::Size protocols::topology_broker::TMHTopologySamplerClaimer::tmhelix_

private

◆ topology_root_res_

core::Size protocols::topology_broker::TMHTopologySamplerClaimer::topology_root_res_

private

◆ translation_mag_

core::Real protocols::topology_broker::TMHTopologySamplerClaimer::translation_mag_

private

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

src/protocols/topology_broker/TMHTopologySamplerClaimer.hh
src/protocols/topology_broker/TMHTopologySamplerClaimer.cc

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Types

Private Attributes

Member Typedef Documentation

◆ Parent

Constructor & Destructor Documentation

◆ TMHTopologySamplerClaimer() [1/2]

◆ TMHTopologySamplerClaimer() [2/2]

◆ ~TMHTopologySamplerClaimer()

Member Function Documentation

◆ _static_type_name()

◆ add_mover()

◆ build_fold_tree()

◆ claimer_builds_own_fold_tree()

◆ clone()

◆ generate_claims()

◆ get_fold_tree()

◆ get_membrane_embed()

◆ get_membrane_topology()

◆ get_pose_from_claimer()

◆ initialize_dofs()

◆ move_spans()

◆ output_membrane_vector()

◆ pre_compute_grid_points()

◆ pre_process()

◆ read_tag()

◆ register_options()

◆ set_defaults()

◆ set_pose_from_broker()

◆ set_pose_torsions()

◆ type()

Member Data Documentation

◆ current_pose_

◆ cuts_

◆ jump_array_

◆ njumps_

◆ nres_

◆ rb_mover_stage1_weight_

◆ rotation_mag_

◆ tmhelix_

◆ topology_root_res_

◆ translation_mag_