#include <PseudocontactShiftEnergyController.hh>

Inheritance diagram for protocols::topology_broker::PseudocontactShiftEnergyController:

Collaboration diagram for protocols::topology_broker::PseudocontactShiftEnergyController:

Public Member Functions
	PseudocontactShiftEnergyController ()

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

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

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

virtual void	set_defaults ()

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...

virtual void	init_after_reading ()

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	generate_claims (DofClaims &)
	generate first round of DOF claims 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 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 ()

Private Types
typedef TopologyClaimer	Parent

Private Member Functions
void	control_grid_param ()

Private Attributes
core::Real	grid_edge_stage1_

core::Real	grid_edge_stage2_

core::Real	grid_edge_stage3_

core::Real	grid_edge_stage4_

core::Real	grid_step_stage1_

core::Real	grid_step_stage2_

core::Real	grid_step_stage3_

core::Real	grid_step_stage4_

core::Real	grid_small_cutoff_stage1_

core::Real	grid_small_cutoff_stage2_

core::Real	grid_small_cutoff_stage3_

core::Real	grid_small_cutoff_stage4_

core::Real	grid_large_cutoff_stage1_

core::Real	grid_large_cutoff_stage2_

core::Real	grid_large_cutoff_stage3_

core::Real	grid_large_cutoff_stage4_

core::Real	grid_cone_angle_cutoff_stage1_

core::Real	grid_cone_angle_cutoff_stage2_

core::Real	grid_cone_angle_cutoff_stage3_

core::Real	grid_cone_angle_cutoff_stage4_

std::string	grid_atom_name_1_stage1_

std::string	grid_atom_name_1_stage2_

std::string	grid_atom_name_1_stage3_

std::string	grid_atom_name_1_stage4_

std::string	grid_atom_name_2_stage1_

std::string	grid_atom_name_2_stage2_

std::string	grid_atom_name_2_stage3_

std::string	grid_atom_name_2_stage4_

core::SSize	grid_residue_num_1_stage1_

core::SSize	grid_residue_num_1_stage2_

core::SSize	grid_residue_num_1_stage3_

core::SSize	grid_residue_num_1_stage4_

core::SSize	grid_residue_num_2_stage1_

core::SSize	grid_residue_num_2_stage2_

core::SSize	grid_residue_num_2_stage3_

core::SSize	grid_residue_num_2_stage4_

core::Real	grid_k_vector_stage1_

core::Real	grid_k_vector_stage2_

core::Real	grid_k_vector_stage3_

core::Real	grid_k_vector_stage4_

bool	minimize_best_tensor_stage1_

bool	minimize_best_tensor_stage2_

bool	minimize_best_tensor_stage3_

bool	minimize_best_tensor_stage4_

core::Real	pcs_weight_stage1_

core::Real	pcs_weight_stage2_

core::Real	pcs_weight_stage3_

core::Real	pcs_weight_stage4_

utility::vector1< std::string >	filenames_

utility::vector1< core::Real >	individual_weights_

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...

Detailed Description

Definition at line 48 of file PseudocontactShiftEnergyController.hh.

Member Typedef Documentation

typedef TopologyClaimer protocols::topology_broker::PseudocontactShiftEnergyController::Parent

private

Definition at line 50 of file PseudocontactShiftEnergyController.hh.

Constructor & Destructor Documentation

protocols::topology_broker::PseudocontactShiftEnergyController::PseudocontactShiftEnergyController ( )

Definition at line 66 of file PseudocontactShiftEnergyController.cc.

Referenced by clone().

Member Function Documentation

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

inlinestatic

Definition at line 63 of file PseudocontactShiftEnergyController.hh.

Referenced by type().

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

virtual

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.

Definition at line 346 of file PseudocontactShiftEnergyController.cc.

References core::scoring::pcs, protocols::abinitio::STAGE_1, protocols::abinitio::STAGE_2, protocols::abinitio::STAGE_3a, protocols::abinitio::STAGE_3b, and protocols::abinitio::STAGE_4.

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

inlinevirtual

clone it!

Implements protocols::topology_broker::TopologyClaimer.

Definition at line 54 of file PseudocontactShiftEnergyController.hh.

References PseudocontactShiftEnergyController().

void protocols::topology_broker::PseudocontactShiftEnergyController::control_grid_param ( )

private

Definition at line 486 of file PseudocontactShiftEnergyController.cc.

void protocols::topology_broker::PseudocontactShiftEnergyController::init_after_reading ( )

virtual

Reimplemented from protocols::topology_broker::TopologyClaimer.

Definition at line 454 of file PseudocontactShiftEnergyController.cc.

References core::scoring::pcs.

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

virtual

Reimplemented from protocols::topology_broker::TopologyClaimer.

Definition at line 133 of file PseudocontactShiftEnergyController.cc.

References protocols::match::upstream::b, core::pack::dunbrack::c, protocols::abinitio::filename(), and core::scoring::pcs.

void protocols::topology_broker::PseudocontactShiftEnergyController::set_defaults ( )

virtual

Reimplemented from protocols::topology_broker::TopologyClaimer.

Definition at line 129 of file PseudocontactShiftEnergyController.cc.

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

inlinevirtual

type() is specifying the output name of the TopologyClaimer

Implements protocols::topology_broker::TopologyClaimer.

Definition at line 59 of file PseudocontactShiftEnergyController.hh.

References _static_type_name().

Member Data Documentation

utility::vector1<std::string> protocols::topology_broker::PseudocontactShiftEnergyController::filenames_

private

Definition at line 146 of file PseudocontactShiftEnergyController.hh.

std::string protocols::topology_broker::PseudocontactShiftEnergyController::grid_atom_name_1_stage1_

private

Definition at line 111 of file PseudocontactShiftEnergyController.hh.

std::string protocols::topology_broker::PseudocontactShiftEnergyController::grid_atom_name_1_stage2_

private

Definition at line 112 of file PseudocontactShiftEnergyController.hh.

std::string protocols::topology_broker::PseudocontactShiftEnergyController::grid_atom_name_1_stage3_

private

Definition at line 113 of file PseudocontactShiftEnergyController.hh.

std::string protocols::topology_broker::PseudocontactShiftEnergyController::grid_atom_name_1_stage4_

private

Definition at line 114 of file PseudocontactShiftEnergyController.hh.

std::string protocols::topology_broker::PseudocontactShiftEnergyController::grid_atom_name_2_stage1_

private

Definition at line 116 of file PseudocontactShiftEnergyController.hh.

std::string protocols::topology_broker::PseudocontactShiftEnergyController::grid_atom_name_2_stage2_

private

Definition at line 117 of file PseudocontactShiftEnergyController.hh.

std::string protocols::topology_broker::PseudocontactShiftEnergyController::grid_atom_name_2_stage3_

private

Definition at line 118 of file PseudocontactShiftEnergyController.hh.

std::string protocols::topology_broker::PseudocontactShiftEnergyController::grid_atom_name_2_stage4_

private

Definition at line 119 of file PseudocontactShiftEnergyController.hh.

core::Real protocols::topology_broker::PseudocontactShiftEnergyController::grid_cone_angle_cutoff_stage1_

private

Definition at line 106 of file PseudocontactShiftEnergyController.hh.

core::Real protocols::topology_broker::PseudocontactShiftEnergyController::grid_cone_angle_cutoff_stage2_

private

Definition at line 107 of file PseudocontactShiftEnergyController.hh.

core::Real protocols::topology_broker::PseudocontactShiftEnergyController::grid_cone_angle_cutoff_stage3_

private

Definition at line 108 of file PseudocontactShiftEnergyController.hh.

core::Real protocols::topology_broker::PseudocontactShiftEnergyController::grid_cone_angle_cutoff_stage4_

private

Definition at line 109 of file PseudocontactShiftEnergyController.hh.

core::Real protocols::topology_broker::PseudocontactShiftEnergyController::grid_edge_stage1_

private

Definition at line 86 of file PseudocontactShiftEnergyController.hh.

core::Real protocols::topology_broker::PseudocontactShiftEnergyController::grid_edge_stage2_

private

Definition at line 87 of file PseudocontactShiftEnergyController.hh.

core::Real protocols::topology_broker::PseudocontactShiftEnergyController::grid_edge_stage3_

private

Definition at line 88 of file PseudocontactShiftEnergyController.hh.

core::Real protocols::topology_broker::PseudocontactShiftEnergyController::grid_edge_stage4_

private

Definition at line 89 of file PseudocontactShiftEnergyController.hh.

core::Real protocols::topology_broker::PseudocontactShiftEnergyController::grid_k_vector_stage1_

private

Definition at line 131 of file PseudocontactShiftEnergyController.hh.

core::Real protocols::topology_broker::PseudocontactShiftEnergyController::grid_k_vector_stage2_

private

Definition at line 132 of file PseudocontactShiftEnergyController.hh.

core::Real protocols::topology_broker::PseudocontactShiftEnergyController::grid_k_vector_stage3_

private

Definition at line 133 of file PseudocontactShiftEnergyController.hh.

core::Real protocols::topology_broker::PseudocontactShiftEnergyController::grid_k_vector_stage4_

private

Definition at line 134 of file PseudocontactShiftEnergyController.hh.

core::Real protocols::topology_broker::PseudocontactShiftEnergyController::grid_large_cutoff_stage1_

private

Definition at line 101 of file PseudocontactShiftEnergyController.hh.

core::Real protocols::topology_broker::PseudocontactShiftEnergyController::grid_large_cutoff_stage2_

private

Definition at line 102 of file PseudocontactShiftEnergyController.hh.

core::Real protocols::topology_broker::PseudocontactShiftEnergyController::grid_large_cutoff_stage3_

private

Definition at line 103 of file PseudocontactShiftEnergyController.hh.

core::Real protocols::topology_broker::PseudocontactShiftEnergyController::grid_large_cutoff_stage4_

private

Definition at line 104 of file PseudocontactShiftEnergyController.hh.

core::SSize protocols::topology_broker::PseudocontactShiftEnergyController::grid_residue_num_1_stage1_

private

Definition at line 121 of file PseudocontactShiftEnergyController.hh.

core::SSize protocols::topology_broker::PseudocontactShiftEnergyController::grid_residue_num_1_stage2_

private

Definition at line 122 of file PseudocontactShiftEnergyController.hh.

core::SSize protocols::topology_broker::PseudocontactShiftEnergyController::grid_residue_num_1_stage3_

private

Definition at line 123 of file PseudocontactShiftEnergyController.hh.

core::SSize protocols::topology_broker::PseudocontactShiftEnergyController::grid_residue_num_1_stage4_

private

Definition at line 124 of file PseudocontactShiftEnergyController.hh.

core::SSize protocols::topology_broker::PseudocontactShiftEnergyController::grid_residue_num_2_stage1_

private

Definition at line 126 of file PseudocontactShiftEnergyController.hh.

core::SSize protocols::topology_broker::PseudocontactShiftEnergyController::grid_residue_num_2_stage2_

private

Definition at line 127 of file PseudocontactShiftEnergyController.hh.

core::SSize protocols::topology_broker::PseudocontactShiftEnergyController::grid_residue_num_2_stage3_

private

Definition at line 128 of file PseudocontactShiftEnergyController.hh.

core::SSize protocols::topology_broker::PseudocontactShiftEnergyController::grid_residue_num_2_stage4_

private

Definition at line 129 of file PseudocontactShiftEnergyController.hh.

core::Real protocols::topology_broker::PseudocontactShiftEnergyController::grid_small_cutoff_stage1_

private

Definition at line 96 of file PseudocontactShiftEnergyController.hh.

core::Real protocols::topology_broker::PseudocontactShiftEnergyController::grid_small_cutoff_stage2_

private

Definition at line 97 of file PseudocontactShiftEnergyController.hh.

core::Real protocols::topology_broker::PseudocontactShiftEnergyController::grid_small_cutoff_stage3_

private

Definition at line 98 of file PseudocontactShiftEnergyController.hh.

core::Real protocols::topology_broker::PseudocontactShiftEnergyController::grid_small_cutoff_stage4_

private

Definition at line 99 of file PseudocontactShiftEnergyController.hh.

core::Real protocols::topology_broker::PseudocontactShiftEnergyController::grid_step_stage1_

private

Definition at line 91 of file PseudocontactShiftEnergyController.hh.

core::Real protocols::topology_broker::PseudocontactShiftEnergyController::grid_step_stage2_

private

Definition at line 92 of file PseudocontactShiftEnergyController.hh.

core::Real protocols::topology_broker::PseudocontactShiftEnergyController::grid_step_stage3_

private

Definition at line 93 of file PseudocontactShiftEnergyController.hh.

core::Real protocols::topology_broker::PseudocontactShiftEnergyController::grid_step_stage4_

private

Definition at line 94 of file PseudocontactShiftEnergyController.hh.

utility::vector1<core::Real> protocols::topology_broker::PseudocontactShiftEnergyController::individual_weights_

private

Definition at line 147 of file PseudocontactShiftEnergyController.hh.

bool protocols::topology_broker::PseudocontactShiftEnergyController::minimize_best_tensor_stage1_

private

Definition at line 136 of file PseudocontactShiftEnergyController.hh.

bool protocols::topology_broker::PseudocontactShiftEnergyController::minimize_best_tensor_stage2_

private

Definition at line 137 of file PseudocontactShiftEnergyController.hh.

bool protocols::topology_broker::PseudocontactShiftEnergyController::minimize_best_tensor_stage3_

private

Definition at line 138 of file PseudocontactShiftEnergyController.hh.

bool protocols::topology_broker::PseudocontactShiftEnergyController::minimize_best_tensor_stage4_

private

Definition at line 139 of file PseudocontactShiftEnergyController.hh.

core::Real protocols::topology_broker::PseudocontactShiftEnergyController::pcs_weight_stage1_

private

Definition at line 141 of file PseudocontactShiftEnergyController.hh.

core::Real protocols::topology_broker::PseudocontactShiftEnergyController::pcs_weight_stage2_

private

Definition at line 142 of file PseudocontactShiftEnergyController.hh.

core::Real protocols::topology_broker::PseudocontactShiftEnergyController::pcs_weight_stage3_

private

Definition at line 143 of file PseudocontactShiftEnergyController.hh.

core::Real protocols::topology_broker::PseudocontactShiftEnergyController::pcs_weight_stage4_

private

Definition at line 144 of file PseudocontactShiftEnergyController.hh.

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

src/protocols/topology_broker/PseudocontactShiftEnergyController.hh
src/protocols/topology_broker/PseudocontactShiftEnergyController.cc

Public Member Functions

Static Public Member Functions

Private Types

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation