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protocols::topology_broker::PseudocontactShiftEnergyController_Ts4 Class Reference

#include <PseudocontactShiftEnergyController_Ts4.hh>

Inheritance diagram for protocols::topology_broker::PseudocontactShiftEnergyController_Ts4:
Inheritance graph
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Public Member Functions

 PseudocontactShiftEnergyController_Ts4 ()
 
TopologyClaimerOP clone () const override
 clone it! More...
 
std::string type () const override
 type() is specifying the output name of the TopologyClaimer More...
 
bool read_tag (std::string tag, std::istream &) override
 
void set_defaults () override
 
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 init_after_reading () override
 
- 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 bool claimer_builds_own_fold_tree ()
 
virtual
core::kinematics::FoldTreeOP 
get_fold_tree (core::pose::Pose &)
 in case a claimer has its own fold_tree. get_fold_tree() is called by the broker More...
 
virtual void build_fold_tree (core::pose::Pose &, core::kinematics::FoldTree &)
 
virtual void set_pose_from_broker (core::pose::Pose &)
 
virtual void read (std::istream &)
 read definition of Claimer from setup file, i.e., a CLAIMER <type> ... END_CLAIMER block More...
 
virtual void pre_process (core::pose::Pose &)
 
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 generate_claims (claims::DofClaims &)
 generate first round of DOF claims 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 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::AbinitioMoverWeightmover_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 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::Realindividual_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...
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::PseudocontactShiftEnergyController_Ts4 ( )

Member Function Documentation

static std::string protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::_static_type_name ( )
inlinestatic

Referenced by type().

void protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::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 core::scoring::pcsTs4, protocols::abinitio::STAGE_1, protocols::abinitio::STAGE_2, protocols::abinitio::STAGE_3a, protocols::abinitio::STAGE_3b, and protocols::abinitio::STAGE_4.

TopologyClaimerOP protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::clone ( ) const
inlineoverridevirtual
void protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::control_grid_param ( )
private
void protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::init_after_reading ( )
overridevirtual
bool protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::read_tag ( std::string  tag,
std::istream &  is 
)
overridevirtual
void protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::set_defaults ( )
overridevirtual
std::string protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::type ( ) const
inlineoverridevirtual

type() is specifying the output name of the TopologyClaimer

Implements protocols::topology_broker::TopologyClaimer.

References _static_type_name().

Member Data Documentation

utility::vector1<std::string> protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::filenames_
private
std::string protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::grid_atom_name_1_stage1_
private
std::string protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::grid_atom_name_1_stage2_
private
std::string protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::grid_atom_name_1_stage3_
private
std::string protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::grid_atom_name_1_stage4_
private
std::string protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::grid_atom_name_2_stage1_
private
std::string protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::grid_atom_name_2_stage2_
private
std::string protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::grid_atom_name_2_stage3_
private
std::string protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::grid_atom_name_2_stage4_
private
core::Real protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::grid_cone_angle_cutoff_stage1_
private
core::Real protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::grid_cone_angle_cutoff_stage2_
private
core::Real protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::grid_cone_angle_cutoff_stage3_
private
core::Real protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::grid_cone_angle_cutoff_stage4_
private
core::Real protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::grid_edge_stage1_
private
core::Real protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::grid_edge_stage2_
private
core::Real protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::grid_edge_stage3_
private
core::Real protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::grid_edge_stage4_
private
core::Real protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::grid_k_vector_stage1_
private
core::Real protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::grid_k_vector_stage2_
private
core::Real protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::grid_k_vector_stage3_
private
core::Real protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::grid_k_vector_stage4_
private
core::Real protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::grid_large_cutoff_stage1_
private
core::Real protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::grid_large_cutoff_stage2_
private
core::Real protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::grid_large_cutoff_stage3_
private
core::Real protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::grid_large_cutoff_stage4_
private
core::SSize protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::grid_residue_num_1_stage1_
private
core::SSize protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::grid_residue_num_1_stage2_
private
core::SSize protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::grid_residue_num_1_stage3_
private
core::SSize protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::grid_residue_num_1_stage4_
private
core::SSize protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::grid_residue_num_2_stage1_
private
core::SSize protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::grid_residue_num_2_stage2_
private
core::SSize protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::grid_residue_num_2_stage3_
private
core::SSize protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::grid_residue_num_2_stage4_
private
core::Real protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::grid_small_cutoff_stage1_
private
core::Real protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::grid_small_cutoff_stage2_
private
core::Real protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::grid_small_cutoff_stage3_
private
core::Real protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::grid_small_cutoff_stage4_
private
core::Real protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::grid_step_stage1_
private
core::Real protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::grid_step_stage2_
private
core::Real protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::grid_step_stage3_
private
core::Real protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::grid_step_stage4_
private
utility::vector1<core::Real> protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::individual_weights_
private
bool protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::minimize_best_tensor_stage1_
private
bool protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::minimize_best_tensor_stage2_
private
bool protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::minimize_best_tensor_stage3_
private
bool protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::minimize_best_tensor_stage4_
private
core::Real protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::pcs_weight_stage1_
private
core::Real protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::pcs_weight_stage2_
private
core::Real protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::pcs_weight_stage3_
private
core::Real protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::pcs_weight_stage4_
private

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