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protocols::topology_broker::DisulfJumpClaimer Class Reference

Claimer that works with the old system of BaseJumpSetup it supports only JumpFrames of type [ BBTorsion ] UpJump DownJump [ BBTorsion ] the class JumpSample is still used to transport the information jumps and jump_atoms, but cuts are ignored all functionality of JumpSample is not used anymore. More...

#include <DisulfJumpClaimer.hh>

Inheritance diagram for protocols::topology_broker::DisulfJumpClaimer:
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Collaboration diagram for protocols::topology_broker::DisulfJumpClaimer:
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Public Member Functions

 DisulfJumpClaimer ()
 
virtual TopologyClaimerOP clone () const
 clone it! More...
 
void generate_jump_frags (protocols::jumping::DisulfPairingLibrary const &lib, core::fragment::FrameList &all_frames) const
 
virtual void generate_claims (DofClaims &)
 generate first round of DOF claims 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...
 
virtual void new_decoy ()
 a new decoy — random choices to be made ? make them here More...
 
virtual std::string type () const
 type() is specifying the output name of the TopologyClaimer More...
 
virtual void initialize_dofs (core::pose::Pose &, DofClaims const &init_claims, DofClaims &failed_to_init)
 is called after all round1 claims have been approved or retracted – additional claims can be issued in this round More...
 
virtual bool read_tag (std::string tag, std::istream &is)
 
- Public Member Functions inherited from protocols::topology_broker::FragmentClaimer
 FragmentClaimer ()
 
 FragmentClaimer (simple_moves::FragmentMoverOP, std::string mover_tag, weights::AbinitioMoverWeightOP weight)
 
 FragmentClaimer (simple_moves::FragmentMoverOP)
 
 FragmentClaimer (FragmentClaimer const &src)
 
 ~FragmentClaimer ()
 
virtual bool accept_declined_claim (DofClaim const &was_declined)
 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...
 
void set_mover (simple_moves::FragmentMoverOP mover)
 
void set_mover_tag (std::string const &str)
 
void set_bInitDofs (bool set)
 
std::string const & mover_tag () const
 
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...
 
void get_sequence_region (std::set< core::Size > &start_region) const
 
- 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 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 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 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...
 
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::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...
 
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 Public Member Functions inherited from protocols::topology_broker::FragmentClaimer
static std::string _static_type_name ()
 

Private Types

typedef FragmentClaimer Parent
 

Private Attributes

utility::vector1
< protocols::jumping::DisulfPairing
all_jump_pairings_
 
core::fragment::FrameList all_frames_
 
bool bKeepJumpsFromInputPose_
 

Additional Inherited Members

- Protected Member Functions inherited from protocols::topology_broker::FragmentClaimer
simple_moves::FragmentMover const & mover () const
 
simple_moves::FragmentMoverOP get_frag_mover_ptr ()
 
void set_claim_right (DofClaim::ClaimRight setting)
 
virtual void init_after_reading ()
 
- Protected Attributes inherited from protocols::topology_broker::FragmentClaimer
core::kinematics::MoveMapOP movemap_
 

Detailed Description

Claimer that works with the old system of BaseJumpSetup it supports only JumpFrames of type [ BBTorsion ] UpJump DownJump [ BBTorsion ] the class JumpSample is still used to transport the information jumps and jump_atoms, but cuts are ignored all functionality of JumpSample is not used anymore.

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::topology_broker::DisulfJumpClaimer::DisulfJumpClaimer ( )

Member Function Documentation

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

Referenced by type().

virtual TopologyClaimerOP protocols::topology_broker::DisulfJumpClaimer::clone ( ) const
inlinevirtual

clone it!

Reimplemented from protocols::topology_broker::FragmentClaimer.

References DisulfJumpClaimer().

void protocols::topology_broker::DisulfJumpClaimer::generate_claims ( DofClaims )
virtual
void protocols::topology_broker::DisulfJumpClaimer::generate_jump_frags ( protocols::jumping::DisulfPairingLibrary const &  lib,
core::fragment::FrameList all_frames 
) const
void protocols::topology_broker::DisulfJumpClaimer::initialize_dofs ( core::pose::Pose pose,
DofClaims const &  init_claims,
DofClaims failed_to_init 
)
virtual

is called after all round1 claims have been approved or retracted – additional claims can be issued in this round

Reimplemented from protocols::topology_broker::FragmentClaimer.

References protocols::topology_broker::FragmentClaimer::initialize_dofs().

void protocols::topology_broker::DisulfJumpClaimer::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 new_decoy().

void protocols::topology_broker::DisulfJumpClaimer::new_decoy ( )
virtual
bool protocols::topology_broker::DisulfJumpClaimer::read_tag ( std::string  tag,
std::istream &  is 
)
virtual
virtual std::string protocols::topology_broker::DisulfJumpClaimer::type ( ) const
inlinevirtual

type() is specifying the output name of the TopologyClaimer

Reimplemented from protocols::topology_broker::FragmentClaimer.

References _static_type_name().

Member Data Documentation

core::fragment::FrameList protocols::topology_broker::DisulfJumpClaimer::all_frames_
private

Referenced by new_decoy().

utility::vector1< protocols::jumping::DisulfPairing > protocols::topology_broker::DisulfJumpClaimer::all_jump_pairings_
private
bool protocols::topology_broker::DisulfJumpClaimer::bKeepJumpsFromInputPose_
private

Referenced by read_tag().


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