Rosetta 3.4
Public Member Functions | Protected Member Functions
protocols::topology_broker::TopologyClaimer Class Reference

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#include <TopologyClaimer.hh>

Inheritance diagram for protocols::topology_broker::TopologyClaimer:
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Collaboration diagram for protocols::topology_broker::TopologyClaimer:
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List of all members.

Public Member Functions

 TopologyClaimer ()
 TopologyClaimer (weights::AbinitioMoverWeightOP weight)
 construct with weight-set ( how important is mover for different abinitio stages ? )
virtual TopologyClaimerOP clone () const =0
 clone it!
virtual std::string type () const =0
 name of Claimer
virtual void read (std::istream &)
 read definition of Claimer from setup file, i.e., a CLAIMER <type> ... END_CLAIMER block
virtual void generate_sequence_claims (DofClaims &)
 generate claims that affect the sequence of the pose
virtual void generate_claims (DofClaims &)
 generate first round of DOF claims
virtual void finalize_claims (DofClaims &)
 is called after all round1 claims have been approved or retracted -- additional claims can be issued in this round
virtual bool allow_claim (DofClaim const &)
 allow a claim from a foreign Claimer
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
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
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
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
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 ... )
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.
virtual void add_constraints (core::pose::Pose &)
 add constraints to pose... might make this stage dependent as with movers...
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
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_
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_
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
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
TopologyBroker const & broker () const
 return the broker we are collaborating with
virtual void new_decoy ()
 a new decoy --- random choices to be made ? make them here
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
std::string const & label () const
void set_label (std::string const &str)
virtual void receive_message (ClaimerMessage &)

Protected Member Functions

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
virtual bool read_tag (std::string tag, std::istream &is)
virtual void set_defaults ()
virtual void init_after_reading ()

Detailed Description


Constructor & Destructor Documentation

protocols::topology_broker::TopologyClaimer::TopologyClaimer ( ) [inline]
protocols::topology_broker::TopologyClaimer::TopologyClaimer ( weights::AbinitioMoverWeightOP  weight) [inline]

construct with weight-set ( how important is mover for different abinitio stages ? )


Member Function Documentation

virtual bool protocols::topology_broker::TopologyClaimer::accept_declined_claim ( DofClaim const &  ) [inline, virtual]

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 ... )

Reimplemented in protocols::topology_broker::DensityScoringClaimer, protocols::topology_broker::FragmentClaimer, and protocols::topology_broker::RigidChunkClaimer.

virtual void protocols::topology_broker::TopologyClaimer::add_constraints ( core::pose::Pose ) [inline, virtual]

add constraints to pose... might make this stage dependent as with movers...

Reimplemented in protocols::topology_broker::ConstraintClaimer, protocols::topology_broker::CoordConstraintClaimer, and protocols::topology_broker::MetalloClaimer.

void protocols::topology_broker::TopologyClaimer::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 in protocols::topology_broker::AsymFoldandDockClaimer, protocols::topology_broker::FibrilModelingClaimer, protocols::topology_broker::FoldandDockClaimer, protocols::topology_broker::MembraneTopologyClaimer, protocols::topology_broker::PcsEnergyController, and protocols::topology_broker::PseudocontactShiftEnergyController.

References protocols::moves::MoverContainer::add_mover().

virtual void protocols::topology_broker::TopologyClaimer::adjust_relax_movemap ( core::kinematics::MoveMap ) const [inline, virtual]
virtual bool protocols::topology_broker::TopologyClaimer::allow_claim ( DofClaim const &  ) [inline, virtual]

allow a claim from a foreign Claimer

Reimplemented in protocols::topology_broker::FibrilModelingClaimer, and protocols::topology_broker::RigidChunkClaimer.

TopologyBroker const& protocols::topology_broker::TopologyClaimer::broker ( ) const [inline]
virtual void protocols::topology_broker::TopologyClaimer::claim_accepted ( DofClaimOP  my_claim) [inline, virtual]

this claim of yours was accepted.... I so far haven't done anything with this... might go away.

virtual TopologyClaimerOP protocols::topology_broker::TopologyClaimer::clone ( ) const [pure virtual]
virtual void protocols::topology_broker::TopologyClaimer::finalize_claims ( DofClaims ) [inline, virtual]

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

Reimplemented in protocols::topology_broker::RigidChunkClaimer.

virtual void protocols::topology_broker::TopologyClaimer::generate_claims ( DofClaims ) [inline, virtual]
virtual void protocols::topology_broker::TopologyClaimer::generate_sequence_claims ( DofClaims ) [inline, virtual]
virtual moves::MoverOP protocols::topology_broker::TopologyClaimer::get_mover ( core::pose::Pose const &  ) const [inline, protected, virtual]

what is your mover ... called by add_mover --- overload this or add_mover if you have movers too supply

Reimplemented in protocols::topology_broker::FragmentClaimer, protocols::topology_broker::LoopFragmentClaimer, and protocols::topology_broker::StartStructClaimer.

virtual void protocols::topology_broker::TopologyClaimer::init_after_reading ( ) [inline, protected, virtual]
void protocols::topology_broker::TopologyClaimer::initialize_dofs ( core::pose::Pose ,
DofClaims const &  init_claims,
DofClaims failed_to_init 
) [virtual]
void protocols::topology_broker::TopologyClaimer::initialize_residues ( core::pose::Pose ,
SequenceClaimOP  init_claim,
DofClaims failed_to_init 
) [virtual]

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

Reimplemented in protocols::topology_broker::DensityScoringClaimer, protocols::topology_broker::MetalloClaimer, protocols::topology_broker::SequenceClaimer, and protocols::topology_broker::StartStructClaimer.

References tr().

std::string const& protocols::topology_broker::TopologyClaimer::label ( ) const [inline]
virtual core::fragment::FragSetCOP protocols::topology_broker::TopologyClaimer::loop_frags ( core::kinematics::MoveMap ) const [inline, virtual]

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

Reimplemented in protocols::topology_broker::LoopFragmentClaimer.

virtual void protocols::topology_broker::TopologyClaimer::manipulate_cut_bias ( utility::vector1< core::Real > &  ) [inline, virtual]

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

Reimplemented in protocols::topology_broker::CutBiasClaimer, and protocols::topology_broker::RigidChunkClaimer.

weights::AbinitioMoverWeight& protocols::topology_broker::TopologyClaimer::mover_weight ( ) [inline]
virtual void protocols::topology_broker::TopologyClaimer::new_decoy ( ) [inline, virtual]
virtual void protocols::topology_broker::TopologyClaimer::new_decoy ( core::pose::Pose const &  ) [inline, virtual]

an input pose is given, i.e., a starting structure for resampling don't make random choices, base choices on given pose

Reimplemented in protocols::topology_broker::CoordConstraintClaimer, protocols::topology_broker::DisulfJumpClaimer, protocols::topology_broker::JumpClaimer, protocols::topology_broker::RigidChunkClaimer, and protocols::topology_broker::StartStructClaimer.

References new_decoy().

Referenced by new_decoy().

virtual bool protocols::topology_broker::TopologyClaimer::passes_filter ( core::pose::Pose const &  ,
abinitio::StageID  ,
core::Real  ,
std::ostringstream &   
) [inline, 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_

void protocols::topology_broker::TopologyClaimer::read ( std::istream &  is) [virtual]

read definition of Claimer from setup file, i.e., a CLAIMER <type> ... END_CLAIMER block

Reimplemented in protocols::topology_broker::CutBiasClaimer.

References tr().

Referenced by protocols::topology_broker::operator>>().

void protocols::topology_broker::TopologyClaimer::read_mover_weight ( std::istream &  is)

read mover weight from Stream. - so far recognizes: LargeStage, SmallStage, SmoothStage, AllStage

Referenced by protocols::topology_broker::TemplateJumpClaimer::read_tag(), protocols::topology_broker::DisulfJumpClaimer::read_tag(), and protocols::topology_broker::TemplateFragmentClaimer::read_tag().

bool protocols::topology_broker::TopologyClaimer::read_tag ( std::string  tag,
std::istream &  is 
) [protected, virtual]
virtual void protocols::topology_broker::TopologyClaimer::receive_message ( ClaimerMessage ) [inline, virtual]
void protocols::topology_broker::TopologyClaimer::set_broker ( TopologyBrokerCAP  ptr) [inline]

don't use this --- it is called by TopologyBroker add_claim only

void protocols::topology_broker::TopologyClaimer::set_defaults ( ) [protected, virtual]
void protocols::topology_broker::TopologyClaimer::set_label ( std::string const &  str) [inline]
void protocols::topology_broker::TopologyClaimer::set_mover_weight ( weights::AbinitioMoverWeightOP  wset) [inline]
virtual void protocols::topology_broker::TopologyClaimer::switch_to_fullatom ( core::pose::Pose ,
utility::vector1< bool  
) const [inline, virtual]

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

Reimplemented in protocols::topology_broker::RigidChunkClaimer.

virtual std::string protocols::topology_broker::TopologyClaimer::type ( ) const [pure virtual]

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