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protocols::topology_broker::FibrilModelingClaimer Class Reference

#include <FibrilModelingClaimer.hh>

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

 FibrilModelingClaimer ()
 
 FibrilModelingClaimer (core::pose::Pose const &input_pose, loops::Loops rigid, int shift=0)
 
 FibrilModelingClaimer (core::pose::Pose const &input_pose, loops::Loops rigid, loops::Loops input_rigid)
 
void make_fibril (core::pose::Pose &pose)
 
virtual TopologyClaimerOP clone () const
 clone it! More...
 
virtual std::string type () const
 type() is specifying the output name of the TopologyClaimer More...
 
virtual void add_mover (moves::RandomMover &random_mover, core::pose::Pose const &pose, abinitio::StageID stageID, core::scoring::ScoreFunction const &scorefxn, core::Real progress)
 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 initialize_dofs (core::pose::Pose &, DofClaims const &init_claims, DofClaims &)
 initialize dofs – e.g., torsions, jumps – Claimer searches init_claims for claims owned by *this More...
 
virtual void generate_claims (DofClaims &new_claims)
 generate first round of DOF claims More...
 
virtual bool allow_claim (DofClaim const &)
 has to decline foreign BB claims for slave regions More...
 
- 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 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 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::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 &)
 

Static Public Member Functions

static std::string _static_type_name ()
 

Protected Member Functions

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

Private Types

typedef TopologyClaimer Parent
 

Private Attributes

core::pose::Pose input_pose_
 monomer pose More...
 
loops::Loops rigid_core_
 regions that can be used for rigid core More...
 
loops::Loops input_rigid_core_
 
bool bAlign_
 align to the monomer before create symmetry More...
 
int sequence_shift_
 
core::conformation::symmetry::SymmetryInfoOP symminfo_
 symmetry information More...
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::topology_broker::FibrilModelingClaimer::FibrilModelingClaimer ( )

Referenced by clone().

protocols::topology_broker::FibrilModelingClaimer::FibrilModelingClaimer ( core::pose::Pose const &  input_pose,
loops::Loops  rigid,
int  shift = 0 
)
protocols::topology_broker::FibrilModelingClaimer::FibrilModelingClaimer ( core::pose::Pose const &  input_pose,
loops::Loops  rigid,
loops::Loops  input_rigid 
)

Member Function Documentation

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

Referenced by type().

void protocols::topology_broker::FibrilModelingClaimer::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.

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

bool protocols::topology_broker::FibrilModelingClaimer::allow_claim ( DofClaim const &  foreign_claim)
virtual
virtual TopologyClaimerOP protocols::topology_broker::FibrilModelingClaimer::clone ( ) const
inlinevirtual
void protocols::topology_broker::FibrilModelingClaimer::generate_claims ( DofClaims )
virtual
void protocols::topology_broker::FibrilModelingClaimer::initialize_dofs ( core::pose::Pose ,
DofClaims const &  init_claims,
DofClaims failed_to_init 
)
virtual

initialize dofs – e.g., torsions, jumps – Claimer searches init_claims for claims owned by *this

Reimplemented from protocols::topology_broker::TopologyClaimer.

References protocols::simple_moves::symmetry::SymDockingInitialPerturbation::apply(), make_fibril(), and core::pose::symmetry::make_symmetric_movemap().

void protocols::topology_broker::FibrilModelingClaimer::make_fibril ( core::pose::Pose pose)
bool protocols::topology_broker::FibrilModelingClaimer::read_tag ( std::string  tag,
std::istream &  is 
)
protectedvirtual
virtual std::string protocols::topology_broker::FibrilModelingClaimer::type ( ) const
inlinevirtual

type() is specifying the output name of the TopologyClaimer

Implements protocols::topology_broker::TopologyClaimer.

References _static_type_name().

Referenced by read_tag().

Member Data Documentation

bool protocols::topology_broker::FibrilModelingClaimer::bAlign_
private

align to the monomer before create symmetry

Referenced by FibrilModelingClaimer(), make_fibril(), and read_tag().

core::pose::Pose protocols::topology_broker::FibrilModelingClaimer::input_pose_
private

monomer pose

Referenced by generate_claims(), make_fibril(), and read_tag().

loops::Loops protocols::topology_broker::FibrilModelingClaimer::input_rigid_core_
private
loops::Loops protocols::topology_broker::FibrilModelingClaimer::rigid_core_
private

regions that can be used for rigid core

Referenced by FibrilModelingClaimer(), make_fibril(), and read_tag().

int protocols::topology_broker::FibrilModelingClaimer::sequence_shift_
private

Referenced by FibrilModelingClaimer(), and read_tag().

core::conformation::symmetry::SymmetryInfoOP protocols::topology_broker::FibrilModelingClaimer::symminfo_
private

symmetry information

Referenced by allow_claim(), and make_fibril().


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