Rosetta  2020.46
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Protected Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::topology_broker::TopologyClaimer Class Referenceabstract

More...

#include <TopologyClaimer.hh>

Inheritance diagram for protocols::topology_broker::TopologyClaimer:
Inheritance graph
[legend]

Public Member Functions

 ~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 TopologyClaimerOP clone () const =0
 clone it! More...
 
virtual std::string type () const =0
 name of Claimer More...
 
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...
 
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...
 
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 ()
 

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

Private Member Functions

void unknown_tag (std::string tag, std::istream &is) const
 

Private Attributes

claims::DofClaims current_claims_
 currently accepted claims... dunno haven't used that yet. More...
 
weights::AbinitioMoverWeightOP abinitio_mover_weight_
 weight set .. how often shall this claimer's mover be sampled during different stages ? More...
 
TopologyBrokerCAP broker_
 oh, our master. (use broker() to get this ). More...
 
std::string label_
 a user defined string, can be used to send messages from claimer to claimer More...
 

Detailed Description

Constructor & Destructor Documentation

protocols::topology_broker::TopologyClaimer::~TopologyClaimer ( )
overridedefault

Automatically generated virtual destructor for class deriving directly from VirtualBase.

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 ? )

References abinitio_mover_weight_.

Member Function Documentation

virtual bool protocols::topology_broker::TopologyClaimer::accept_declined_claim ( claims::DofClaim const &  )
inlinevirtual

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

virtual void protocols::topology_broker::TopologyClaimer::add_constraints ( core::pose::Pose ) const
inlinevirtual
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
virtual void protocols::topology_broker::TopologyClaimer::adjust_relax_movemap ( core::kinematics::MoveMap ) const
inlinevirtual
virtual bool protocols::topology_broker::TopologyClaimer::allow_claim ( claims::DofClaim const &  )
inlinevirtual

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::build_fold_tree ( core::pose::Pose ,
core::kinematics::FoldTree  
)
inlinevirtual
virtual void protocols::topology_broker::TopologyClaimer::claim_accepted ( claims::DofClaimOP  my_claim)
inlinevirtual

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

References current_claims_.

virtual bool protocols::topology_broker::TopologyClaimer::claimer_builds_own_fold_tree ( )
inlinevirtual
virtual TopologyClaimerOP protocols::topology_broker::TopologyClaimer::clone ( ) const
pure virtual
virtual void protocols::topology_broker::TopologyClaimer::finalize_claims ( claims::DofClaims )
inlinevirtual

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 ( claims::DofClaims )
inlinevirtual
virtual void protocols::topology_broker::TopologyClaimer::generate_sequence_claims ( claims::DofClaims )
inlinevirtual
virtual void protocols::topology_broker::TopologyClaimer::generate_symmetry_claims ( claims::SymmetryClaims )
inlinevirtual

generate claims that affect the sequence of the pose

Reimplemented in protocols::topology_broker::SymmetryClaimer.

virtual core::kinematics::FoldTreeOP protocols::topology_broker::TopologyClaimer::get_fold_tree ( core::pose::Pose )
inlinevirtual

in case a claimer has its own fold_tree. get_fold_tree() is called by the broker

Reimplemented in protocols::topology_broker::TMHTopologySamplerClaimer, and protocols::topology_broker::MembraneTopologyClaimer.

virtual moves::MoverOP protocols::topology_broker::TopologyClaimer::get_mover ( core::pose::Pose const &  ) const
inlineprotectedvirtual

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::StartStructClaimer, and protocols::topology_broker::LoopFragmentClaimer.

virtual core::pose::PoseOP protocols::topology_broker::TopologyClaimer::get_pose_from_claimer ( )
inlinevirtual
TopologyClaimerCOP protocols::topology_broker::TopologyClaimer::get_self_ptr ( ) const
inline

self pointers

TopologyClaimerOP protocols::topology_broker::TopologyClaimer::get_self_ptr ( )
inline
TopologyClaimerCAP protocols::topology_broker::TopologyClaimer::get_self_weak_ptr ( ) const
inline
TopologyClaimerAP protocols::topology_broker::TopologyClaimer::get_self_weak_ptr ( )
inline
virtual void protocols::topology_broker::TopologyClaimer::init_after_reading ( )
inlineprotectedvirtual
void protocols::topology_broker::TopologyClaimer::initialize_dofs ( core::pose::Pose ,
claims::DofClaims const &  init_claims,
claims::DofClaims failed_to_init 
)
virtual
std::string const& protocols::topology_broker::TopologyClaimer::label ( ) const
inline
virtual core::fragment::FragSetCOP protocols::topology_broker::TopologyClaimer::loop_frags ( core::kinematics::MoveMap ) const
inlinevirtual

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 > &  )
inlinevirtual

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

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

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::StartStructClaimer, protocols::topology_broker::CoordConstraintClaimer, protocols::topology_broker::FragmentJumpClaimer, protocols::topology_broker::RigidChunkClaimer, and protocols::topology_broker::DisulfJumpClaimer.

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 &   
)
inlinevirtual

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 protocols::topology_broker::TopologyClaimer::pre_process ( core::pose::Pose )
inlinevirtual
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::TemplateFragmentClaimer::read_tag(), protocols::topology_broker::DisulfJumpClaimer::read_tag(), and protocols::topology_broker::TemplateJumpClaimer::read_tag().

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

Reimplemented in protocols::topology_broker::FragmentClaimer, protocols::topology_broker::MetalloClaimer, protocols::topology_broker::RigidChunkClaimer, protocols::topology_broker::TMHTopologySamplerClaimer, protocols::topology_broker::CoordConstraintClaimer, protocols::topology_broker::StartStructClaimer, protocols::topology_broker::DensityScoringClaimer, protocols::topology_broker::FibrilModelingClaimer, protocols::topology_broker::FragmentJumpClaimer, protocols::topology_broker::BasicJumpClaimer, protocols::topology_broker::TemplateJumpClaimer, protocols::topology_broker::DisulfJumpClaimer, protocols::topology_broker::SequenceClaimer, protocols::topology_broker::ConstraintClaimer, protocols::topology_broker::TemplateFragmentClaimer, protocols::topology_broker::SymmetryClaimer, protocols::topology_broker::PcsEnergyController, protocols::topology_broker::AsymFoldandDockClaimer, protocols::topology_broker::PseudocontactShiftEnergyController_Ts2, protocols::topology_broker::PseudocontactShiftEnergyController_Ts3, protocols::topology_broker::PseudocontactShiftEnergyController_Ts4, protocols::topology_broker::PseudocontactShiftEnergyController_Ts1, and protocols::topology_broker::PseudocontactShiftEnergyController.

References tr().

Referenced by protocols::topology_broker::SymmetryClaimer::read_tag(), protocols::topology_broker::ConstraintClaimer::read_tag(), protocols::topology_broker::SequenceClaimer::read_tag(), protocols::topology_broker::BasicJumpClaimer::read_tag(), protocols::topology_broker::FibrilModelingClaimer::read_tag(), protocols::topology_broker::CoordConstraintClaimer::read_tag(), protocols::topology_broker::RigidChunkClaimer::read_tag(), and protocols::topology_broker::FragmentClaimer::read_tag().

virtual void protocols::topology_broker::TopologyClaimer::receive_message ( ClaimerMessage )
inlinevirtual
void protocols::topology_broker::TopologyClaimer::set_broker ( TopologyBrokerCAP  ptr)
inline

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

References broker_.

void protocols::topology_broker::TopologyClaimer::set_defaults ( )
protectedvirtual
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::set_pose_from_broker ( core::pose::Pose )
inlinevirtual
virtual void protocols::topology_broker::TopologyClaimer::switch_to_fullatom ( core::pose::Pose ,
utility::vector1< bool  
) const
inlinevirtual

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
void protocols::topology_broker::TopologyClaimer::unknown_tag ( std::string  tag,
std::istream &  is 
) const
private

Member Data Documentation

weights::AbinitioMoverWeightOP protocols::topology_broker::TopologyClaimer::abinitio_mover_weight_
private

weight set .. how often shall this claimer's mover be sampled during different stages ?

Referenced by mover_weight(), set_mover_weight(), and TopologyClaimer().

TopologyBrokerCAP protocols::topology_broker::TopologyClaimer::broker_
private

oh, our master. (use broker() to get this ).

Referenced by broker(), and set_broker().

claims::DofClaims protocols::topology_broker::TopologyClaimer::current_claims_
private

currently accepted claims... dunno haven't used that yet.

Referenced by claim_accepted().

std::string protocols::topology_broker::TopologyClaimer::label_
private

a user defined string, can be used to send messages from claimer to claimer

Referenced by label(), and set_label().


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