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protocols::topology_broker::FragmentClaimer Class Reference

#include <FragmentClaimer.hh>

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

 FragmentClaimer ()
 
 FragmentClaimer (simple_moves::FragmentMoverOP, std::string const &mover_tag, weights::AbinitioMoverWeightOP weight)
 
 FragmentClaimer (simple_moves::FragmentMoverOP, std::string const &mover_tag, weights::AbinitioMoverWeightOP weight, std::string label, core::fragment::FragSetOP fags)
 
 FragmentClaimer (simple_moves::FragmentMoverOP)
 
 FragmentClaimer (FragmentClaimer const &src)
 
 ~FragmentClaimer () override
 
FragmentClaimerOP shared_from_this ()
 
TopologyClaimerOP clone () const override
 clone it! More...
 
void generate_claims (claims::DofClaims &) override
 generate first round of DOF claims More...
 
void initialize_dofs (core::pose::Pose &, claims::DofClaims const &init_claims, claims::DofClaims &failed_to_init) override
 is called after all round1 claims have been approved or retracted – additional claims can be issued in this round More...
 
bool accept_declined_claim (claims::DofClaim const &was_declined) override
 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...
 
std::string type () const override
 type() is specifying the output name of the TopologyClaimer 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
 
moves::MoverOP get_mover (core::pose::Pose const &) const override
 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
 ~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 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 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 (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 ()
 

Static Public Member Functions

static std::string _static_type_name ()
 

Protected Member Functions

simple_moves::FragmentMover const & mover () const
 
simple_moves::FragmentMoverOP get_frag_mover_ptr ()
 
core::fragment::FragSetCOP fragments ()
 
void set_fragments (core::fragment::FragSetOP)
 
void set_claim_right (claims::DofClaim::ClaimRight setting)
 
bool read_tag (std::string tag, std::istream &) override
 
void init_after_reading () override
 
- Protected Member Functions inherited from protocols::topology_broker::TopologyClaimer
virtual void set_defaults ()
 

Protected Attributes

core::kinematics::MoveMapOP movemap_
 

Private Types

typedef TopologyClaimer Parent
 

Private Attributes

simple_moves::FragmentMoverOP mover_
 
std::string mover_tag_
 
bool bInitDofs_
 
claims::DofClaim::ClaimRight claim_right_
 
loops::Loops region_
 regions that can be used for fragment insertions More...
 
utility::vector1< std::string > active_sequence_labels_
 if non-empty this claimer operates only on the sequences with these labels... create std::set< core::Size > with residue numbers by get_sequence_region(); More...
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::topology_broker::FragmentClaimer::FragmentClaimer ( )

References movemap_.

protocols::topology_broker::FragmentClaimer::FragmentClaimer ( simple_moves::FragmentMoverOP  mover,
std::string const &  mover_tag,
weights::AbinitioMoverWeightOP  weight 
)

References fragments(), and movemap_.

protocols::topology_broker::FragmentClaimer::FragmentClaimer ( simple_moves::FragmentMoverOP  mover,
std::string const &  mover_tag,
weights::AbinitioMoverWeightOP  weight,
std::string  label,
core::fragment::FragSetOP  fags 
)
protocols::topology_broker::FragmentClaimer::FragmentClaimer ( simple_moves::FragmentMoverOP  mover)

References fragments(), movemap_, mover_, and mover_tag_.

protocols::topology_broker::FragmentClaimer::FragmentClaimer ( FragmentClaimer const &  src)

SHALLOW COPY to duplicate the pre-9/7/2009 behavior provided by the compiler.

References bInitDofs_, claim_right_, movemap_, mover_, mover_tag_, and region_.

protocols::topology_broker::FragmentClaimer::~FragmentClaimer ( )
overridedefault

Member Function Documentation

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

Referenced by type().

bool protocols::topology_broker::FragmentClaimer::accept_declined_claim ( claims::DofClaim const &  )
overridevirtual

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 from protocols::topology_broker::TopologyClaimer.

References movemap_, protocols::topology_broker::claims::DofClaim::toggle(), and tr().

TopologyClaimerOP protocols::topology_broker::FragmentClaimer::clone ( ) const
inlineoverridevirtual
core::fragment::FragSetCOP protocols::topology_broker::FragmentClaimer::fragments ( )
protected

References mover_.

Referenced by FragmentClaimer(), generate_claims(), and initialize_dofs().

void protocols::topology_broker::FragmentClaimer::generate_claims ( claims::DofClaims )
overridevirtual
simple_moves::FragmentMoverOP protocols::topology_broker::FragmentClaimer::get_frag_mover_ptr ( )
protected
moves::MoverOP protocols::topology_broker::FragmentClaimer::get_mover ( core::pose::Pose const &  ) const
overridevirtual

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

Reimplemented from protocols::topology_broker::TopologyClaimer.

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

References mover_.

void protocols::topology_broker::FragmentClaimer::get_sequence_region ( std::set< core::Size > &  start_region) const
void protocols::topology_broker::FragmentClaimer::init_after_reading ( )
overrideprotectedvirtual
void protocols::topology_broker::FragmentClaimer::initialize_dofs ( core::pose::Pose pose,
claims::DofClaims const &  init_claims,
claims::DofClaims failed_to_init 
)
overridevirtual
simple_moves::FragmentMover const& protocols::topology_broker::FragmentClaimer::mover ( ) const
inlineprotected
std::string const& protocols::topology_broker::FragmentClaimer::mover_tag ( ) const
inline
bool protocols::topology_broker::FragmentClaimer::read_tag ( std::string  tag,
std::istream &  is 
)
overrideprotectedvirtual
void protocols::topology_broker::FragmentClaimer::set_bInitDofs ( bool  set)
inline
void protocols::topology_broker::FragmentClaimer::set_claim_right ( claims::DofClaim::ClaimRight  setting)
inlineprotected
void protocols::topology_broker::FragmentClaimer::set_fragments ( core::fragment::FragSetOP  frags)
protected
void protocols::topology_broker::FragmentClaimer::set_mover ( simple_moves::FragmentMoverOP  mover)
void protocols::topology_broker::FragmentClaimer::set_mover_tag ( std::string const &  str)
FragmentClaimerOP protocols::topology_broker::FragmentClaimer::shared_from_this ( )
inline
std::string protocols::topology_broker::FragmentClaimer::type ( ) const
inlineoverridevirtual

Member Data Documentation

utility::vector1< std::string > protocols::topology_broker::FragmentClaimer::active_sequence_labels_
private

if non-empty this claimer operates only on the sequences with these labels... create std::set< core::Size > with residue numbers by get_sequence_region();

Referenced by get_sequence_region(), init_after_reading(), and read_tag().

bool protocols::topology_broker::FragmentClaimer::bInitDofs_
private
claims::DofClaim::ClaimRight protocols::topology_broker::FragmentClaimer::claim_right_
private
core::kinematics::MoveMapOP protocols::topology_broker::FragmentClaimer::movemap_
protected
simple_moves::FragmentMoverOP protocols::topology_broker::FragmentClaimer::mover_
private
std::string protocols::topology_broker::FragmentClaimer::mover_tag_
private
loops::Loops protocols::topology_broker::FragmentClaimer::region_
private

regions that can be used for fragment insertions

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


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