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protocols::topology_broker::FragmentJumpClaimer 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 <FragmentJumpClaimer.hh>

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

 FragmentJumpClaimer ()
 
 FragmentJumpClaimer (jumping::BaseJumpSetupOP jump_def, std::string const &mover_tag="JumpMove", weights::AbinitioMoverWeightOP weight=nullptr)
 
 FragmentJumpClaimer (FragmentJumpClaimer const &src)
 
 ~FragmentJumpClaimer () override
 
TopologyClaimerOP clone () const override
 clone it! More...
 
void generate_claims (claims::DofClaims &) override
 generate first round of DOF claims More...
 
void new_decoy (core::pose::Pose const &) override
 an input pose is given, i.e., a starting structure for resampling don't make random choices, base choices on given pose More...
 
void new_decoy () override
 a new decoy — random choices to be made ? make them here More...
 
std::string type () const override
 type() is specifying the output name of the TopologyClaimer 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 read_tag (std::string tag, std::istream &is) override
 
- Public Member Functions inherited from protocols::topology_broker::FragmentClaimer
 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 ()
 
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...
 
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...
 
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 ()
 
- Static Public Member Functions inherited from protocols::topology_broker::FragmentClaimer
static std::string _static_type_name ()
 

Protected Member Functions

void set_jump_def (jumping::BaseJumpSetupOP jump_def)
 
virtual void generate_claims (claims::DofClaims &, std::string, std::string)
 
jumping::BaseJumpSetupOP jump_def ()
 
void set_keep_jumps_from_input_pose (bool setting)
 
void init_jumps ()
 
- Protected Member Functions inherited from protocols::topology_broker::FragmentClaimer
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)
 
void init_after_reading () override
 
- Protected Member Functions inherited from protocols::topology_broker::TopologyClaimer
virtual void set_defaults ()
 

Private Types

typedef FragmentClaimer Parent
 

Private Attributes

jumping::BaseJumpSetupOP jump_def_
 
jumping::JumpSample current_jumps_
 
simple_moves::ClassicFragmentMoverOP init_mover_
 
bool bKeepJumpsFromInputPose_
 
core::pose::Pose input_pose_
 
bool discard_jumps_
 

Additional Inherited Members

- 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::FragmentJumpClaimer::FragmentJumpClaimer ( )
protocols::topology_broker::FragmentJumpClaimer::FragmentJumpClaimer ( jumping::BaseJumpSetupOP  jump_def,
std::string const &  mover_tag = "JumpMove",
weights::AbinitioMoverWeightOP  weight = nullptr 
)
protocols::topology_broker::FragmentJumpClaimer::FragmentJumpClaimer ( FragmentJumpClaimer const &  src)
protocols::topology_broker::FragmentJumpClaimer::~FragmentJumpClaimer ( )
overridedefault

Member Function Documentation

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

Referenced by type().

TopologyClaimerOP protocols::topology_broker::FragmentJumpClaimer::clone ( ) const
overridevirtual
void protocols::topology_broker::FragmentJumpClaimer::generate_claims ( claims::DofClaims )
overridevirtual
void protocols::topology_broker::FragmentJumpClaimer::generate_claims ( claims::DofClaims new_claims,
std::string  uplabel,
std::string  downlabel 
)
protectedvirtual
void protocols::topology_broker::FragmentJumpClaimer::init_jumps ( )
protected
void protocols::topology_broker::FragmentJumpClaimer::initialize_dofs ( core::pose::Pose pose,
claims::DofClaims const &  init_claims,
claims::DofClaims failed_to_init 
)
overridevirtual
jumping::BaseJumpSetupOP protocols::topology_broker::FragmentJumpClaimer::jump_def ( )
inlineprotected
void protocols::topology_broker::FragmentJumpClaimer::new_decoy ( core::pose::Pose const &  )
overridevirtual

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 input_pose_, and new_decoy().

void protocols::topology_broker::FragmentJumpClaimer::new_decoy ( )
overridevirtual

a new decoy — random choices to be made ? make them here

Reimplemented from protocols::topology_broker::TopologyClaimer.

References core::pose::Pose::clear(), discard_jumps_, and input_pose_.

Referenced by protocols::topology_broker::MetalloClaimer::generate_claims(), and new_decoy().

bool protocols::topology_broker::FragmentJumpClaimer::read_tag ( std::string  tag,
std::istream &  is 
)
overridevirtual
void protocols::topology_broker::FragmentJumpClaimer::set_jump_def ( jumping::BaseJumpSetupOP  jump_def)
inlineprotected
void protocols::topology_broker::FragmentJumpClaimer::set_keep_jumps_from_input_pose ( bool  setting)
inlineprotected
std::string protocols::topology_broker::FragmentJumpClaimer::type ( ) const
inlineoverridevirtual

Member Data Documentation

bool protocols::topology_broker::FragmentJumpClaimer::bKeepJumpsFromInputPose_
private
jumping::JumpSample protocols::topology_broker::FragmentJumpClaimer::current_jumps_
private
bool protocols::topology_broker::FragmentJumpClaimer::discard_jumps_
private
simple_moves::ClassicFragmentMoverOP protocols::topology_broker::FragmentJumpClaimer::init_mover_
private
core::pose::Pose protocols::topology_broker::FragmentJumpClaimer::input_pose_
private

Referenced by init_jumps(), and new_decoy().

jumping::BaseJumpSetupOP protocols::topology_broker::FragmentJumpClaimer::jump_def_
private

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