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Rosetta 3.5
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Rosetta 3.5
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#include <LoopFragmentClaimer.hh>
Public Member Functions | |
| LoopFragmentClaimer (core::fragment::FragSetOP) | |
| virtual std::string | type () const |
| type() is specifying the output name of the TopologyClaimer More... | |
| 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... | |
| core::fragment::FragSetCOP | loop_frags (core::kinematics::MoveMap &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... | |
 Public Member Functions inherited from protocols::topology_broker::FragmentClaimer | |
| FragmentClaimer () | |
| FragmentClaimer (simple_moves::FragmentMoverOP, std::string mover_tag, weights::AbinitioMoverWeightOP weight) | |
| FragmentClaimer (simple_moves::FragmentMoverOP) | |
| FragmentClaimer (FragmentClaimer const &src) | |
| ~FragmentClaimer () | |
| virtual TopologyClaimerOP | clone () const |
| clone it! More... | |
| virtual void | generate_claims (DofClaims &) |
| generate first round of DOF claims More... | |
| virtual void | initialize_dofs (core::pose::Pose &, DofClaims const &init_claims, DofClaims &failed_to_init) |
| is called after all round1 claims have been approved or retracted – additional claims can be issued in this round More... | |
| virtual bool | accept_declined_claim (DofClaim const &was_declined) |
| 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 |
| void | get_sequence_region (std::set< core::Size > &start_region) const |
| 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 bool | allow_claim (DofClaim const &) |
| allow a claim from a foreign Claimer 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 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 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::AbinitioMoverWeight & | mover_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 () |
| Static Public Member Functions inherited from protocols::topology_broker::FragmentClaimer | |
| static std::string | _static_type_name () |
Additional Inherited Members | |
| Protected Member Functions inherited from protocols::topology_broker::FragmentClaimer | |
| simple_moves::FragmentMover const & | mover () const |
| simple_moves::FragmentMoverOP | get_frag_mover_ptr () |
| void | set_claim_right (DofClaim::ClaimRight setting) |
| virtual bool | read_tag (std::string tag, std::istream &) |
| virtual void | init_after_reading () |
| Protected Attributes inherited from protocols::topology_broker::FragmentClaimer | |
| core::kinematics::MoveMapOP | movemap_ |
Definition at line 58 of file LoopFragmentClaimer.hh.
| protocols::topology_broker::LoopFragmentClaimer::LoopFragmentClaimer | ( | core::fragment::FragSetOP | frags) |
Definition at line 55 of file LoopFragmentClaimer.cc.
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inlinestatic |
Definition at line 67 of file LoopFragmentClaimer.hh.
Referenced by type().
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inlinevirtual |
what is your mover ... called by add_mover — overload this or add_mover if you have movers too supply
Reimplemented from protocols::topology_broker::FragmentClaimer.
Definition at line 71 of file LoopFragmentClaimer.hh.
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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 from protocols::topology_broker::TopologyClaimer.
Definition at line 62 of file LoopFragmentClaimer.cc.
References protocols::simple_moves::FragmentMover::fragments(), protocols::simple_moves::FragmentMover::movemap(), and protocols::topology_broker::FragmentClaimer::mover().
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inlinevirtual |
type() is specifying the output name of the TopologyClaimer
Reimplemented from protocols::topology_broker::FragmentClaimer.
Definition at line 63 of file LoopFragmentClaimer.hh.
References _static_type_name().
1.8.4