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Rosetta 3.5
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Rosetta 3.5
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#include <CutBiasClaimer.hh>
Public Member Functions | |
| CutBiasClaimer () | |
| CutBiasClaimer (utility::vector1< core::Real > const &) | |
| CutBiasClaimer (core::fragment::SecondaryStructure const &ss_def) | |
| virtual TopologyClaimerOP | clone () const |
| clone it! More... | |
| virtual void | generate_claims (DofClaims &) |
| generate first round of DOF claims More... | |
| virtual void | read (std::istream &) |
| read definition of Claimer from setup file, i.e., a CLAIMER <type> ... END_CLAIMER block More... | |
| virtual std::string | type () const |
| type() is specifying the output name of the TopologyClaimer 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... | |
 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 | 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 | initialize_dofs (core::pose::Pose &, DofClaims const &init_claims, DofClaims &failed_to_init) |
| initialize dofs – e.g., torsions, jumps – 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 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... | |
| 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 () |
Private Attributes | |
| utility::vector1< core::Real > | cut_bias_ |
Additional Inherited Members | |
| 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 bool | read_tag (std::string tag, std::istream &is) |
| virtual void | set_defaults () |
| virtual void | init_after_reading () |
Definition at line 54 of file CutBiasClaimer.hh.
| protocols::topology_broker::CutBiasClaimer::CutBiasClaimer | ( | ) |
Definition at line 49 of file CutBiasClaimer.cc.
Referenced by clone().
| protocols::topology_broker::CutBiasClaimer::CutBiasClaimer | ( | utility::vector1< core::Real > const & | set) |
Definition at line 60 of file CutBiasClaimer.cc.
| protocols::topology_broker::CutBiasClaimer::CutBiasClaimer | ( | core::fragment::SecondaryStructure const & | ss_def) |
Definition at line 51 of file CutBiasClaimer.cc.
References core::fragment::SecondaryStructure::loop_fraction(), and core::fragment::SecondaryStructure::total_residue().
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inlinestatic |
Definition at line 74 of file CutBiasClaimer.hh.
Referenced by type().
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inlinevirtual |
clone it!
Implements protocols::topology_broker::TopologyClaimer.
Definition at line 60 of file CutBiasClaimer.hh.
References CutBiasClaimer().
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inlinevirtual |
generate first round of DOF claims
Reimplemented from protocols::topology_broker::TopologyClaimer.
Definition at line 64 of file CutBiasClaimer.hh.
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virtual |
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 from protocols::topology_broker::TopologyClaimer.
Definition at line 65 of file CutBiasClaimer.cc.
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inlinevirtual |
read definition of Claimer from setup file, i.e., a CLAIMER <type> ... END_CLAIMER block
Reimplemented from protocols::topology_broker::TopologyClaimer.
Definition at line 67 of file CutBiasClaimer.hh.
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inlinevirtual |
type() is specifying the output name of the TopologyClaimer
Implements protocols::topology_broker::TopologyClaimer.
Definition at line 70 of file CutBiasClaimer.hh.
References _static_type_name().
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private |
Definition at line 82 of file CutBiasClaimer.hh.
1.8.4