Rosetta Protocols  2014.35
Public Member Functions | Static Public Member Functions | Protected Member Functions | Private Attributes | List of all members
protocols::topology_broker::DensityScoringClaimer Class Reference

#include <DensityScoringClaimer.hh>

Public Member Functions

 DensityScoringClaimer ()
 
virtual TopologyClaimerOP clone () const
 clone it! More...
 
virtual void generate_sequence_claims (claims::DofClaims &)
 mainly calls parent function... but is also used to figure out what residue number we are jumping to. More...
 
virtual void generate_claims (protocols::topology_broker::claims::DofClaims &dc)
 generate first round of DOF claims More...
 
virtual std::string type () const
 type() is specifying the output name of the TopologyClaimer More...
 
virtual void add_constraints (core::pose::Pose &) const
 add constraints to pose... might make this stage dependent as with movers... More...
 
virtual bool accept_declined_claim (claims::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...
 
- 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 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_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 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 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 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

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

Private Attributes

core::Size anchor_residue_
 
std::string anchor_chain_
 
core::Size resolved_anchor_residue_
 
core::Size vrt_id_
 

Constructor & Destructor Documentation

protocols::topology_broker::DensityScoringClaimer::DensityScoringClaimer ( )

Member Function Documentation

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

Referenced by type().

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

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 tr.

void protocols::topology_broker::DensityScoringClaimer::add_constraints ( core::pose::Pose ) const
virtual

add constraints to pose... might make this stage dependent as with movers...

Reimplemented from protocols::topology_broker::TopologyClaimer.

TopologyClaimerOP protocols::topology_broker::DensityScoringClaimer::clone ( ) const
virtual
void protocols::topology_broker::DensityScoringClaimer::generate_claims ( protocols::topology_broker::claims::DofClaims )
virtual

generate first round of DOF claims

Reimplemented from protocols::topology_broker::TopologyClaimer.

References protocols::topology_broker::claims::DofClaim::EXCLUSIVE.

void protocols::topology_broker::DensityScoringClaimer::generate_sequence_claims ( claims::DofClaims new_claims)
virtual

mainly calls parent function... but is also used to figure out what residue number we are jumping to.

Reimplemented from protocols::topology_broker::TopologyClaimer.

void protocols::topology_broker::DensityScoringClaimer::init_after_reading ( )
protectedvirtual
bool protocols::topology_broker::DensityScoringClaimer::read_tag ( std::string  tag,
std::istream &  is 
)
protectedvirtual

Reimplemented from protocols::topology_broker::TopologyClaimer.

References jumping, and tr.

void protocols::topology_broker::DensityScoringClaimer::set_defaults ( )
protectedvirtual
virtual std::string protocols::topology_broker::DensityScoringClaimer::type ( ) const
inlinevirtual

type() is specifying the output name of the TopologyClaimer

Implements protocols::topology_broker::TopologyClaimer.

References _static_type_name().

Member Data Documentation

std::string protocols::topology_broker::DensityScoringClaimer::anchor_chain_
private
core::Size protocols::topology_broker::DensityScoringClaimer::anchor_residue_
private
core::Size protocols::topology_broker::DensityScoringClaimer::resolved_anchor_residue_
private
core::Size protocols::topology_broker::DensityScoringClaimer::vrt_id_
private

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