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protocols::topology_broker::CoordConstraintClaimer Class Reference

#include <CoordConstraintClaimer.hh>

Inheritance diagram for protocols::topology_broker::CoordConstraintClaimer:
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Collaboration diagram for protocols::topology_broker::CoordConstraintClaimer:
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Public Member Functions

 CoordConstraintClaimer ()
 
 ~CoordConstraintClaimer ()
 
 CoordConstraintClaimer (std::string pdb_file)
 
virtual TopologyClaimerOP clone () const
 clone it! More...
 
virtual void generate_claims (DofClaims &)
 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 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...
 
void superimpose (core::pose::Pose const &) const
 superimpose xyz coords in constraints_ with pose 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 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 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 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 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 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 &)
 

Static Public Member Functions

static std::string _static_type_name ()
 

Protected Member Functions

virtual bool read_tag (std::string tag, std::istream &)
 virtual functions for IO More...
 
virtual void set_defaults ()
 read setup file More...
 
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 Types

typedef TopologyClaimer Parent
 

Private Member Functions

void read_cst_pose ()
 
void set_cst_root ()
 
void generate_constraints (core::pose::Pose const &cst_pose) const
 
void read_constraints_from_file (core::pose::Pose const &cst_pose) const
 

Private Attributes

std::string filename_
 
std::string cst_filename_
 
loops::Loops rigid_
 
core::scoring::constraints::ConstraintSetOP constraints_
 
std::string sequence_
 
core::scoring::constraints::FuncOP cst_func_
 
Size root_
 
std::string root_from_label_
 
bool bRegenerateFromInputPose_
 
bool bUseXYZ_in_cstfile_
 
core::pose::PoseOP cst_pose_
 
bool bCentroid_
 true if constraints are active in centroid mode More...
 
bool bFullatom_
 true if constraints are active in full-atom mode More...
 
bool bLocal_
 tmp for backwards compatibility More...
 
core::Real perturb_
 add 0..perturb_ random number to xyz-coords. More...
 
bool bSuperimpose_
 superimpose xyz coordinates with pose in add_constraints() More...
 
loops::Loops superimpose_regions_
 superimpose on these residues More...
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::topology_broker::CoordConstraintClaimer::CoordConstraintClaimer ( )

Referenced by clone().

protocols::topology_broker::CoordConstraintClaimer::~CoordConstraintClaimer ( )
protocols::topology_broker::CoordConstraintClaimer::CoordConstraintClaimer ( std::string  pdb_file)

Member Function Documentation

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

Referenced by type().

void protocols::topology_broker::CoordConstraintClaimer::add_constraints ( core::pose::Pose ) const
virtual
virtual TopologyClaimerOP protocols::topology_broker::CoordConstraintClaimer::clone ( ) const
inlinevirtual
void protocols::topology_broker::CoordConstraintClaimer::generate_claims ( DofClaims )
virtual
void protocols::topology_broker::CoordConstraintClaimer::generate_constraints ( core::pose::Pose const &  cst_pose) const
private
void protocols::topology_broker::CoordConstraintClaimer::init_after_reading ( )
protectedvirtual
void protocols::topology_broker::CoordConstraintClaimer::new_decoy ( )
virtual

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

Reimplemented from protocols::topology_broker::TopologyClaimer.

References bUseXYZ_in_cstfile_, constraints_, cst_pose_, and generate_constraints().

Referenced by new_decoy().

void protocols::topology_broker::CoordConstraintClaimer::new_decoy ( core::pose::Pose const &  )
virtual

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 bRegenerateFromInputPose_, bSuperimpose_, cst_pose_, new_decoy(), and sequence_.

void protocols::topology_broker::CoordConstraintClaimer::read_constraints_from_file ( core::pose::Pose const &  cst_pose) const
private
void protocols::topology_broker::CoordConstraintClaimer::read_cst_pose ( )
private
bool protocols::topology_broker::CoordConstraintClaimer::read_tag ( std::string  tag,
std::istream &  is 
)
protectedvirtual
void protocols::topology_broker::CoordConstraintClaimer::set_cst_root ( )
private
void protocols::topology_broker::CoordConstraintClaimer::set_defaults ( )
protectedvirtual
void protocols::topology_broker::CoordConstraintClaimer::superimpose ( core::pose::Pose const &  pose) const
virtual std::string protocols::topology_broker::CoordConstraintClaimer::type ( ) const
inlinevirtual

type() is specifying the output name of the TopologyClaimer

Implements protocols::topology_broker::TopologyClaimer.

References _static_type_name().

Referenced by init_after_reading(), and read_tag().

Member Data Documentation

bool protocols::topology_broker::CoordConstraintClaimer::bCentroid_
private

true if constraints are active in centroid mode

Referenced by add_constraints(), and read_tag().

bool protocols::topology_broker::CoordConstraintClaimer::bFullatom_
private

true if constraints are active in full-atom mode

Referenced by add_constraints(), and read_tag().

bool protocols::topology_broker::CoordConstraintClaimer::bLocal_
private

tmp for backwards compatibility

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

bool protocols::topology_broker::CoordConstraintClaimer::bRegenerateFromInputPose_
private

Referenced by new_decoy(), and read_tag().

bool protocols::topology_broker::CoordConstraintClaimer::bSuperimpose_
private

superimpose xyz coordinates with pose in add_constraints()

Referenced by add_constraints(), new_decoy(), read_tag(), and set_defaults().

bool protocols::topology_broker::CoordConstraintClaimer::bUseXYZ_in_cstfile_
private
core::scoring::constraints::ConstraintSetOP protocols::topology_broker::CoordConstraintClaimer::constraints_
mutableprivate
std::string protocols::topology_broker::CoordConstraintClaimer::cst_filename_
private
core::scoring::constraints::FuncOP protocols::topology_broker::CoordConstraintClaimer::cst_func_
private
core::pose::PoseOP protocols::topology_broker::CoordConstraintClaimer::cst_pose_
private
std::string protocols::topology_broker::CoordConstraintClaimer::filename_
private
core::Real protocols::topology_broker::CoordConstraintClaimer::perturb_
private

add 0..perturb_ random number to xyz-coords.

Referenced by generate_constraints(), read_tag(), and set_defaults().

loops::Loops protocols::topology_broker::CoordConstraintClaimer::rigid_
private

Referenced by generate_constraints(), and read_tag().

Size protocols::topology_broker::CoordConstraintClaimer::root_
private
std::string protocols::topology_broker::CoordConstraintClaimer::root_from_label_
private
std::string protocols::topology_broker::CoordConstraintClaimer::sequence_
mutableprivate
loops::Loops protocols::topology_broker::CoordConstraintClaimer::superimpose_regions_
private

superimpose on these residues

Referenced by read_tag(), set_defaults(), and superimpose().


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