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protocols::topology_broker::CoordConstraintClaimer Class Reference

#include <CoordConstraintClaimer.hh>

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

 CoordConstraintClaimer ()
 
 ~CoordConstraintClaimer () override
 
 CoordConstraintClaimer (std::string const &pdb_file)
 
TopologyClaimerOP clone () const override
 clone it! More...
 
void generate_claims (claims::DofClaims &) override
 generate first round of DOF claims More...
 
std::string type () const override
 type() is specifying the output name of the TopologyClaimer More...
 
void add_constraints (core::pose::Pose &) const override
 add constraints to pose... might make this stage dependent as with movers... More...
 
void new_decoy () override
 a new decoy — random choices to be made ? make them here 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 superimpose (core::pose::Pose const &) const
 superimpose xyz coords in constraints_ with pose More...
 
- 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 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 bool accept_declined_claim (claims::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 (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...
 
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

bool read_tag (std::string tag, std::istream &) override
 virtual functions for IO More...
 
void set_defaults () override
 read setup file More...
 
void init_after_reading () override
 
- 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_ = "NoFile"
 
std::string cst_filename_ = "NoFile"
 
loops::Loops rigid_
 
core::scoring::constraints::ConstraintSetOP constraints_
 
std::string sequence_
 
core::scoring::func::FuncOP cst_func_
 
core::Size root_ = 1
 
std::string root_from_label_ = "ALL"
 
bool bRegenerateFromInputPose_ = false
 
bool bUseXYZ_in_cstfile_ = false
 
core::pose::PoseOP cst_pose_
 
bool bCentroid_ = true
 true if constraints are active in centroid mode More...
 
bool bFullatom_ = false
 true if constraints are active in full-atom mode More...
 
bool bLocal_ = false
 tmp for backwards compatibility More...
 
core::Real perturb_ = 0
 add 0..perturb_ random number to xyz-coords. More...
 
bool bSuperimpose_ = false
 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 ( )
protocols::topology_broker::CoordConstraintClaimer::~CoordConstraintClaimer ( )
overridedefault
protocols::topology_broker::CoordConstraintClaimer::CoordConstraintClaimer ( std::string const &  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
overridevirtual
TopologyClaimerOP protocols::topology_broker::CoordConstraintClaimer::clone ( ) const
inlineoverridevirtual
void protocols::topology_broker::CoordConstraintClaimer::generate_claims ( claims::DofClaims )
overridevirtual
void protocols::topology_broker::CoordConstraintClaimer::generate_constraints ( core::pose::Pose const &  cst_pose) const
private
void protocols::topology_broker::CoordConstraintClaimer::init_after_reading ( )
overrideprotectedvirtual
void protocols::topology_broker::CoordConstraintClaimer::new_decoy ( )
overridevirtual

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 &  )
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 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

References constraints_, cst_filename_, and tr().

Referenced by generate_claims(), and init_after_reading().

void protocols::topology_broker::CoordConstraintClaimer::read_cst_pose ( )
private
bool protocols::topology_broker::CoordConstraintClaimer::read_tag ( std::string  tag,
std::istream &  is 
)
overrideprotectedvirtual
void protocols::topology_broker::CoordConstraintClaimer::set_cst_root ( )
private
void protocols::topology_broker::CoordConstraintClaimer::set_defaults ( )
overrideprotectedvirtual
void protocols::topology_broker::CoordConstraintClaimer::superimpose ( core::pose::Pose const &  pose) const
std::string protocols::topology_broker::CoordConstraintClaimer::type ( ) const
inlineoverridevirtual

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_ = true
private

true if constraints are active in centroid mode

Referenced by add_constraints(), and read_tag().

bool protocols::topology_broker::CoordConstraintClaimer::bFullatom_ = false
private

true if constraints are active in full-atom mode

Referenced by add_constraints(), and read_tag().

bool protocols::topology_broker::CoordConstraintClaimer::bLocal_ = false
private

tmp for backwards compatibility

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

bool protocols::topology_broker::CoordConstraintClaimer::bRegenerateFromInputPose_ = false
private

Referenced by new_decoy(), and read_tag().

bool protocols::topology_broker::CoordConstraintClaimer::bSuperimpose_ = false
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_ = false
private
core::scoring::constraints::ConstraintSetOP protocols::topology_broker::CoordConstraintClaimer::constraints_
mutableprivate
std::string protocols::topology_broker::CoordConstraintClaimer::cst_filename_ = "NoFile"
private
core::scoring::func::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_ = "NoFile"
private
core::Real protocols::topology_broker::CoordConstraintClaimer::perturb_ = 0
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().

core::Size protocols::topology_broker::CoordConstraintClaimer::root_ = 1
private
std::string protocols::topology_broker::CoordConstraintClaimer::root_from_label_ = "ALL"
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: