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protocols::topology_broker::ConstraintClaimer Class Reference

#include <ConstraintClaimer.hh>

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

 ConstraintClaimer ()
 
 ConstraintClaimer (std::string const &cst_file, std::string const &tag="")
 
 ConstraintClaimer (bool CmdFlag, bool centroid=true, bool fullatom=false)
 
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 new_decoy () override
 a new decoy — random choices to be made ? make them here More...
 
bool read_tag (std::string tag, std::istream &) override
 
void add_constraints (core::pose::Pose &) const override
 add constraints to pose... might make this stage dependent as with movers... More...
 
core::Real filter_weight () const
 
std::string const & filter_name () const
 
core::Size combine_ratio () const
 
core::Real drop_random_rate () const
 
std::string const & tag () const
 
void set_cst_file (std::string const &)
 
void set_fullatom (bool setting)
 
void set_centroid (bool setting)
 
void set_skip_redundant (core::Size setting)
 
void set_combine_ratio (core::Size setting)
 
void set_filter_weight (core::Real weight)
 
- 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...
 
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 ()
 

Private Types

typedef TopologyClaimer Parent
 

Private Attributes

std::string filename_
 
std::string fa_filename_
 
std::string cst_filename_
 
std::string tag_
 
core::scoring::constraints::ConstraintSetOP constraints_
 
core::scoring::constraints::ConstraintSetOP fa_constraints_
 
core::pose::Pose constraint_ref_pose_
 
std::string sequence_
 
utility::vector1< boolcombine_exclude_res_
 
bool bCentroid_
 true if constraints are active in centroid mode More...
 
bool bFullatom_
 true if constraints are active in full-atom mode if true use fa_constraints if available... normal constraints otherwise More...
 
bool bCmdFlag_
 use constraints defined via command line More...
 
core::Size combine_ratio_
 combine constraints randomly into Ambiguous Constraints More...
 
core::Real drop_random_rate_
 drop restraints with this rate randomly – default 0 – no dropping More...
 
bool skip_redundant_
 at most one constraint per residue pair ( does not look at bounds... ) More...
 
core::Size skip_redundant_width_
 how many residues left and right do we exclude other "redundant" constraints... More...
 
core::Real filter_weight_
 which weight should this constraint set have when used as a filter More...
 
std::string filter_name_
 

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 void set_defaults ()
 
virtual void init_after_reading ()
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::topology_broker::ConstraintClaimer::ConstraintClaimer ( )
protocols::topology_broker::ConstraintClaimer::ConstraintClaimer ( std::string const &  cst_file,
std::string const &  tag = "" 
)
protocols::topology_broker::ConstraintClaimer::ConstraintClaimer ( bool  CmdFlag,
bool  centroid = true,
bool  fullatom = false 
)

Member Function Documentation

static std::string protocols::topology_broker::ConstraintClaimer::_static_type_name ( )
inlinestatic
void protocols::topology_broker::ConstraintClaimer::add_constraints ( core::pose::Pose ) const
overridevirtual
TopologyClaimerOP protocols::topology_broker::ConstraintClaimer::clone ( ) const
inlineoverridevirtual
core::Size protocols::topology_broker::ConstraintClaimer::combine_ratio ( ) const
inline

References combine_ratio_.

core::Real protocols::topology_broker::ConstraintClaimer::drop_random_rate ( ) const
inline

References drop_random_rate_.

std::string const& protocols::topology_broker::ConstraintClaimer::filter_name ( ) const
inline

References filter_name_.

core::Real protocols::topology_broker::ConstraintClaimer::filter_weight ( ) const
inline

References filter_weight_.

void protocols::topology_broker::ConstraintClaimer::generate_claims ( claims::DofClaims )
overridevirtual

generate first round of DOF claims

Reimplemented from protocols::topology_broker::TopologyClaimer.

void protocols::topology_broker::ConstraintClaimer::new_decoy ( )
overridevirtual
bool protocols::topology_broker::ConstraintClaimer::read_tag ( std::string  tag,
std::istream &  is 
)
overridevirtual
void protocols::topology_broker::ConstraintClaimer::set_centroid ( bool  setting)
void protocols::topology_broker::ConstraintClaimer::set_combine_ratio ( core::Size  setting)
void protocols::topology_broker::ConstraintClaimer::set_cst_file ( std::string const &  file)
void protocols::topology_broker::ConstraintClaimer::set_filter_weight ( core::Real  weight)

References filter_weight_.

void protocols::topology_broker::ConstraintClaimer::set_fullatom ( bool  setting)
void protocols::topology_broker::ConstraintClaimer::set_skip_redundant ( core::Size  setting)
std::string const& protocols::topology_broker::ConstraintClaimer::tag ( ) const
inline

References tag_.

std::string protocols::topology_broker::ConstraintClaimer::type ( ) const
inlineoverridevirtual

type() is specifying the output name of the TopologyClaimer

Implements protocols::topology_broker::TopologyClaimer.

References _static_type_name().

Member Data Documentation

bool protocols::topology_broker::ConstraintClaimer::bCentroid_
private

true if constraints are active in centroid mode

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

bool protocols::topology_broker::ConstraintClaimer::bCmdFlag_
private

use constraints defined via command line

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

bool protocols::topology_broker::ConstraintClaimer::bFullatom_
private

true if constraints are active in full-atom mode if true use fa_constraints if available... normal constraints otherwise

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

utility::vector1< bool > protocols::topology_broker::ConstraintClaimer::combine_exclude_res_
mutableprivate

Referenced by add_constraints().

core::Size protocols::topology_broker::ConstraintClaimer::combine_ratio_
private

combine constraints randomly into Ambiguous Constraints

Referenced by add_constraints(), combine_ratio(), new_decoy(), read_tag(), and set_combine_ratio().

core::pose::Pose protocols::topology_broker::ConstraintClaimer::constraint_ref_pose_
mutableprivate

Referenced by add_constraints().

core::scoring::constraints::ConstraintSetOP protocols::topology_broker::ConstraintClaimer::constraints_
mutableprivate
std::string protocols::topology_broker::ConstraintClaimer::cst_filename_
private
core::Real protocols::topology_broker::ConstraintClaimer::drop_random_rate_
private

drop restraints with this rate randomly – default 0 – no dropping

Referenced by add_constraints(), drop_random_rate(), and read_tag().

core::scoring::constraints::ConstraintSetOP protocols::topology_broker::ConstraintClaimer::fa_constraints_
mutableprivate
std::string protocols::topology_broker::ConstraintClaimer::fa_filename_
private
std::string protocols::topology_broker::ConstraintClaimer::filename_
private
std::string protocols::topology_broker::ConstraintClaimer::filter_name_
private

Referenced by filter_name(), and read_tag().

core::Real protocols::topology_broker::ConstraintClaimer::filter_weight_
private

which weight should this constraint set have when used as a filter

Referenced by filter_weight(), read_tag(), and set_filter_weight().

std::string protocols::topology_broker::ConstraintClaimer::sequence_
mutableprivate

Referenced by add_constraints().

bool protocols::topology_broker::ConstraintClaimer::skip_redundant_
private

at most one constraint per residue pair ( does not look at bounds... )

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

core::Size protocols::topology_broker::ConstraintClaimer::skip_redundant_width_
private

how many residues left and right do we exclude other "redundant" constraints...

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

std::string protocols::topology_broker::ConstraintClaimer::tag_
private

Referenced by add_constraints(), and tag().


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