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protocols::topology_broker::MetalloClaimer Class Reference

#include <MetalloClaimer.hh>

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

 MetalloClaimer ()
 
 ~MetalloClaimer () override=default
 
MetalloClaimerOP shared_from_this ()
 
TopologyClaimerOP clone () const override
 clone it! More...
 
void generate_sequence_claims (claims::DofClaims &dc) override
 generate claims that affect the sequence of the pose More...
 
void generate_claims (protocols::topology_broker::claims::DofClaims &dc) override
 mainly calls parent function... but is also used to figure out what residue number we are jumping to. More...
 
void initialize_dofs (core::pose::Pose &pose, claims::DofClaims const &init_claims, claims::DofClaims &failed_to_init) override
 is called after all round1 claims have been approved or retracted – additional claims can be issued in this round 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...
 
- Public Member Functions inherited from protocols::topology_broker::SequenceClaimer
 SequenceClaimer ()
 
 SequenceClaimer (std::string const &sequence, std::string const &label, std::string rsd_type_set_identifier)
 
SequenceClaimerOP shared_from_this ()
 
TopologyClaimerOP clone () const override
 clone it! More...
 
void generate_sequence_claims (claims::DofClaims &) override
 generate claims that affect the sequence of the pose More...
 
void generate_claims (claims::DofClaims &) override
 is called after all round1 claims have been approved or retracted – additional claims can be issued in this round if this Sequence has been moved from position 1 — needs to issue a fixed CUT in the fold-tree More...
 
std::string type () const override
 type() is specifying the output name of the TopologyClaimer 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_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 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...
 
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 ()
 
- Public Member Functions inherited from protocols::topology_broker::FragmentJumpClaimer
 FragmentJumpClaimer ()
 
 FragmentJumpClaimer (jumping::BaseJumpSetupOP jump_def, std::string const &mover_tag="JumpMove", weights::AbinitioMoverWeightOP weight=nullptr)
 
 FragmentJumpClaimer (FragmentJumpClaimer const &src)
 
 ~FragmentJumpClaimer () override
 
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 new_decoy () override
 a new decoy — random choices to be made ? make them here More...
 
- Public Member Functions inherited from protocols::topology_broker::FragmentClaimer
 FragmentClaimer ()
 
 FragmentClaimer (simple_moves::FragmentMoverOP, std::string const &mover_tag, weights::AbinitioMoverWeightOP weight)
 
 FragmentClaimer (simple_moves::FragmentMoverOP, std::string const &mover_tag, weights::AbinitioMoverWeightOP weight, std::string label, core::fragment::FragSetOP fags)
 
 FragmentClaimer (simple_moves::FragmentMoverOP)
 
 FragmentClaimer (FragmentClaimer const &src)
 
 ~FragmentClaimer () override
 
FragmentClaimerOP shared_from_this ()
 
bool accept_declined_claim (claims::DofClaim const &was_declined) override
 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...
 
void set_mover (simple_moves::FragmentMoverOP mover)
 
void set_mover_tag (std::string const &str)
 
void set_bInitDofs (bool set)
 
std::string const & mover_tag () const
 
moves::MoverOP get_mover (core::pose::Pose const &) const override
 what is your mover ... called by add_mover — overload this or add_mover if you have movers too supply More...
 
void get_sequence_region (std::set< core::Size > &start_region) const
 

Static Public Member Functions

static std::string _static_type_name ()
 
- Static Public Member Functions inherited from protocols::topology_broker::SequenceClaimer
static std::string _static_type_name ()
 
- Static Public Member Functions inherited from protocols::topology_broker::FragmentJumpClaimer
static std::string _static_type_name ()
 
- Static Public Member Functions inherited from protocols::topology_broker::FragmentClaimer
static std::string _static_type_name ()
 

Protected Member Functions

void set_defaults () override
 
bool read_tag (std::string tag, std::istream &) override
 
void init_after_reading () override
 
- Protected Member Functions inherited from protocols::topology_broker::SequenceClaimer
bool read_tag (std::string tag, std::istream &) override
 
void init_after_reading () override
 
void make_sequence_claim ()
 
void set_sequence (std::string const &str)
 
void set_priority (core::Real pr)
 
- Protected Member Functions inherited from protocols::topology_broker::FragmentJumpClaimer
void set_jump_def (jumping::BaseJumpSetupOP jump_def)
 
virtual void generate_claims (claims::DofClaims &, std::string, std::string)
 
jumping::BaseJumpSetupOP jump_def ()
 
void set_keep_jumps_from_input_pose (bool setting)
 
void init_jumps ()
 
- Protected Member Functions inherited from protocols::topology_broker::FragmentClaimer
simple_moves::FragmentMover const & mover () const
 
simple_moves::FragmentMoverOP get_frag_mover_ptr ()
 
core::fragment::FragSetCOP fragments ()
 
void set_fragments (core::fragment::FragSetOP)
 
void set_claim_right (claims::DofClaim::ClaimRight setting)
 

Private Attributes

jumping::ResiduePairJumpSetupOP jump_setup_
 
jumping::ResiduePairJumpOP residue_pair_jump_
 
std::string ligand_
 
core::Size anchor_residue_
 
std::string anchor_chain_
 
core::Size resolved_anchor_residue_
 

Additional Inherited Members

- Protected Attributes inherited from protocols::topology_broker::FragmentClaimer
core::kinematics::MoveMapOP movemap_
 

Constructor & Destructor Documentation

protocols::topology_broker::MetalloClaimer::MetalloClaimer ( )
protocols::topology_broker::MetalloClaimer::~MetalloClaimer ( )
overridedefault

Member Function Documentation

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

Referenced by type().

void protocols::topology_broker::MetalloClaimer::add_constraints ( core::pose::Pose ) const
overridevirtual

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

Reimplemented from protocols::topology_broker::TopologyClaimer.

TopologyClaimerOP protocols::topology_broker::MetalloClaimer::clone ( ) const
inlineoverridevirtual

clone it!

Reimplemented from protocols::topology_broker::FragmentJumpClaimer.

void protocols::topology_broker::MetalloClaimer::generate_claims ( protocols::topology_broker::claims::DofClaims dc)
overridevirtual
void protocols::topology_broker::MetalloClaimer::generate_sequence_claims ( claims::DofClaims )
inlineoverridevirtual
void protocols::topology_broker::MetalloClaimer::init_after_reading ( )
overrideprotectedvirtual
void protocols::topology_broker::MetalloClaimer::initialize_dofs ( core::pose::Pose pose,
claims::DofClaims const &  init_claims,
claims::DofClaims failed_to_init 
)
inlineoverridevirtual

is called after all round1 claims have been approved or retracted – additional claims can be issued in this round

Reimplemented from protocols::topology_broker::FragmentJumpClaimer.

References protocols::topology_broker::FragmentJumpClaimer::initialize_dofs(), and protocols::topology_broker::TopologyClaimer::initialize_dofs().

bool protocols::topology_broker::MetalloClaimer::read_tag ( std::string  tag,
std::istream &  is 
)
overrideprotectedvirtual
void protocols::topology_broker::MetalloClaimer::set_defaults ( )
overrideprotectedvirtual
MetalloClaimerOP protocols::topology_broker::MetalloClaimer::shared_from_this ( )
inline
std::string protocols::topology_broker::MetalloClaimer::type ( ) const
inlineoverridevirtual

type() is specifying the output name of the TopologyClaimer

Reimplemented from protocols::topology_broker::FragmentJumpClaimer.

References _static_type_name().

Member Data Documentation

std::string protocols::topology_broker::MetalloClaimer::anchor_chain_
private
core::Size protocols::topology_broker::MetalloClaimer::anchor_residue_
private
jumping::ResiduePairJumpSetupOP protocols::topology_broker::MetalloClaimer::jump_setup_
private
std::string protocols::topology_broker::MetalloClaimer::ligand_
private

Referenced by init_after_reading(), and read_tag().

jumping::ResiduePairJumpOP protocols::topology_broker::MetalloClaimer::residue_pair_jump_
private
core::Size protocols::topology_broker::MetalloClaimer::resolved_anchor_residue_
private

Referenced by generate_claims().


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