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protocols::topology_broker::MetalloClaimer Class Reference

#include <MetalloClaimer.hh>

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

 MetalloClaimer ()
 
 ~MetalloClaimer ()
 
virtual TopologyClaimerOP clone () const
 clone it! More...
 
virtual void generate_sequence_claims (DofClaims &dc)
 generate claims that affect the sequence of the pose More...
 
virtual void initialize_residues (core::pose::Pose &, SequenceClaimOP init_claim, DofClaims &failed_to_init)
 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::DofClaims &dc)
 generate first round of DOF claims More...
 
virtual void initialize_dofs (core::pose::Pose &pose, DofClaims const &init_claims, DofClaims &failed_to_init)
 is called after all round1 claims have been approved or retracted – additional claims can be issued in this round 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...
 
- Public Member Functions inherited from protocols::topology_broker::SequenceClaimer
 SequenceClaimer ()
 
 SequenceClaimer (std::string const &sequence, std::string const &rsd_type_set_identifier, std::string label)
 
core::Size offset ()
 
void set_sequence (std::string const &str)
 
- 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 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 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 (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 &)
 
- Public Member Functions inherited from protocols::topology_broker::JumpClaimer
 JumpClaimer ()
 
 JumpClaimer (jumping::BaseJumpSetupOP jump_def, std::string const &mover_tag="JumpMove", weights::AbinitioMoverWeightOP weight=NULL)
 
 JumpClaimer (JumpClaimer const &src)
 
 ~JumpClaimer ()
 
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...
 
virtual void new_decoy ()
 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 mover_tag, weights::AbinitioMoverWeightOP weight)
 
 FragmentClaimer (simple_moves::FragmentMoverOP)
 
 FragmentClaimer (FragmentClaimer const &src)
 
 ~FragmentClaimer ()
 
virtual bool accept_declined_claim (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...
 
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
 
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...
 
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::JumpClaimer
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

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::JumpClaimer
void set_jump_def (jumping::BaseJumpSetupOP jump_def)
 
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 ()
 
void set_claim_right (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 ( )

Referenced by clone().

protocols::topology_broker::MetalloClaimer::~MetalloClaimer ( )
inline

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
virtual

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

Reimplemented from protocols::topology_broker::TopologyClaimer.

virtual TopologyClaimerOP protocols::topology_broker::MetalloClaimer::clone ( ) const
inlinevirtual

clone it!

Reimplemented from protocols::topology_broker::JumpClaimer.

References MetalloClaimer().

virtual void protocols::topology_broker::MetalloClaimer::generate_claims ( protocols::topology_broker::DofClaims )
inlinevirtual
virtual void protocols::topology_broker::MetalloClaimer::generate_sequence_claims ( DofClaims )
inlinevirtual
void protocols::topology_broker::MetalloClaimer::init_after_reading ( )
protectedvirtual
virtual void protocols::topology_broker::MetalloClaimer::initialize_dofs ( core::pose::Pose pose,
DofClaims const &  init_claims,
DofClaims failed_to_init 
)
inlinevirtual

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

Reimplemented from protocols::topology_broker::JumpClaimer.

References protocols::topology_broker::SequenceClaimer::initialize_dofs(), and protocols::topology_broker::JumpClaimer::initialize_dofs().

void protocols::topology_broker::MetalloClaimer::initialize_residues ( core::pose::Pose pose,
SequenceClaimOP  init_claim,
DofClaims failed_to_init 
)
virtual
bool protocols::topology_broker::MetalloClaimer::read_tag ( std::string  tag,
std::istream &  is 
)
protectedvirtual
void protocols::topology_broker::MetalloClaimer::set_defaults ( )
protectedvirtual
virtual std::string protocols::topology_broker::MetalloClaimer::type ( ) const
inlinevirtual

type() is specifying the output name of the TopologyClaimer

Reimplemented from protocols::topology_broker::JumpClaimer.

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 initialize_residues().


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