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protocols::topology_broker::TMHTopologySamplerClaimer Class Reference

#include <TMHTopologySamplerClaimer.hh>

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

 TMHTopologySamplerClaimer ()
 
 TMHTopologySamplerClaimer (topology_broker::TopologyBrokerOP broker)
 constructor: supply mover classes for Fragment Moves More...
 
 ~TMHTopologySamplerClaimer () override
 destructor More...
 
TopologyClaimerOP clone () const override
 TMHTopologySamplerClaimer has virtual functions... use this to obtain a new instance. More...
 
std::string type () const override
 type() is specifying the output name of the TopologyClaimer More...
 
void set_pose_from_broker (core::pose::Pose &pose) override
 get the pose from the boker and set it as this object's pose More...
 
void pre_process (core::pose::Pose &pose) override
 read in the pose's spans via the MembraneTopology store din the pose, determine jumps, TMHs, loops, etc. More...
 
bool claimer_builds_own_fold_tree () override
 the broker checks if the claimer builds its own fold tree to figure out if needs to build one itself More...
 
core::kinematics::FoldTreeOP get_fold_tree (core::pose::Pose &pose) override
 in case a claimer has its own fold_tree. get_fold_tree() is called by the broker More...
 
core::pose::PoseOP get_pose_from_claimer () override
 
void generate_claims (claims::DofClaims &dof_claims) override
 generate DofClaims More...
 
void initialize_dofs (core::pose::Pose &pose, claims::DofClaims const &init_dofs, claims::DofClaims &failed_to_init) override
 make move_map and add the DoF claims from generate_claims() to the movemap. Now we can move certain parts with certain DOFs. More...
 
void add_mover (moves::RandomMover &, core::pose::Pose const &, abinitio::StageID, core::scoring::ScoreFunction const &, core::Real) override
 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 build_fold_tree (core::pose::Pose &pose, core::kinematics::FoldTree &fold_tree) override
 this claimer builds its own radial fold tree based on read-in spanfile More...
 
bool read_tag (std::string tag, std::istream &is) override
 read tag from topology broker file (setup.tpb) 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 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 (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 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 void add_constraints (core::pose::Pose &) const
 add constraints to pose... might make this stage dependent as with movers... 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...
 
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 ()
 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...
 
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 ()
 
static void register_options ()
 register cmd-line options in option system ( call before core::init ) More...
 

Protected Member Functions

void set_defaults () override
 called by constructor — calls all set_default_XXX methods More...
 
void set_pose_torsions (core::pose::Pose &pose)
 Make extended chain an idealized helix. More...
 
void move_spans (core::pose::Pose &pose)
 move helices closer together More...
 
core::Vector output_membrane_vector (core::pose::Pose &pose)
 output membrane center and normal as virtual atoms More...
 
utility::vector1< core::Vectorpre_compute_grid_points (core::pose::Pose &pose)
 pre-compute grid points where you want to move the helices More...
 
core::scoring::MembraneTopologyOP get_membrane_topology (core::pose::Pose &pose)
 get membrane topology information More...
 
core::scoring::MembraneEmbed get_membrane_embed (core::pose::Pose &pose)
 get membrane embedding information More...
 
- 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 init_after_reading ()
 

Private Types

typedef TopologyClaimer Parent
 

Private Attributes

core::Real rotation_mag_
 
core::Real translation_mag_
 
core::Real rb_mover_stage1_weight_
 
core::pose::Pose current_pose_
 
core::Size nres_
 
core::Size njumps_
 
ObjexxFCL::FArray2D< core::Sizejump_array_
 
ObjexxFCL::FArray1D< core::Sizecuts_
 
core::Size topology_root_res_
 
core::Size tmhelix_
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::topology_broker::TMHTopologySamplerClaimer::TMHTopologySamplerClaimer ( )

References set_defaults().

protocols::topology_broker::TMHTopologySamplerClaimer::TMHTopologySamplerClaimer ( topology_broker::TopologyBrokerOP  broker)

constructor: supply mover classes for Fragment Moves

References set_defaults().

protocols::topology_broker::TMHTopologySamplerClaimer::~TMHTopologySamplerClaimer ( )
overridedefault

destructor

Member Function Documentation

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

Referenced by type().

void protocols::topology_broker::TMHTopologySamplerClaimer::add_mover ( moves::RandomMover random_mover,
core::pose::Pose const &  ,
abinitio::StageID  stageID,
core::scoring::ScoreFunction const &  ,
core::Real   
)
overridevirtual

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_

Reimplemented from protocols::topology_broker::TopologyClaimer.

References protocols::moves::MoverContainer::add_mover(), and tr().

void protocols::topology_broker::TMHTopologySamplerClaimer::build_fold_tree ( core::pose::Pose pose,
core::kinematics::FoldTree fold_tree 
)
overridevirtual
bool protocols::topology_broker::TMHTopologySamplerClaimer::claimer_builds_own_fold_tree ( )
overridevirtual

the broker checks if the claimer builds its own fold tree to figure out if needs to build one itself

Reimplemented from protocols::topology_broker::TopologyClaimer.

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

TMHTopologySamplerClaimer has virtual functions... use this to obtain a new instance.

Implements protocols::topology_broker::TopologyClaimer.

void protocols::topology_broker::TMHTopologySamplerClaimer::generate_claims ( claims::DofClaims dof_claims)
overridevirtual

generate DofClaims

generate DoF Claims to be read in by broker

Reimplemented from protocols::topology_broker::TopologyClaimer.

References protocols::topology_broker::claims::DofClaim::CAN_INIT, and protocols::topology_broker::TopologyClaimer::label().

core::kinematics::FoldTreeOP protocols::topology_broker::TMHTopologySamplerClaimer::get_fold_tree ( core::pose::Pose )
overridevirtual

in case a claimer has its own fold_tree. get_fold_tree() is called by the broker

Reimplemented from protocols::topology_broker::TopologyClaimer.

References core::pose::Pose::fold_tree().

core::scoring::MembraneEmbed protocols::topology_broker::TMHTopologySamplerClaimer::get_membrane_embed ( core::pose::Pose pose)
protected
core::scoring::MembraneTopologyOP protocols::topology_broker::TMHTopologySamplerClaimer::get_membrane_topology ( core::pose::Pose pose)
protected
core::pose::PoseOP protocols::topology_broker::TMHTopologySamplerClaimer::get_pose_from_claimer ( )
overridevirtual
void protocols::topology_broker::TMHTopologySamplerClaimer::initialize_dofs ( core::pose::Pose pose,
claims::DofClaims const &  init_dofs,
claims::DofClaims failed_to_init 
)
overridevirtual

make move_map and add the DoF claims from generate_claims() to the movemap. Now we can move certain parts with certain DOFs.

Reimplemented from protocols::topology_broker::TopologyClaimer.

References tr().

void protocols::topology_broker::TMHTopologySamplerClaimer::move_spans ( core::pose::Pose pose)
protected
core::Vector protocols::topology_broker::TMHTopologySamplerClaimer::output_membrane_vector ( core::pose::Pose pose)
protected
utility::vector1< core::Vector > protocols::topology_broker::TMHTopologySamplerClaimer::pre_compute_grid_points ( core::pose::Pose pose)
protected

pre-compute grid points where you want to move the helices

References core::conformation::membrane::center, and tr().

void protocols::topology_broker::TMHTopologySamplerClaimer::pre_process ( core::pose::Pose pose)
overridevirtual

read in the pose's spans via the MembraneTopology store din the pose, determine jumps, TMHs, loops, etc.

read in the pose's spans via the MembraneTopology stored in the pose, determine jumps, TMHs, loops, etc.

Reimplemented from protocols::topology_broker::TopologyClaimer.

References core::conformation::Residue::atom_name(), core::kinematics::FoldTree::begin(), core::pose::Pose::fold_tree(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::pose::residue_center_of_mass(), core::scoring::rg, core::kinematics::FoldTree::root(), core::pose::Pose::size(), and tr().

bool protocols::topology_broker::TMHTopologySamplerClaimer::read_tag ( std::string  tag,
std::istream &  is 
)
overridevirtual

read tag from topology broker file (setup.tpb)

Reimplemented from protocols::topology_broker::TopologyClaimer.

void protocols::topology_broker::TMHTopologySamplerClaimer::register_options ( )
static

register cmd-line options in option system ( call before core::init )

void protocols::topology_broker::TMHTopologySamplerClaimer::set_defaults ( )
overrideprotectedvirtual

called by constructor — calls all set_default_XXX methods

Reimplemented from protocols::topology_broker::TopologyClaimer.

Referenced by TMHTopologySamplerClaimer().

void protocols::topology_broker::TMHTopologySamplerClaimer::set_pose_from_broker ( core::pose::Pose pose)
overridevirtual

get the pose from the boker and set it as this object's pose

Reimplemented from protocols::topology_broker::TopologyClaimer.

void protocols::topology_broker::TMHTopologySamplerClaimer::set_pose_torsions ( core::pose::Pose pose)
protected
std::string protocols::topology_broker::TMHTopologySamplerClaimer::type ( ) const
inlineoverridevirtual

type() is specifying the output name of the TopologyClaimer

Implements protocols::topology_broker::TopologyClaimer.

References _static_type_name().

Member Data Documentation

core::pose::Pose protocols::topology_broker::TMHTopologySamplerClaimer::current_pose_
private
ObjexxFCL::FArray1D< core::Size > protocols::topology_broker::TMHTopologySamplerClaimer::cuts_
private
ObjexxFCL::FArray2D< core::Size > protocols::topology_broker::TMHTopologySamplerClaimer::jump_array_
private
core::Size protocols::topology_broker::TMHTopologySamplerClaimer::njumps_
private
core::Size protocols::topology_broker::TMHTopologySamplerClaimer::nres_
private
core::Real protocols::topology_broker::TMHTopologySamplerClaimer::rb_mover_stage1_weight_
private
core::Real protocols::topology_broker::TMHTopologySamplerClaimer::rotation_mag_
private
core::Size protocols::topology_broker::TMHTopologySamplerClaimer::tmhelix_
private
core::Size protocols::topology_broker::TMHTopologySamplerClaimer::topology_root_res_
private
core::Real protocols::topology_broker::TMHTopologySamplerClaimer::translation_mag_
private

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