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protocols::topology_broker::RigidChunkClaimer Class Reference

defines a rigid part of structure... imagine a loop-relax application core structure is fixed via jumps and loops can move the rigid chunk takes a definition of rigid regions in form of an instance of Loops (just taken as bunch of start-end residue numbers — here defining the rigid residues and not the loops). the rigid chunk to keep its integrity will need jumps, the claimer will reuse jumps if somebody else claims them, or submit in finalize_claims his own jumps, if not enough jumps are present. in "bExclusive_ mode" the RigidChunk will reclaim any jump claim that is useful and wihin the rigid region. (i.e., foreign claim is dissallowed but own claim with same residues is issued — in this way the claimer uses e.g., beta-sheet jumps, where they are suggested the input pose is used to initialize the rigid region ( via copying of internal coordinates ) e.g., a hole in the structure shouldn't pose a problem, since we basically copy the atom-tree. More...

#include <RigidChunkClaimer.hh>

Inheritance diagram for protocols::topology_broker::RigidChunkClaimer:
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Collaboration diagram for protocols::topology_broker::RigidChunkClaimer:
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Classes

class  CM_SuggestFixResidue
 
class  JumpCalculator
 helper class – computes if we have all jupms needed to rigidify the chosen chunk and generate more jumps if needed. More...
 

Public Member Functions

 RigidChunkClaimer ()
 
 RigidChunkClaimer (core::pose::Pose const &input_pose, loops::Loops rigid)
 
virtual TopologyClaimerOP clone () const
 clone it! More...
 
virtual std::string type () const
 type() is specifying the output name of the TopologyClaimer 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...
 
virtual void generate_claims (DofClaims &)
 generate DofClaims for BB More...
 
virtual bool allow_claim (DofClaim const &)
 has to decline foreign BB claims for rigid regions, reclaim jumps where appropriate More...
 
virtual void finalize_claims (DofClaims &)
 issue jump-claims for jumps yet missing to keep rigid regions fixed More...
 
virtual void initialize_dofs (core::pose::Pose &, DofClaims const &init_claims, DofClaims &failed_to_init)
 initialize BB residues and rigid-internal jumps from starting structure — copying atom-tree dofs More...
 
virtual void switch_to_fullatom (core::pose::Pose &, utility::vector1< bool > bNeedToRepack) const
 rigid-chunk can probably provide some side-chain info from full-length model More...
 
virtual bool accept_declined_claim (DofClaim const &was_declined)
 will fail if a BB torsion claim of the rigid region has been declined More...
 
virtual void manipulate_cut_bias (utility::vector1< core::Real > &cut_bias)
 multiply your bias to this – if its zero don't change that, i.e., multiply only More...
 
virtual void adjust_relax_movemap (core::kinematics::MoveMap &) const
 disallow torsion moves in relax if bRigidInRelax More...
 
virtual void receive_message (ClaimerMessage &cm)
 
bool use_loops_from_threading_job () const
 Returns true if we are using loop definitions from ThreadingJob. More...
 
void use_loops_from_threading_job (bool setting)
 Sets whether we should use loop definitions from ThreadingJob. More...
 
- 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 generate_sequence_claims (DofClaims &)
 generate claims that affect the sequence of the pose More...
 
virtual void initialize_residues (core::pose::Pose &, SequenceClaimOP init_claim, 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 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 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...
 
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...
 
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)
 

Static Public Member Functions

static std::string _static_type_name ()
 

Protected Member Functions

void select_parts ()
 select sub-regions from rigid_core_, if skip-rate is specified More...
 
virtual bool read_tag (std::string tag, std::istream &is)
 
virtual void set_defaults ()
 
virtual void init_after_reading ()
 
- 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
 
typedef
utility::pointer::owning_ptr
< JumpCalculator
JumpCalculatorOP
 

Private Attributes

core::pose::Pose input_pose_
 starting pose More...
 
core::pose::Pose centroid_input_pose_
 starting pose in centroid mode More...
 
loops::Loops rigid_core_
 regions that can be used for rigid core More...
 
loops::Loops current_rigid_core_
 if skip-rate is given (in loop-definitions) current_rigid_core_ will contain the current "choice" of regions... set in generate_claims() More...
 
DofClaims current_jumps_
 jumps used this round — since generate_claims() More...
 
bool bExclusive_
 flag used to specify if the rigid regions should really be treated exclusivity — i.e., are they really rigid ? More...
 
bool bAllowAdjacentJumps_
 jump residues that are just next to rigid region are probably leading to impossibl fold-trees (not always – but most of the time) if false we don't allow such jumps More...
 
bool bUseInputPose_
 use the pose in new_decoy( pose ) More...
 
bool bUseThreadingJobLoops_
 use loop-definition from ThreadingJob More...
 
core::Size min_loop_size_
 min_loop_size for Threading-loops More...
 
core::Real random_grow_loops_by_
 same effect as OptionKeys::loops::random_grow_loops_by ]() for looprelax More...
 
bool bRigidInRelax_
 keep this chunk rigid in relax — adjust movemap to keep BB-Torsions fixed... More...
 
JumpCalculatorOP current_jump_calculator_
 

Detailed Description

defines a rigid part of structure... imagine a loop-relax application core structure is fixed via jumps and loops can move the rigid chunk takes a definition of rigid regions in form of an instance of Loops (just taken as bunch of start-end residue numbers — here defining the rigid residues and not the loops). the rigid chunk to keep its integrity will need jumps, the claimer will reuse jumps if somebody else claims them, or submit in finalize_claims his own jumps, if not enough jumps are present. in "bExclusive_ mode" the RigidChunk will reclaim any jump claim that is useful and wihin the rigid region. (i.e., foreign claim is dissallowed but own claim with same residues is issued — in this way the claimer uses e.g., beta-sheet jumps, where they are suggested the input pose is used to initialize the rigid region ( via copying of internal coordinates ) e.g., a hole in the structure shouldn't pose a problem, since we basically copy the atom-tree.

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::topology_broker::RigidChunkClaimer::RigidChunkClaimer ( )

Referenced by clone().

protocols::topology_broker::RigidChunkClaimer::RigidChunkClaimer ( core::pose::Pose const &  input_pose,
loops::Loops  rigid 
)

Member Function Documentation

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

Referenced by type().

bool protocols::topology_broker::RigidChunkClaimer::accept_declined_claim ( DofClaim const &  was_declined)
virtual

will fail if a BB torsion claim of the rigid region has been declined

Reimplemented from protocols::topology_broker::TopologyClaimer.

References tr().

void protocols::topology_broker::RigidChunkClaimer::adjust_relax_movemap ( core::kinematics::MoveMap mm) const
virtual

disallow torsion moves in relax if bRigidInRelax

Reimplemented from protocols::topology_broker::TopologyClaimer.

References core::id::BB, bRigidInRelax_, rigid_core_, and protocols::loops::Loops::switch_movemap().

bool protocols::topology_broker::RigidChunkClaimer::allow_claim ( DofClaim const &  foreign_claim)
virtual
virtual TopologyClaimerOP protocols::topology_broker::RigidChunkClaimer::clone ( ) const
inlinevirtual
void protocols::topology_broker::RigidChunkClaimer::finalize_claims ( DofClaims new_claims)
virtual

issue jump-claims for jumps yet missing to keep rigid regions fixed

Reimplemented from protocols::topology_broker::TopologyClaimer.

References current_jump_calculator_, and current_jumps_.

void protocols::topology_broker::RigidChunkClaimer::generate_claims ( DofClaims new_claims)
virtual

generate DofClaims for BB

generate exclusive backbone claims for each residue of the rigid-chunk jumps are not exclusive and are added later in final_claims — want to reuse other jumps if possible

Reimplemented from protocols::topology_broker::TopologyClaimer.

References protocols::loops::Loops::begin(), current_rigid_core_, protocols::loops::Loops::end(), protocols::topology_broker::DofClaim::EXCLUSIVE, and tr().

void protocols::topology_broker::RigidChunkClaimer::init_after_reading ( )
protectedvirtual
void protocols::topology_broker::RigidChunkClaimer::initialize_dofs ( core::pose::Pose pose,
DofClaims const &  init_claims,
DofClaims failed_to_init 
)
virtual
void protocols::topology_broker::RigidChunkClaimer::manipulate_cut_bias ( utility::vector1< core::Real > &  cut_bias)
virtual

multiply your bias to this – if its zero don't change that, i.e., multiply only

Reimplemented from protocols::topology_broker::TopologyClaimer.

References current_rigid_core_, and protocols::loops::Loops::transfer_to_residue_vector().

void protocols::topology_broker::RigidChunkClaimer::new_decoy ( )
virtual

a new decoy — random choices to be made ? make them here

Reimplemented from protocols::topology_broker::TopologyClaimer.

References bAllowAdjacentJumps_, current_jump_calculator_, current_jumps_, current_rigid_core_, and select_parts().

Referenced by new_decoy().

void protocols::topology_broker::RigidChunkClaimer::new_decoy ( core::pose::Pose const &  )
virtual
bool protocols::topology_broker::RigidChunkClaimer::read_tag ( std::string  tag,
std::istream &  is 
)
protectedvirtual
void protocols::topology_broker::RigidChunkClaimer::receive_message ( ClaimerMessage cm)
virtual
void protocols::topology_broker::RigidChunkClaimer::select_parts ( )
protected
void protocols::topology_broker::RigidChunkClaimer::set_defaults ( )
protectedvirtual
void protocols::topology_broker::RigidChunkClaimer::switch_to_fullatom ( core::pose::Pose pose,
utility::vector1< bool bNeedToRepack 
) const
virtual
virtual std::string protocols::topology_broker::RigidChunkClaimer::type ( ) const
inlinevirtual

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().

bool protocols::topology_broker::RigidChunkClaimer::use_loops_from_threading_job ( ) const
inline

Returns true if we are using loop definitions from ThreadingJob.

References bUseThreadingJobLoops_.

void protocols::topology_broker::RigidChunkClaimer::use_loops_from_threading_job ( bool  setting)
inline

Sets whether we should use loop definitions from ThreadingJob.

References bUseThreadingJobLoops_.

Member Data Documentation

bool protocols::topology_broker::RigidChunkClaimer::bAllowAdjacentJumps_
private

jump residues that are just next to rigid region are probably leading to impossibl fold-trees (not always – but most of the time) if false we don't allow such jumps

Referenced by protocols::topology_broker::RigidChunkClaimer::JumpCalculator::good_jump(), protocols::topology_broker::RigidChunkClaimer::JumpCalculator::irrelevant_jump(), and new_decoy().

bool protocols::topology_broker::RigidChunkClaimer::bExclusive_
private

flag used to specify if the rigid regions should really be treated exclusivity — i.e., are they really rigid ?

changing this flag to false, will allow everything to move, but together with coordinate constraints this might yield a pose that is easier sampled ?

Referenced by allow_claim(), and read_tag().

bool protocols::topology_broker::RigidChunkClaimer::bRigidInRelax_
private

keep this chunk rigid in relax — adjust movemap to keep BB-Torsions fixed...

Referenced by adjust_relax_movemap(), and read_tag().

bool protocols::topology_broker::RigidChunkClaimer::bUseInputPose_
private

use the pose in new_decoy( pose )

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

bool protocols::topology_broker::RigidChunkClaimer::bUseThreadingJobLoops_
private

use loop-definition from ThreadingJob

Referenced by new_decoy(), read_tag(), set_defaults(), and use_loops_from_threading_job().

core::pose::Pose protocols::topology_broker::RigidChunkClaimer::centroid_input_pose_
private

starting pose in centroid mode

Referenced by init_after_reading(), initialize_dofs(), new_decoy(), and RigidChunkClaimer().

JumpCalculatorOP protocols::topology_broker::RigidChunkClaimer::current_jump_calculator_
private
DofClaims protocols::topology_broker::RigidChunkClaimer::current_jumps_
private

jumps used this round — since generate_claims()

Referenced by allow_claim(), finalize_claims(), and new_decoy().

loops::Loops protocols::topology_broker::RigidChunkClaimer::current_rigid_core_
private

if skip-rate is given (in loop-definitions) current_rigid_core_ will contain the current "choice" of regions... set in generate_claims()

Referenced by allow_claim(), generate_claims(), initialize_dofs(), manipulate_cut_bias(), new_decoy(), receive_message(), select_parts(), and switch_to_fullatom().

core::pose::Pose protocols::topology_broker::RigidChunkClaimer::input_pose_
private
core::Size protocols::topology_broker::RigidChunkClaimer::min_loop_size_
private

min_loop_size for Threading-loops

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

core::Real protocols::topology_broker::RigidChunkClaimer::random_grow_loops_by_
private

same effect as OptionKeys::loops::random_grow_loops_by ]() for looprelax

Referenced by read_tag(), select_parts(), and set_defaults().

loops::Loops protocols::topology_broker::RigidChunkClaimer::rigid_core_
private

regions that can be used for rigid core

Referenced by adjust_relax_movemap(), init_after_reading(), new_decoy(), read_tag(), and select_parts().


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