Rosetta 3.4
Public Member Functions
protocols::topology_broker::TopologyBroker Class Reference

#include <TopologyBroker.hh>

Inheritance diagram for protocols::topology_broker::TopologyBroker:
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List of all members.

Public Member Functions

 TopologyBroker ()
 constructor
 ~TopologyBroker ()
 TopologyBroker (TopologyBroker const &)
TopologyBroker const & operator= (TopologyBroker const &)
void add (TopologyClaimerOP cl)
 add new Claimers to the broker ---- useful before a job is started
void use_job_pose (bool setting)
 use the input pose from the job (i.e., call new_decoy( pose ) )
bool use_job_pose () const
 Returns true if we are using the input pose from the job (i.e. new_decoy(pose)), false otherwise.
const TopologyClaimerOPclaimer (core::Size i) const
 Returns the ith topology claimer if it exists.
core::Size num_claimers () const
 Returns the number of claimers associated with the broker.
void apply (core::pose::Pose &)
 at the start of a job this is called, e.g., by the AbrelaxMover it generates a pose with appropriate foldtree and initializes dofs, adds constraints, etc.
moves::MoverOP mover (core::pose::Pose const &, abinitio::StageID, core::scoring::ScoreFunction const &scorefxn, core::Real progress) const
 return a set of Movers ( RandomMover, i.e. container of movers )
void apply_filter (core::pose::Pose const &, abinitio::StageID, core::Real progress) const
 apply filter (TopologyClaimer::passes_filter() ) and raise exception EXCN_FILTER_FAILED if failed
void adjust_relax_movemap (core::kinematics::MoveMap &) const
 if some claimer wants to influence the movemap for relax he can do it here:
core::fragment::FragSetCOP loop_frags (core::kinematics::MoveMap &) const
 the SlidingWindowLoopClosure needs pure fragments, because it changes the the residue number in the ShortLoopClosure part thus extra hook for this --- > only some Claimers will answer
bool has_chainbreaks_to_close () const
 do we need to close loops ( unphysical chainbreaks have been introduced? )
void add_chainbreak_variants (core::pose::Pose &pose, core::Size max_dist=0, core::kinematics::ShortestPathInFoldTreeCOP sp=NULL) const
 add chainbreak variant residue to the unphysical chainbreaks
bool check_chainbreak_variants (core::pose::Pose &pose) const
 check that each chainbreak residue has a chainbreak variant
void switch_to_fullatom (core::pose::Pose &)
 switch to fullatom --- some Claimers might help by providing template based side-chain information
core::kinematics::FoldTreefinal_fold_tree () const
 access for hacky claimers
SequenceClaimresolve_sequence_label (std::string const &label) const
 get the sequence claim that is consistent with the label, throws EXCN_Unknown_SequenceLabel if not found
core::Size resolve_residue (std::string const &chain_label, core::Size pos) const
void relay_message (ClaimerMessage &msg) const
bool has_sequence_claimer ()
core::pose::Pose const & current_pose () const

Constructor & Destructor Documentation

protocols::topology_broker::TopologyBroker::TopologyBroker ( )

constructor

protocols::topology_broker::TopologyBroker::~TopologyBroker ( )
protocols::topology_broker::TopologyBroker::TopologyBroker ( TopologyBroker const &  tp)

Member Function Documentation

void protocols::topology_broker::TopologyBroker::add ( TopologyClaimerOP  cl)

add new Claimers to the broker ---- useful before a job is started

---------------- Application Setup ------------------------------------

Referenced by protocols::topology_broker::add_claims_from_stream(), and protocols::topology_broker::add_cmdline_claims().

void protocols::topology_broker::TopologyBroker::add_chainbreak_variants ( core::pose::Pose pose,
core::Size  max_dist = 0,
core::kinematics::ShortestPathInFoldTreeCOP  sp = NULL 
) const
void protocols::topology_broker::TopologyBroker::adjust_relax_movemap ( core::kinematics::MoveMap mm) const

if some claimer wants to influence the movemap for relax he can do it here:

void protocols::topology_broker::TopologyBroker::apply ( core::pose::Pose pose)
void protocols::topology_broker::TopologyBroker::apply_filter ( core::pose::Pose const &  pose,
abinitio::StageID  stage_id,
core::Real  progress 
) const

apply filter (TopologyClaimer::passes_filter() ) and raise exception EXCN_FILTER_FAILED if failed

References tr().

Referenced by protocols::abinitio::FragmentSampler::apply(), and protocols::abinitio::FragmentSampler::mover().

bool protocols::topology_broker::TopologyBroker::check_chainbreak_variants ( core::pose::Pose pose) const
const TopologyClaimerOP& protocols::topology_broker::TopologyBroker::claimer ( core::Size  i) const [inline]

Returns the ith topology claimer if it exists.

core::pose::Pose const& protocols::topology_broker::TopologyBroker::current_pose ( ) const [inline]
core::kinematics::FoldTree& protocols::topology_broker::TopologyBroker::final_fold_tree ( ) const [inline]
bool protocols::topology_broker::TopologyBroker::has_chainbreaks_to_close ( ) const

do we need to close loops ( unphysical chainbreaks have been introduced? )

bool protocols::topology_broker::TopologyBroker::has_sequence_claimer ( )
core::fragment::FragSetCOP protocols::topology_broker::TopologyBroker::loop_frags ( core::kinematics::MoveMap movemap) const

the SlidingWindowLoopClosure needs pure fragments, because it changes the the residue number in the ShortLoopClosure part thus extra hook for this --- > only some Claimers will answer

moves::MoverOP protocols::topology_broker::TopologyBroker::mover ( core::pose::Pose const &  pose,
abinitio::StageID  stage_id,
core::scoring::ScoreFunction const &  scorefxn,
core::Real  progress 
) const

return a set of Movers ( RandomMover, i.e. container of movers )

---------------------------------- Consulting ---------------------------------------------------- the following interface is for the Mover to consult the Broker during the course of a simulation usually these calls a relayed to the Claimers only some will answer, others will ignore it. e.g., ConstraintClaimer will not add a Mover, JumpClaimer and RigidChunkClaimer will add chainbreaks a basic FragmentClaimer will not

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

Referenced by protocols::abinitio::FragmentSampler::mover().

core::Size protocols::topology_broker::TopologyBroker::num_claimers ( ) const [inline]

Returns the number of claimers associated with the broker.

TopologyBroker const & protocols::topology_broker::TopologyBroker::operator= ( TopologyBroker const &  src)
void protocols::topology_broker::TopologyBroker::relay_message ( ClaimerMessage msg) const
core::Size protocols::topology_broker::TopologyBroker::resolve_residue ( std::string const &  chain_label,
core::Size  pos 
) const
SequenceClaim & protocols::topology_broker::TopologyBroker::resolve_sequence_label ( std::string const &  label) const

get the sequence claim that is consistent with the label, throws EXCN_Unknown_SequenceLabel if not found

Referenced by protocols::topology_broker::FragmentClaimer::get_sequence_region(), and resolve_residue().

void protocols::topology_broker::TopologyBroker::switch_to_fullatom ( core::pose::Pose pose)
bool protocols::topology_broker::TopologyBroker::use_job_pose ( ) const [inline]

Returns true if we are using the input pose from the job (i.e. new_decoy(pose)), false otherwise.

void protocols::topology_broker::TopologyBroker::use_job_pose ( bool  setting) [inline]

use the input pose from the job (i.e., call new_decoy( pose ) )

Referenced by protocols::topology_broker::add_claims_from_stream().


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