Rosetta 3.4
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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>

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List of all members.

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.

Public Member Functions

 RigidChunkClaimer ()
 RigidChunkClaimer (core::pose::Pose const &input_pose, loops::Loops rigid)
virtual TopologyClaimerOP clone () const
 clone it!
virtual std::string type () const
 type() is specifying the output name of the TopologyClaimer
virtual void new_decoy ()
 a new decoy --- random choices to be made ? make them here
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
virtual void generate_claims (DofClaims &)
 generate DofClaims for BB
virtual bool allow_claim (DofClaim const &)
 has to decline foreign BB claims for rigid regions, reclaim jumps where appropriate
virtual void finalize_claims (DofClaims &)
 issue jump-claims for jumps yet missing to keep rigid regions fixed
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
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
virtual bool accept_declined_claim (DofClaim const &was_declined)
 will fail if a BB torsion claim of the rigid region has been declined
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
virtual void adjust_relax_movemap (core::kinematics::MoveMap &) const
 disallow torsion moves in relax if bRigidInRelax
virtual void receive_message (ClaimerMessage &cm)
bool use_loops_from_threading_job () const
 Returns true if we are using loop definitions from ThreadingJob.
void use_loops_from_threading_job (bool setting)
 Sets whether we should use loop definitions from ThreadingJob.

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
virtual bool read_tag (std::string tag, std::istream &is)
virtual void set_defaults ()
virtual void init_after_reading ()

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.


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 ( ) [inline, static]

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, 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 [inline, virtual]
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.

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::topology_broker::DofClaim::EXCLUSIVE, and tr().

void protocols::topology_broker::RigidChunkClaimer::init_after_reading ( ) [protected, virtual]
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 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 select_parts().

Referenced by new_decoy().

void protocols::topology_broker::RigidChunkClaimer::new_decoy ( core::pose::Pose const &  ) [virtual]

an input pose is given, i.e., a starting structure for resampling don't make random choices, base choices on given pose

Reimplemented from protocols::topology_broker::TopologyClaimer.

References core::chemical::CENTROID, protocols::topology_broker::generate_rigid_from_alignment(), core::pose::Pose::is_fullatom(), new_decoy(), core::util::switch_to_residue_type_set(), core::pose::Pose::total_residue(), and tr().

bool protocols::topology_broker::RigidChunkClaimer::read_tag ( std::string  tag,
std::istream &  is 
) [protected, virtual]
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 ( ) [protected, virtual]
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 [inline, virtual]

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.

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

Sets whether we should use loop definitions from ThreadingJob.


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