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protocols::topology_broker Namespace Reference

Namespaces

 weights
 

Classes

class  AsymFoldandDockClaimer
 
class  ClaimerMessage
 
class  SuggestValueMessage
 
class  ConstraintClaimer
 
class  ConstraintEvaluatorWrapper
 
class  ConstraintEvaluatorWrapperCreator
 creator for the ConstraintsEvaluatorWrapperCreator class More...
 
class  CoordConstraintClaimer
 
class  CutBiasClaimer
 
class  DensityScoringClaimer
 
class  DisulfJumpClaimer
 Claimer that works with the old system of BaseJumpSetup it supports only JumpFrames of type [ BBTorsion ] UpJump DownJump [ BBTorsion ] the class JumpSample is still used to transport the information jumps and jump_atoms, but cuts are ignored all functionality of JumpSample is not used anymore. More...
 
class  DofClaim
 
class  SequenceClaim
 
class  BBClaim
 
class  JumpClaim
 
class  CutClaim
 
class  RootClaim
 
class  EXCN_TopologyBroker
 
class  EXCN_Input
 
class  EXCN_Unknown
 
class  EXCN_FailedBroking
 
class  EXCN_FilterFailed
 
class  FibrilModelingClaimer
 
class  FoldandDockClaimer
 
class  FragmentClaimer
 
class  JumpClaimer
 Claimer that works with the old system of BaseJumpSetup it supports only JumpFrames of type [ BBTorsion ] UpJump DownJump [ BBTorsion ] the class JumpSample is still used to transport the information jumps and jump_atoms, but cuts are ignored all functionality of JumpSample is not used anymore. More...
 
class  LoopFragmentClaimer
 
class  MembraneTopologyClaimer
 
class  MetalloClaimer
 
class  PcsEnergyController
 
class  PseudocontactShiftEnergyController
 
class  RigidChunkClaimer
 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...
 
class  SequenceClaimer
 
class  StartStructClaimer
 
class  TemplateFragmentClaimer
 hacky wrapper to keep the old Template code alive a bit longer this claimer deals with the Jumpy part of the Templates. More...
 
class  TemplateJumpClaimer
 hacky wrapper to keep the old Template code alive a bit longer this claimer deals with the Jumpy part of the Templates. More...
 
class  TopologyBroker
 
class  TopologyClaimer
 
class  TopologyClaimerFactory
 A non-copyable factory for instantiating TopologyClaimers by name. Commonly used TopologyClaimers are registered in the constructor. Additional claimers can be registered after the fact using the add_type() method. More...
 
struct  CmdLineData
 

Typedefs

typedef
utility::pointer::owning_ptr
< AsymFoldandDockClaimer > 		AsymFoldandDockClaimerOP
 
typedef
utility::pointer::owning_ptr
< AsymFoldandDockClaimer const > 		AsymFoldandDockClaimerCOP
 
typedef
utility::pointer::access_ptr
< AsymFoldandDockClaimer > 		AsymFoldandDockClaimerAP
 
typedef
utility::pointer::access_ptr
< AsymFoldandDockClaimer const > 		AsymFoldandDockClaimerCAP
 
typedef
utility::pointer::owning_ptr
< ClaimerMessage > 		ClaimerMessageOP
 
typedef
utility::pointer::owning_ptr
< ClaimerMessage const > 		ClaimerMessageCOP
 
typedef
utility::pointer::access_ptr
< ClaimerMessage > 		ClaimerMessageAP
 
typedef
utility::pointer::access_ptr
< ClaimerMessage const > 		ClaimerMessageCAP
 
typedef
utility::pointer::owning_ptr
< ConstraintClaimer > 		ConstraintClaimerOP
 
typedef
utility::pointer::owning_ptr
< ConstraintClaimer const > 		ConstraintClaimerCOP
 
typedef
utility::pointer::access_ptr
< ConstraintClaimer > 		ConstraintClaimerAP
 
typedef
utility::pointer::access_ptr
< ConstraintClaimer const > 		ConstraintClaimerCAP
 
typedef
utility::pointer::owning_ptr
< ConstraintEvaluatorWrapper > 		ConstraintEvaluatorWrapperOP
 
typedef
utility::pointer::owning_ptr
< ConstraintEvaluatorWrapper
const > 		ConstraintEvaluatorWrapperCOP
 
typedef
utility::pointer::access_ptr
< ConstraintEvaluatorWrapper > 		ConstraintEvaluatorWrapperAP
 
typedef
utility::pointer::access_ptr
< ConstraintEvaluatorWrapper
const > 		ConstraintEvaluatorWrapperCAP
 
typedef
utility::pointer::owning_ptr
< CutBiasClaimer > 		CutBiasClaimerOP
 
typedef
utility::pointer::owning_ptr
< CutBiasClaimer const > 		CutBiasClaimerCOP
 
typedef
utility::pointer::access_ptr
< CutBiasClaimer > 		CutBiasClaimerAP
 
typedef
utility::pointer::access_ptr
< CutBiasClaimer const > 		CutBiasClaimerCAP
 
typedef
utility::pointer::owning_ptr
< DensityScoringClaimer > 		DensityScoringClaimerOP
 
typedef
utility::pointer::owning_ptr
< DensityScoringClaimer const > 		DensityScoringClaimerCOP
 
typedef
utility::pointer::access_ptr
< DensityScoringClaimer > 		DensityScoringClaimerAP
 
typedef
utility::pointer::access_ptr
< DensityScoringClaimer const > 		DensityScoringClaimerCAP
 
typedef
utility::pointer::owning_ptr
< DisulfJumpClaimer > 		DisulfJumpClaimerOP
 
typedef
utility::pointer::owning_ptr
< DisulfJumpClaimer const > 		DisulfJumpClaimerCOP
 
typedef
utility::pointer::access_ptr
< DisulfJumpClaimer > 		DisulfJumpClaimerAP
 
typedef
utility::pointer::access_ptr
< DisulfJumpClaimer const > 		DisulfJumpClaimerCAP
 
typedef
utility::pointer::owning_ptr
< DofClaim > 		DofClaimOP
 
typedef
utility::pointer::owning_ptr
< DofClaim const > 		DofClaimCOP
 
typedef
utility::pointer::access_ptr
< DofClaim > 		DofClaimAP
 
typedef
utility::pointer::access_ptr
< DofClaim const > 		DofClaimCAP
 
typedef utility::vector1
< DofClaimOP > 		DofClaims
 
typedef
utility::pointer::owning_ptr
< SequenceClaim > 		SequenceClaimOP
 
typedef
utility::pointer::owning_ptr
< SequenceClaim const > 		SequenceClaimCOP
 
typedef
utility::pointer::access_ptr
< SequenceClaim > 		SequenceClaimAP
 
typedef
utility::pointer::access_ptr
< SequenceClaim const > 		SequenceClaimCAP
 
typedef utility::vector1
< SequenceClaimOP > 		SequenceClaims
 
typedef
utility::pointer::owning_ptr
< JumpClaim > 		JumpClaimOP
 
typedef
utility::pointer::owning_ptr
< JumpClaim const > 		JumpClaimCOP
 
typedef
utility::pointer::access_ptr
< JumpClaim > 		JumpClaimAP
 
typedef
utility::pointer::access_ptr
< JumpClaim const > 		JumpClaimCAP
 
typedef
utility::pointer::owning_ptr
< BBClaim > 		BBClaimOP
 
typedef
utility::pointer::owning_ptr
< BBClaim const > 		BBClaimCOP
 
typedef
utility::pointer::access_ptr
< BBClaim > 		BBClaimAP
 
typedef
utility::pointer::access_ptr
< BBClaim const > 		BBClaimCAP
 
typedef
utility::pointer::owning_ptr
< FibrilModelingClaimer > 		FibrilModelingClaimerOP
 
typedef
utility::pointer::owning_ptr
< FibrilModelingClaimer const > 		FibrilModelingClaimerCOP
 
typedef
utility::pointer::access_ptr
< FibrilModelingClaimer > 		FibrilModelingClaimerAP
 
typedef
utility::pointer::access_ptr
< FibrilModelingClaimer const > 		FibrilModelingClaimerCAP
 
typedef
utility::pointer::owning_ptr
< FoldandDockClaimer > 		FoldandDockClaimerOP
 
typedef
utility::pointer::owning_ptr
< FoldandDockClaimer const > 		FoldandDockClaimerCOP
 
typedef
utility::pointer::access_ptr
< FoldandDockClaimer > 		FoldandDockClaimerAP
 
typedef
utility::pointer::access_ptr
< FoldandDockClaimer const > 		FoldandDockClaimerCAP
 
typedef
utility::pointer::owning_ptr
< FragmentClaimer > 		FragmentClaimerOP
 
typedef
utility::pointer::owning_ptr
< FragmentClaimer const > 		FragmentClaimerCOP
 
typedef
utility::pointer::access_ptr
< FragmentClaimer > 		FragmentClaimerAP
 
typedef
utility::pointer::access_ptr
< FragmentClaimer const > 		FragmentClaimerCAP
 
typedef
utility::pointer::owning_ptr
< JumpClaimer > 		JumpClaimerOP
 
typedef
utility::pointer::owning_ptr
< JumpClaimer const > 		JumpClaimerCOP
 
typedef
utility::pointer::access_ptr
< JumpClaimer > 		JumpClaimerAP
 
typedef
utility::pointer::access_ptr
< JumpClaimer const > 		JumpClaimerCAP
 
typedef
utility::pointer::owning_ptr
< LoopFragmentClaimer > 		LoopFragmentClaimerOP
 
typedef
utility::pointer::owning_ptr
< LoopFragmentClaimer const > 		LoopFragmentClaimerCOP
 
typedef
utility::pointer::access_ptr
< LoopFragmentClaimer > 		LoopFragmentClaimerAP
 
typedef
utility::pointer::access_ptr
< LoopFragmentClaimer const > 		LoopFragmentClaimerCAP
 
typedef
utility::pointer::owning_ptr
< MetalloClaimer > 		MetalloClaimerOP
 
typedef
utility::pointer::owning_ptr
< MetalloClaimer const > 		MetalloClaimerCOP
 
typedef
utility::pointer::access_ptr
< MetalloClaimer > 		MetalloClaimerAP
 
typedef
utility::pointer::access_ptr
< MetalloClaimer const > 		MetalloClaimerCAP
 
typedef
utility::pointer::owning_ptr
< PcsEnergyController > 		PcsEnergyControllerOP
 
typedef
utility::pointer::owning_ptr
< PcsEnergyController const > 		PcsEnergyControllerCOP
 
typedef
utility::pointer::access_ptr
< PcsEnergyController > 		PcsEnergyControllerAP
 
typedef
utility::pointer::access_ptr
< PcsEnergyController const > 		PcsEnergyControllerCAP
 
typedef
utility::pointer::owning_ptr
< PseudocontactShiftEnergyController > 		PseudocontactShiftEnergyControllerOP
 
typedef
utility::pointer::owning_ptr
< PseudocontactShiftEnergyController
const > 		PseudocontactShiftEnergyControllerCOP
 
typedef
utility::pointer::access_ptr
< PseudocontactShiftEnergyController > 		PseudocontactShiftEnergyControllerAP
 
typedef
utility::pointer::access_ptr
< PseudocontactShiftEnergyController
const > 		PseudocontactShiftEnergyControllerCAP
 
typedef
utility::pointer::owning_ptr
< RigidChunkClaimer > 		RigidChunkClaimerOP
 
typedef
utility::pointer::owning_ptr
< RigidChunkClaimer const > 		RigidChunkClaimerCOP
 
typedef
utility::pointer::access_ptr
< RigidChunkClaimer > 		RigidChunkClaimerAP
 
typedef
utility::pointer::access_ptr
< RigidChunkClaimer const > 		RigidChunkClaimerCAP
 
typedef
utility::pointer::owning_ptr
< SequenceClaimer > 		SequenceClaimerOP
 
typedef
utility::pointer::owning_ptr
< SequenceClaimer const > 		SequenceClaimerCOP
 
typedef
utility::pointer::access_ptr
< SequenceClaimer > 		SequenceClaimerAP
 
typedef
utility::pointer::access_ptr
< SequenceClaimer const > 		SequenceClaimerCAP
 
typedef
utility::pointer::owning_ptr
< StartStructClaimer > 		StartStructClaimerOP
 
typedef
utility::pointer::owning_ptr
< StartStructClaimer const > 		StartStructClaimerCOP
 
typedef
utility::pointer::access_ptr
< StartStructClaimer > 		StartStructClaimerAP
 
typedef
utility::pointer::access_ptr
< StartStructClaimer const > 		StartStructClaimerCAP
 
typedef
utility::pointer::owning_ptr
< TemplateFragmentClaimer > 		TemplateFragmentClaimerOP
 
typedef
utility::pointer::owning_ptr
< TemplateFragmentClaimer
const > 		TemplateFragmentClaimerCOP
 
typedef
utility::pointer::access_ptr
< TemplateFragmentClaimer > 		TemplateFragmentClaimerAP
 
typedef
utility::pointer::access_ptr
< TemplateFragmentClaimer
const > 		TemplateFragmentClaimerCAP
 
typedef
utility::pointer::owning_ptr
< TemplateJumpClaimer > 		TemplateJumpClaimerOP
 
typedef
utility::pointer::owning_ptr
< TemplateJumpClaimer const > 		TemplateJumpClaimerCOP
 
typedef
utility::pointer::access_ptr
< TemplateJumpClaimer > 		TemplateJumpClaimerAP
 
typedef
utility::pointer::access_ptr
< TemplateJumpClaimer const > 		TemplateJumpClaimerCAP
 
typedef
utility::pointer::owning_ptr
< TopologyBroker > 		TopologyBrokerOP
 
typedef
utility::pointer::owning_ptr
< TopologyBroker const > 		TopologyBrokerCOP
 
typedef
utility::pointer::access_ptr
< TopologyBroker > 		TopologyBrokerAP
 
typedef
utility::pointer::access_ptr
< TopologyBroker const > 		TopologyBrokerCAP
 
typedef
utility::pointer::owning_ptr
< TopologyClaimer > 		TopologyClaimerOP
 
typedef
utility::pointer::owning_ptr
< TopologyClaimer const > 		TopologyClaimerCOP
 
typedef
utility::pointer::access_ptr
< TopologyClaimer > 		TopologyClaimerAP
 
typedef
utility::pointer::access_ptr
< TopologyClaimer const > 		TopologyClaimerCAP
 

Functions

std::ostream & operator<< (std::ostream &os, ClaimerMessage const &cm)
 
std::ostream & operator<< (std::ostream &os, DofClaim const &dof)
 
std::ostream & operator<< (std::ostream &os, DofClaims const &dofs)
 
protocols::loops::Loops generate_rigid_from_alignment (pose::Pose query_pose, core::sequence::SequenceAlignment const &align, Size min_loop_size)
 
void fix_internal_coords_of_siblings (pose::Pose &pose, pose::Pose const &ref_pose, id::AtomID atom, id::AtomID ref_atom)
 
void fix_mainchain_connect (pose::Pose &pose, pose::Pose const &ref_pose, core::Size upper_residue)
 
void copy_internal_coords (pose::Pose &pose, pose::Pose const &ref_pose, loops::Loops core)
 
bool is_not_neighbor_to_rigid (loops::Loops const &rigid, Size pos1, Size pos2)
 
bool connects_rigid_regions (loops::Loops const &rigid, Size pos1, Size pos2)
 
std::istream & operator>> (std::istream &is, TopologyClaimer &tc)
 
core::fragment::FragSetOP read_frags (std::istream &is, core::fragment::FragmentIO &io)
 
void add_claims_from_stream (TopologyBroker &broker, std::istream &is, CmdLineData &cmdline_data)
 
void add_claims_from_file (TopologyBroker &broker, std::string const &file, CmdLineData &cmdline_data)
 
void add_cmdline_claims (TopologyBroker &, bool do_I_need_frags=true)
 read broker::setup flag and add all claims to Broker More...
 

Typedef Documentation

typedef utility::pointer::access_ptr< AsymFoldandDockClaimer > protocols::topology_broker::AsymFoldandDockClaimerAP

Definition at line 33 of file AsymFoldandDockClaimer.fwd.hh.

typedef utility::pointer::access_ptr< AsymFoldandDockClaimer const > protocols::topology_broker::AsymFoldandDockClaimerCAP

Definition at line 34 of file AsymFoldandDockClaimer.fwd.hh.

typedef utility::pointer::owning_ptr< AsymFoldandDockClaimer const > protocols::topology_broker::AsymFoldandDockClaimerCOP

Definition at line 31 of file AsymFoldandDockClaimer.fwd.hh.

typedef utility::pointer::owning_ptr< AsymFoldandDockClaimer > protocols::topology_broker::AsymFoldandDockClaimerOP

Definition at line 27 of file AsymFoldandDockClaimer.fwd.hh.

typedef utility::pointer::access_ptr< BBClaim > protocols::topology_broker::BBClaimAP

Definition at line 69 of file DofClaim.fwd.hh.

typedef utility::pointer::access_ptr< BBClaim const > protocols::topology_broker::BBClaimCAP

Definition at line 70 of file DofClaim.fwd.hh.

typedef utility::pointer::owning_ptr< BBClaim const > protocols::topology_broker::BBClaimCOP

Definition at line 67 of file DofClaim.fwd.hh.

typedef utility::pointer::owning_ptr< BBClaim > protocols::topology_broker::BBClaimOP

Definition at line 63 of file DofClaim.fwd.hh.

typedef utility::pointer::access_ptr< ClaimerMessage > protocols::topology_broker::ClaimerMessageAP

Definition at line 34 of file ClaimerMessage.fwd.hh.

typedef utility::pointer::access_ptr< ClaimerMessage const > protocols::topology_broker::ClaimerMessageCAP

Definition at line 35 of file ClaimerMessage.fwd.hh.

typedef utility::pointer::owning_ptr< ClaimerMessage const > protocols::topology_broker::ClaimerMessageCOP

Definition at line 32 of file ClaimerMessage.fwd.hh.

typedef utility::pointer::owning_ptr< ClaimerMessage > protocols::topology_broker::ClaimerMessageOP

Definition at line 28 of file ClaimerMessage.fwd.hh.

typedef utility::pointer::access_ptr< ConstraintClaimer > protocols::topology_broker::ConstraintClaimerAP

Definition at line 34 of file ConstraintClaimer.fwd.hh.

typedef utility::pointer::access_ptr< ConstraintClaimer const > protocols::topology_broker::ConstraintClaimerCAP

Definition at line 35 of file ConstraintClaimer.fwd.hh.

typedef utility::pointer::owning_ptr< ConstraintClaimer const > protocols::topology_broker::ConstraintClaimerCOP

Definition at line 32 of file ConstraintClaimer.fwd.hh.

typedef utility::pointer::owning_ptr< ConstraintClaimer > protocols::topology_broker::ConstraintClaimerOP

Definition at line 28 of file ConstraintClaimer.fwd.hh.

typedef utility::pointer::access_ptr< ConstraintEvaluatorWrapper > protocols::topology_broker::ConstraintEvaluatorWrapperAP

Definition at line 34 of file ConstraintEvaluatorWrapper.fwd.hh.

typedef utility::pointer::access_ptr< ConstraintEvaluatorWrapper const > protocols::topology_broker::ConstraintEvaluatorWrapperCAP

Definition at line 35 of file ConstraintEvaluatorWrapper.fwd.hh.

typedef utility::pointer::owning_ptr< ConstraintEvaluatorWrapper const > protocols::topology_broker::ConstraintEvaluatorWrapperCOP

Definition at line 32 of file ConstraintEvaluatorWrapper.fwd.hh.

typedef utility::pointer::owning_ptr< ConstraintEvaluatorWrapper > protocols::topology_broker::ConstraintEvaluatorWrapperOP

Definition at line 28 of file ConstraintEvaluatorWrapper.fwd.hh.

typedef utility::pointer::access_ptr< CutBiasClaimer > protocols::topology_broker::CutBiasClaimerAP

Definition at line 34 of file CutBiasClaimer.fwd.hh.

typedef utility::pointer::access_ptr< CutBiasClaimer const > protocols::topology_broker::CutBiasClaimerCAP

Definition at line 35 of file CutBiasClaimer.fwd.hh.

typedef utility::pointer::owning_ptr< CutBiasClaimer const > protocols::topology_broker::CutBiasClaimerCOP

Definition at line 32 of file CutBiasClaimer.fwd.hh.

typedef utility::pointer::owning_ptr< CutBiasClaimer > protocols::topology_broker::CutBiasClaimerOP

Definition at line 28 of file CutBiasClaimer.fwd.hh.

typedef utility::pointer::access_ptr< DensityScoringClaimer > protocols::topology_broker::DensityScoringClaimerAP

Definition at line 34 of file DensityScoringClaimer.fwd.hh.

typedef utility::pointer::access_ptr< DensityScoringClaimer const > protocols::topology_broker::DensityScoringClaimerCAP

Definition at line 35 of file DensityScoringClaimer.fwd.hh.

typedef utility::pointer::owning_ptr< DensityScoringClaimer const > protocols::topology_broker::DensityScoringClaimerCOP

Definition at line 32 of file DensityScoringClaimer.fwd.hh.

typedef utility::pointer::owning_ptr< DensityScoringClaimer > protocols::topology_broker::DensityScoringClaimerOP

Definition at line 28 of file DensityScoringClaimer.fwd.hh.

typedef utility::pointer::access_ptr< DisulfJumpClaimer > protocols::topology_broker::DisulfJumpClaimerAP

Definition at line 34 of file DisulfJumpClaimer.fwd.hh.

typedef utility::pointer::access_ptr< DisulfJumpClaimer const > protocols::topology_broker::DisulfJumpClaimerCAP

Definition at line 35 of file DisulfJumpClaimer.fwd.hh.

typedef utility::pointer::owning_ptr< DisulfJumpClaimer const > protocols::topology_broker::DisulfJumpClaimerCOP

Definition at line 32 of file DisulfJumpClaimer.fwd.hh.

typedef utility::pointer::owning_ptr< DisulfJumpClaimer > protocols::topology_broker::DisulfJumpClaimerOP

Definition at line 28 of file DisulfJumpClaimer.fwd.hh.

typedef utility::pointer::access_ptr< DofClaim > protocols::topology_broker::DofClaimAP

Definition at line 37 of file DofClaim.fwd.hh.

typedef utility::pointer::access_ptr< DofClaim const > protocols::topology_broker::DofClaimCAP

Definition at line 38 of file DofClaim.fwd.hh.

typedef utility::pointer::owning_ptr< DofClaim const > protocols::topology_broker::DofClaimCOP

Definition at line 35 of file DofClaim.fwd.hh.

typedef utility::pointer::owning_ptr< DofClaim > protocols::topology_broker::DofClaimOP

Definition at line 31 of file DofClaim.fwd.hh.

typedef utility::vector1< DofClaimOP > protocols::topology_broker::DofClaims

Definition at line 40 of file DofClaim.fwd.hh.

typedef utility::pointer::access_ptr< FibrilModelingClaimer > protocols::topology_broker::FibrilModelingClaimerAP

Definition at line 33 of file FibrilModelingClaimer.fwd.hh.

typedef utility::pointer::access_ptr< FibrilModelingClaimer const > protocols::topology_broker::FibrilModelingClaimerCAP

Definition at line 34 of file FibrilModelingClaimer.fwd.hh.

typedef utility::pointer::owning_ptr< FibrilModelingClaimer const > protocols::topology_broker::FibrilModelingClaimerCOP

Definition at line 31 of file FibrilModelingClaimer.fwd.hh.

typedef utility::pointer::owning_ptr< FibrilModelingClaimer > protocols::topology_broker::FibrilModelingClaimerOP

Definition at line 27 of file FibrilModelingClaimer.fwd.hh.

typedef utility::pointer::access_ptr< FoldandDockClaimer > protocols::topology_broker::FoldandDockClaimerAP

Definition at line 33 of file FoldandDockClaimer.fwd.hh.

typedef utility::pointer::access_ptr< FoldandDockClaimer const > protocols::topology_broker::FoldandDockClaimerCAP

Definition at line 34 of file FoldandDockClaimer.fwd.hh.

typedef utility::pointer::owning_ptr< FoldandDockClaimer const > protocols::topology_broker::FoldandDockClaimerCOP

Definition at line 31 of file FoldandDockClaimer.fwd.hh.

typedef utility::pointer::owning_ptr< FoldandDockClaimer > protocols::topology_broker::FoldandDockClaimerOP

Definition at line 27 of file FoldandDockClaimer.fwd.hh.

typedef utility::pointer::access_ptr< FragmentClaimer > protocols::topology_broker::FragmentClaimerAP

Definition at line 34 of file FragmentClaimer.fwd.hh.

typedef utility::pointer::access_ptr< FragmentClaimer const > protocols::topology_broker::FragmentClaimerCAP

Definition at line 35 of file FragmentClaimer.fwd.hh.

typedef utility::pointer::owning_ptr< FragmentClaimer const > protocols::topology_broker::FragmentClaimerCOP

Definition at line 32 of file FragmentClaimer.fwd.hh.

typedef utility::pointer::owning_ptr< FragmentClaimer > protocols::topology_broker::FragmentClaimerOP

Definition at line 28 of file FragmentClaimer.fwd.hh.

typedef utility::pointer::access_ptr< JumpClaim > protocols::topology_broker::JumpClaimAP

Definition at line 60 of file DofClaim.fwd.hh.

typedef utility::pointer::access_ptr< JumpClaim const > protocols::topology_broker::JumpClaimCAP

Definition at line 61 of file DofClaim.fwd.hh.

typedef utility::pointer::owning_ptr< JumpClaim const > protocols::topology_broker::JumpClaimCOP

Definition at line 58 of file DofClaim.fwd.hh.

typedef utility::pointer::access_ptr< JumpClaimer > protocols::topology_broker::JumpClaimerAP

Definition at line 34 of file JumpClaimer.fwd.hh.

typedef utility::pointer::access_ptr< JumpClaimer const > protocols::topology_broker::JumpClaimerCAP

Definition at line 35 of file JumpClaimer.fwd.hh.

typedef utility::pointer::owning_ptr< JumpClaimer const > protocols::topology_broker::JumpClaimerCOP

Definition at line 32 of file JumpClaimer.fwd.hh.

typedef utility::pointer::owning_ptr< JumpClaimer > protocols::topology_broker::JumpClaimerOP

Definition at line 28 of file JumpClaimer.fwd.hh.

typedef utility::pointer::owning_ptr< JumpClaim > protocols::topology_broker::JumpClaimOP

Definition at line 54 of file DofClaim.fwd.hh.

typedef utility::pointer::access_ptr< LoopFragmentClaimer > protocols::topology_broker::LoopFragmentClaimerAP

Definition at line 34 of file LoopFragmentClaimer.fwd.hh.

typedef utility::pointer::access_ptr< LoopFragmentClaimer const > protocols::topology_broker::LoopFragmentClaimerCAP

Definition at line 35 of file LoopFragmentClaimer.fwd.hh.

typedef utility::pointer::owning_ptr< LoopFragmentClaimer const > protocols::topology_broker::LoopFragmentClaimerCOP

Definition at line 32 of file LoopFragmentClaimer.fwd.hh.

typedef utility::pointer::owning_ptr< LoopFragmentClaimer > protocols::topology_broker::LoopFragmentClaimerOP

Definition at line 28 of file LoopFragmentClaimer.fwd.hh.

typedef utility::pointer::access_ptr< MetalloClaimer > protocols::topology_broker::MetalloClaimerAP

Definition at line 34 of file MetalloClaimer.fwd.hh.

typedef utility::pointer::access_ptr< MetalloClaimer const > protocols::topology_broker::MetalloClaimerCAP

Definition at line 35 of file MetalloClaimer.fwd.hh.

typedef utility::pointer::owning_ptr< MetalloClaimer const > protocols::topology_broker::MetalloClaimerCOP

Definition at line 32 of file MetalloClaimer.fwd.hh.

typedef utility::pointer::owning_ptr< MetalloClaimer > protocols::topology_broker::MetalloClaimerOP

Definition at line 28 of file MetalloClaimer.fwd.hh.

typedef utility::pointer::access_ptr< PcsEnergyController > protocols::topology_broker::PcsEnergyControllerAP

Definition at line 48 of file PcsEnergyController.fwd.hh.

typedef utility::pointer::access_ptr< PcsEnergyController const > protocols::topology_broker::PcsEnergyControllerCAP

Definition at line 49 of file PcsEnergyController.fwd.hh.

typedef utility::pointer::owning_ptr< PcsEnergyController const > protocols::topology_broker::PcsEnergyControllerCOP

Definition at line 46 of file PcsEnergyController.fwd.hh.

typedef utility::pointer::owning_ptr< PcsEnergyController > protocols::topology_broker::PcsEnergyControllerOP

Definition at line 43 of file PcsEnergyController.fwd.hh.

typedef utility::pointer::access_ptr< PseudocontactShiftEnergyController > protocols::topology_broker::PseudocontactShiftEnergyControllerAP

Definition at line 50 of file PseudocontactShiftEnergyController.fwd.hh.

typedef utility::pointer::access_ptr< PseudocontactShiftEnergyController const > protocols::topology_broker::PseudocontactShiftEnergyControllerCAP

Definition at line 51 of file PseudocontactShiftEnergyController.fwd.hh.

typedef utility::pointer::owning_ptr< PseudocontactShiftEnergyController const > protocols::topology_broker::PseudocontactShiftEnergyControllerCOP

Definition at line 48 of file PseudocontactShiftEnergyController.fwd.hh.

typedef utility::pointer::owning_ptr< PseudocontactShiftEnergyController > protocols::topology_broker::PseudocontactShiftEnergyControllerOP

Definition at line 44 of file PseudocontactShiftEnergyController.fwd.hh.

typedef utility::pointer::access_ptr< RigidChunkClaimer > protocols::topology_broker::RigidChunkClaimerAP

Definition at line 34 of file RigidChunkClaimer.fwd.hh.

typedef utility::pointer::access_ptr< RigidChunkClaimer const > protocols::topology_broker::RigidChunkClaimerCAP

Definition at line 35 of file RigidChunkClaimer.fwd.hh.

typedef utility::pointer::owning_ptr< RigidChunkClaimer const > protocols::topology_broker::RigidChunkClaimerCOP

Definition at line 32 of file RigidChunkClaimer.fwd.hh.

typedef utility::pointer::owning_ptr< RigidChunkClaimer > protocols::topology_broker::RigidChunkClaimerOP

Definition at line 28 of file RigidChunkClaimer.fwd.hh.

typedef utility::pointer::access_ptr< SequenceClaim > protocols::topology_broker::SequenceClaimAP

Definition at line 49 of file DofClaim.fwd.hh.

typedef utility::pointer::access_ptr< SequenceClaim const > protocols::topology_broker::SequenceClaimCAP

Definition at line 50 of file DofClaim.fwd.hh.

typedef utility::pointer::owning_ptr< SequenceClaim const > protocols::topology_broker::SequenceClaimCOP

Definition at line 47 of file DofClaim.fwd.hh.

typedef utility::pointer::access_ptr< SequenceClaimer > protocols::topology_broker::SequenceClaimerAP

Definition at line 34 of file SequenceClaimer.fwd.hh.

typedef utility::pointer::access_ptr< SequenceClaimer const > protocols::topology_broker::SequenceClaimerCAP

Definition at line 35 of file SequenceClaimer.fwd.hh.

typedef utility::pointer::owning_ptr< SequenceClaimer const > protocols::topology_broker::SequenceClaimerCOP

Definition at line 32 of file SequenceClaimer.fwd.hh.

typedef utility::pointer::owning_ptr< SequenceClaimer > protocols::topology_broker::SequenceClaimerOP

Definition at line 28 of file SequenceClaimer.fwd.hh.

typedef utility::pointer::owning_ptr< SequenceClaim > protocols::topology_broker::SequenceClaimOP

Definition at line 43 of file DofClaim.fwd.hh.

typedef utility::vector1< SequenceClaimOP > protocols::topology_broker::SequenceClaims

Definition at line 52 of file DofClaim.fwd.hh.

typedef utility::pointer::access_ptr< StartStructClaimer > protocols::topology_broker::StartStructClaimerAP

Definition at line 34 of file StartStructClaimer.fwd.hh.

typedef utility::pointer::access_ptr< StartStructClaimer const > protocols::topology_broker::StartStructClaimerCAP

Definition at line 35 of file StartStructClaimer.fwd.hh.

typedef utility::pointer::owning_ptr< StartStructClaimer const > protocols::topology_broker::StartStructClaimerCOP

Definition at line 32 of file StartStructClaimer.fwd.hh.

typedef utility::pointer::owning_ptr< StartStructClaimer > protocols::topology_broker::StartStructClaimerOP

Definition at line 28 of file StartStructClaimer.fwd.hh.

typedef utility::pointer::access_ptr< TemplateFragmentClaimer > protocols::topology_broker::TemplateFragmentClaimerAP

Definition at line 34 of file TemplateFragmentClaimer.fwd.hh.

typedef utility::pointer::access_ptr< TemplateFragmentClaimer const > protocols::topology_broker::TemplateFragmentClaimerCAP

Definition at line 35 of file TemplateFragmentClaimer.fwd.hh.

typedef utility::pointer::owning_ptr< TemplateFragmentClaimer const > protocols::topology_broker::TemplateFragmentClaimerCOP

Definition at line 32 of file TemplateFragmentClaimer.fwd.hh.

typedef utility::pointer::owning_ptr< TemplateFragmentClaimer > protocols::topology_broker::TemplateFragmentClaimerOP

Definition at line 28 of file TemplateFragmentClaimer.fwd.hh.

typedef utility::pointer::access_ptr< TemplateJumpClaimer > protocols::topology_broker::TemplateJumpClaimerAP

Definition at line 34 of file TemplateJumpClaimer.fwd.hh.

typedef utility::pointer::access_ptr< TemplateJumpClaimer const > protocols::topology_broker::TemplateJumpClaimerCAP

Definition at line 35 of file TemplateJumpClaimer.fwd.hh.

typedef utility::pointer::owning_ptr< TemplateJumpClaimer const > protocols::topology_broker::TemplateJumpClaimerCOP

Definition at line 32 of file TemplateJumpClaimer.fwd.hh.

typedef utility::pointer::owning_ptr< TemplateJumpClaimer > protocols::topology_broker::TemplateJumpClaimerOP

Definition at line 28 of file TemplateJumpClaimer.fwd.hh.

typedef utility::pointer::access_ptr<TopologyBroker> protocols::topology_broker::TopologyBrokerAP

Definition at line 26 of file TopologyBroker.fwd.hh.

typedef utility::pointer::access_ptr<TopologyBroker const> protocols::topology_broker::TopologyBrokerCAP

Definition at line 27 of file TopologyBroker.fwd.hh.

typedef utility::pointer::owning_ptr<TopologyBroker const> protocols::topology_broker::TopologyBrokerCOP

Definition at line 24 of file TopologyBroker.fwd.hh.

typedef utility::pointer::owning_ptr<TopologyBroker> protocols::topology_broker::TopologyBrokerOP

Definition at line 22 of file TopologyBroker.fwd.hh.

typedef utility::pointer::access_ptr< TopologyClaimer > protocols::topology_broker::TopologyClaimerAP

Definition at line 34 of file TopologyClaimer.fwd.hh.

typedef utility::pointer::access_ptr< TopologyClaimer const > protocols::topology_broker::TopologyClaimerCAP

Definition at line 35 of file TopologyClaimer.fwd.hh.

typedef utility::pointer::owning_ptr< TopologyClaimer const > protocols::topology_broker::TopologyClaimerCOP

Definition at line 32 of file TopologyClaimer.fwd.hh.

typedef utility::pointer::owning_ptr< TopologyClaimer > protocols::topology_broker::TopologyClaimerOP

Definition at line 28 of file TopologyClaimer.fwd.hh.

Function Documentation

void protocols::topology_broker::add_claims_from_file ( TopologyBroker &  broker,
std::string const &  file,
CmdLineData &  cmdline_data 
)

Definition at line 146 of file util.cc.

References add_claims_from_stream().

Referenced by add_cmdline_claims().

void protocols::topology_broker::add_claims_from_stream ( TopologyBroker &  broker,
std::istream &  is,
CmdLineData &  cmdline_data 
)

Definition at line 99 of file util.cc.

References protocols::topology_broker::ConstraintClaimer::_static_type_name(), protocols::topology_broker::TopologyBroker::add(), protocols::topology_broker::CmdLineData::b_has_constraint_claimer, protocols::topology_broker::CmdLineData::frags_large, protocols::topology_broker::CmdLineData::frags_small, protocols::topology_broker::TopologyClaimerFactory::get_instance(), protocols::topology_broker::TopologyClaimerFactory::newTopologyClaimer(), read_frags(), tr(), and protocols::topology_broker::TopologyBroker::use_job_pose().

Referenced by add_claims_from_file().

void protocols::topology_broker::add_cmdline_claims ( TopologyBroker &  broker,
bool const  do_I_need_frags 
)

read broker::setup flag and add all claims to Broker

Definition at line 161 of file util.cc.

References protocols::topology_broker::TopologyBroker::add(), add_claims_from_file(), core::chemical::CENTROID, protocols::topology_broker::TopologyBroker::has_sequence_claimer(), core::import_pose::pose_from_pdb(), core::sequence::read_fasta_file(), core::fragment::read_std_frags_from_cmd(), and tr().

Referenced by protocols::abinitio::AbrelaxMover::set_defaults(), protocols::abinitio::IterativeBase::setup_filter_cst(), and protocols::abinitio::IterativeBase::test_broker_settings().

bool protocols::topology_broker::connects_rigid_regions ( loops::Loops const &  rigid,
Size  pos1,
Size  pos2 
)

Definition at line 575 of file RigidChunkClaimer.cc.

References protocols::loops::Loops::loop_index_of_residue().

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

void protocols::topology_broker::copy_internal_coords ( pose::Pose &  pose,
pose::Pose const &  ref_pose,
loops::Loops  core 
)

Definition at line 412 of file RigidChunkClaimer.cc.

References protocols::loops::Loops::begin(), protocols::loops::Loops::end(), fix_mainchain_connect(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_cutpoint(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_upper_terminus(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and tr().

Referenced by protocols::topology_broker::RigidChunkClaimer::initialize_dofs().

void protocols::topology_broker::fix_internal_coords_of_siblings ( pose::Pose &  pose,
pose::Pose const &  ref_pose,
id::AtomID  atom,
id::AtomID  ref_atom 
)

Definition at line 311 of file RigidChunkClaimer.cc.

References core::kinematics::AtomTree::atom(), core::conformation::Conformation::atom_tree(), core::pose::Pose::conformation(), core::kinematics::AtomTree::dof(), core::kinematics::AtomTree::has(), core::kinematics::tree::Atom::parent(), core::id::PHI, core::pose::Pose::residue(), core::id::AtomID::rsd(), core::conformation::Conformation::set_bond_angle(), core::conformation::Conformation::set_dof(), core::pose::Pose::total_residue(), tr(), and core::pose::Pose::xyz().

Referenced by fix_mainchain_connect().

void protocols::topology_broker::fix_mainchain_connect ( pose::Pose &  pose,
pose::Pose const &  ref_pose,
core::Size  upper_residue 
)

Definition at line 357 of file RigidChunkClaimer.cc.

References core::conformation::Residue::atom_index(), core::chemical::ResidueType::atom_index(), core::conformation::Conformation::bond_angle(), core::conformation::Conformation::bond_length(), core::pose::Pose::conformation(), fix_internal_coords_of_siblings(), core::conformation::Residue::has(), core::pose::is_ideal_position(), core::conformation::Residue::mainchain_torsion(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::conformation::Conformation::set_bond_angle(), core::conformation::Conformation::set_bond_length(), core::conformation::Conformation::set_torsion_angle(), core::conformation::Conformation::torsion_angle(), and tr().

Referenced by copy_internal_coords().

protocols::loops::Loops protocols::topology_broker::generate_rigid_from_alignment ( pose::Pose  query_pose,
core::sequence::SequenceAlignment const &  align,
Size  min_loop_size 
)

Definition at line 71 of file RigidChunkClaimer.cc.

References protocols::comparative_modeling::loops_from_alignment(), and core::pose::Pose::total_residue().

Referenced by protocols::topology_broker::RigidChunkClaimer::new_decoy().

bool protocols::topology_broker::is_not_neighbor_to_rigid ( loops::Loops const &  rigid,
Size  pos1,
Size  pos2 
)

Definition at line 562 of file RigidChunkClaimer.cc.

References protocols::loops::Loops::loop_index_of_residue().

Referenced by protocols::topology_broker::RigidChunkClaimer::JumpCalculator::irrelevant_jump().

std::ostream& protocols::topology_broker::operator<< ( std::ostream &  os,
ClaimerMessage const &  cm 
)

Definition at line 36 of file ClaimerMessage.cc.

References protocols::topology_broker::ClaimerMessage::received_by_, protocols::topology_broker::ClaimerMessage::show(), and protocols::topology_broker::ClaimerMessage::type().

std::ostream & protocols::topology_broker::operator<< ( std::ostream &  os,
DofClaim const &  dof 
)

Definition at line 58 of file DofClaim.cc.

References protocols::topology_broker::DofClaim::show().

std::ostream & protocols::topology_broker::operator<< ( std::ostream &  os,
DofClaims const &  dofs 
)

Definition at line 63 of file DofClaim.cc.

std::istream& protocols::topology_broker::operator>> ( std::istream &  is,
TopologyClaimer &  tc 
)
inline

Definition at line 220 of file TopologyClaimer.hh.

References protocols::topology_broker::TopologyClaimer::read().

core::fragment::FragSetOP protocols::topology_broker::read_frags ( std::istream &  is,
core::fragment::FragmentIO &  io 
)

Definition at line 72 of file util.cc.

References core::fragment::FragmentIO::read_data(), core::fragment::FragmentIO::set_ncopies(), core::fragment::FragmentIO::set_read_annotation(), and core::fragment::FragmentIO::set_top_frag_num().

Referenced by add_claims_from_stream().

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