protocols::topology_broker Namespace Reference

Namespaces
	claims
	weights

Classes
class	AsymFoldandDockClaimer
class	BasicJumpClaimer
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	EXCN_TopologyBroker
class	EXCN_Input
class	EXCN_Unknown
class	EXCN_FailedBroking
class	EXCN_FilterFailed
class	FibrilModelingClaimer
class	FoldandDockClaimer
class	FragmentClaimer
class	FragmentJumpClaimer
	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	PseudocontactShiftEnergyController_Ts1
class	PseudocontactShiftEnergyController_Ts2
class	PseudocontactShiftEnergyController_Ts3
class	PseudocontactShiftEnergyController_Ts4
class	RigidBodyRandomTMHMover
class	RigidChunkClaimer
	defines a rigid part of structure... imagine a loop-relax application core structure is fixed via jumps and loops can move @detail 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	SequenceNumberResolver
class	StartStructClaimer
class	SymmetryClaimer
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	TMHTopologySamplerClaimer
class	TopologyBroker
class	TopologyClaimer
	@detail More...
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. APL Question: Should this be one-instance-per-program (singleton) or one-instance-per-job? More...
struct	CmdLineData
class	FragmentContainer

Typedefs
typedef utility::pointer::shared_ptr< AsymFoldandDockClaimer >	AsymFoldandDockClaimerOP
typedef utility::pointer::shared_ptr< AsymFoldandDockClaimer const >	AsymFoldandDockClaimerCOP
typedef utility::pointer::weak_ptr< AsymFoldandDockClaimer >	AsymFoldandDockClaimerAP
typedef utility::pointer::weak_ptr< AsymFoldandDockClaimer const >	AsymFoldandDockClaimerCAP
typedef utility::pointer::shared_ptr< BasicJumpClaimer >	BasicJumpClaimerOP
typedef utility::pointer::shared_ptr< BasicJumpClaimer const >	BasicJumpClaimerCOP
typedef utility::pointer::weak_ptr< BasicJumpClaimer >	BasicJumpClaimerAP
typedef utility::pointer::weak_ptr< BasicJumpClaimer const >	BasicJumpClaimerCAP
typedef utility::pointer::shared_ptr< ClaimerMessage >	ClaimerMessageOP
typedef utility::pointer::shared_ptr< ClaimerMessage const >	ClaimerMessageCOP
typedef utility::pointer::weak_ptr< ClaimerMessage >	ClaimerMessageAP
typedef utility::pointer::weak_ptr< ClaimerMessage const >	ClaimerMessageCAP
typedef utility::pointer::shared_ptr< ConstraintClaimer >	ConstraintClaimerOP
typedef utility::pointer::shared_ptr< ConstraintClaimer const >	ConstraintClaimerCOP
typedef utility::pointer::weak_ptr< ConstraintClaimer >	ConstraintClaimerAP
typedef utility::pointer::weak_ptr< ConstraintClaimer const >	ConstraintClaimerCAP
typedef utility::pointer::shared_ptr< ConstraintEvaluatorWrapper >	ConstraintEvaluatorWrapperOP
typedef utility::pointer::shared_ptr< ConstraintEvaluatorWrapper const >	ConstraintEvaluatorWrapperCOP
typedef utility::pointer::weak_ptr< ConstraintEvaluatorWrapper >	ConstraintEvaluatorWrapperAP
typedef utility::pointer::weak_ptr< ConstraintEvaluatorWrapper const >	ConstraintEvaluatorWrapperCAP
typedef utility::pointer::shared_ptr< CutBiasClaimer >	CutBiasClaimerOP
typedef utility::pointer::shared_ptr< CutBiasClaimer const >	CutBiasClaimerCOP
typedef utility::pointer::weak_ptr< CutBiasClaimer >	CutBiasClaimerAP
typedef utility::pointer::weak_ptr< CutBiasClaimer const >	CutBiasClaimerCAP
typedef utility::pointer::shared_ptr< DensityScoringClaimer >	DensityScoringClaimerOP
typedef utility::pointer::shared_ptr< DensityScoringClaimer const >	DensityScoringClaimerCOP
typedef utility::pointer::weak_ptr< DensityScoringClaimer >	DensityScoringClaimerAP
typedef utility::pointer::weak_ptr< DensityScoringClaimer const >	DensityScoringClaimerCAP
typedef utility::pointer::shared_ptr< DisulfJumpClaimer >	DisulfJumpClaimerOP
typedef utility::pointer::shared_ptr< DisulfJumpClaimer const >	DisulfJumpClaimerCOP
typedef utility::pointer::weak_ptr< DisulfJumpClaimer >	DisulfJumpClaimerAP
typedef utility::pointer::weak_ptr< DisulfJumpClaimer const >	DisulfJumpClaimerCAP
typedef utility::pointer::shared_ptr< FibrilModelingClaimer >	FibrilModelingClaimerOP
typedef utility::pointer::shared_ptr< FibrilModelingClaimer const >	FibrilModelingClaimerCOP
typedef utility::pointer::weak_ptr< FibrilModelingClaimer >	FibrilModelingClaimerAP
typedef utility::pointer::weak_ptr< FibrilModelingClaimer const >	FibrilModelingClaimerCAP
typedef utility::pointer::shared_ptr< FoldandDockClaimer >	FoldandDockClaimerOP
typedef utility::pointer::shared_ptr< FoldandDockClaimer const >	FoldandDockClaimerCOP
typedef utility::pointer::weak_ptr< FoldandDockClaimer >	FoldandDockClaimerAP
typedef utility::pointer::weak_ptr< FoldandDockClaimer const >	FoldandDockClaimerCAP
typedef utility::pointer::shared_ptr< FragmentClaimer >	FragmentClaimerOP
typedef utility::pointer::shared_ptr< FragmentClaimer const >	FragmentClaimerCOP
typedef utility::pointer::weak_ptr< FragmentClaimer >	FragmentClaimerAP
typedef utility::pointer::weak_ptr< FragmentClaimer const >	FragmentClaimerCAP
typedef utility::pointer::shared_ptr< FragmentJumpClaimer >	FragmentJumpClaimerOP
typedef utility::pointer::shared_ptr< FragmentJumpClaimer const >	FragmentJumpClaimerCOP
typedef utility::pointer::weak_ptr< FragmentJumpClaimer >	FragmentJumpClaimerAP
typedef utility::pointer::weak_ptr< FragmentJumpClaimer const >	FragmentJumpClaimerCAP
typedef utility::pointer::shared_ptr< LoopFragmentClaimer >	LoopFragmentClaimerOP
typedef utility::pointer::shared_ptr< LoopFragmentClaimer const >	LoopFragmentClaimerCOP
typedef utility::pointer::weak_ptr< LoopFragmentClaimer >	LoopFragmentClaimerAP
typedef utility::pointer::weak_ptr< LoopFragmentClaimer const >	LoopFragmentClaimerCAP
typedef utility::pointer::shared_ptr< MembraneTopologyClaimer >	MembraneTopologyClaimerOP
typedef utility::pointer::shared_ptr< MembraneTopologyClaimer const >	MembraneTopologyClaimerCOP
typedef utility::pointer::weak_ptr< MembraneTopologyClaimer >	MembraneTopologyClaimerAP
typedef utility::pointer::weak_ptr< MembraneTopologyClaimer const >	MembraneTopologyClaimerCAP
typedef utility::pointer::shared_ptr< MetalloClaimer >	MetalloClaimerOP
typedef utility::pointer::shared_ptr< MetalloClaimer const >	MetalloClaimerCOP
typedef utility::pointer::weak_ptr< MetalloClaimer >	MetalloClaimerAP
typedef utility::pointer::weak_ptr< MetalloClaimer const >	MetalloClaimerCAP
typedef utility::pointer::shared_ptr< PcsEnergyController >	PcsEnergyControllerOP
typedef utility::pointer::shared_ptr< PcsEnergyController const >	PcsEnergyControllerCOP
typedef utility::pointer::weak_ptr< PcsEnergyController >	PcsEnergyControllerAP
typedef utility::pointer::weak_ptr< PcsEnergyController const >	PcsEnergyControllerCAP
typedef utility::pointer::shared_ptr< PseudocontactShiftEnergyController >	PseudocontactShiftEnergyControllerOP
typedef utility::pointer::shared_ptr< PseudocontactShiftEnergyController const >	PseudocontactShiftEnergyControllerCOP
typedef utility::pointer::weak_ptr< PseudocontactShiftEnergyController >	PseudocontactShiftEnergyControllerAP
typedef utility::pointer::weak_ptr< PseudocontactShiftEnergyController const >	PseudocontactShiftEnergyControllerCAP
typedef utility::pointer::shared_ptr< PseudocontactShiftEnergyController_Ts1 >	PseudocontactShiftEnergyController_Ts1OP
typedef utility::pointer::shared_ptr< PseudocontactShiftEnergyController_Ts1 const >	PseudocontactShiftEnergyController_Ts1COP
typedef utility::pointer::weak_ptr< PseudocontactShiftEnergyController_Ts1 >	PseudocontactShiftEnergyController_Ts1AP
typedef utility::pointer::weak_ptr< PseudocontactShiftEnergyController_Ts1 const >	PseudocontactShiftEnergyController_Ts1CAP
typedef utility::pointer::shared_ptr< PseudocontactShiftEnergyController_Ts2 >	PseudocontactShiftEnergyController_Ts2OP
typedef utility::pointer::shared_ptr< PseudocontactShiftEnergyController_Ts2 const >	PseudocontactShiftEnergyController_Ts2COP
typedef utility::pointer::weak_ptr< PseudocontactShiftEnergyController_Ts2 >	PseudocontactShiftEnergyController_Ts2AP
typedef utility::pointer::weak_ptr< PseudocontactShiftEnergyController_Ts2 const >	PseudocontactShiftEnergyController_Ts2CAP
typedef utility::pointer::shared_ptr< PseudocontactShiftEnergyController_Ts3 >	PseudocontactShiftEnergyController_Ts3OP
typedef utility::pointer::shared_ptr< PseudocontactShiftEnergyController_Ts3 const >	PseudocontactShiftEnergyController_Ts3COP
typedef utility::pointer::weak_ptr< PseudocontactShiftEnergyController_Ts3 >	PseudocontactShiftEnergyController_Ts3AP
typedef utility::pointer::weak_ptr< PseudocontactShiftEnergyController_Ts3 const >	PseudocontactShiftEnergyController_Ts3CAP
typedef utility::pointer::shared_ptr< PseudocontactShiftEnergyController_Ts4 >	PseudocontactShiftEnergyController_Ts4OP
typedef utility::pointer::shared_ptr< PseudocontactShiftEnergyController_Ts4 const >	PseudocontactShiftEnergyController_Ts4COP
typedef utility::pointer::weak_ptr< PseudocontactShiftEnergyController_Ts4 >	PseudocontactShiftEnergyController_Ts4AP
typedef utility::pointer::weak_ptr< PseudocontactShiftEnergyController_Ts4 const >	PseudocontactShiftEnergyController_Ts4CAP
typedef utility::pointer::shared_ptr< RigidBodyRandomTMHMover >	RigidBodyRandomTMHMoverOP
typedef utility::pointer::shared_ptr< RigidBodyRandomTMHMover const >	RigidBodyRandomTMHMoverCOP
typedef utility::pointer::shared_ptr< RigidChunkClaimer >	RigidChunkClaimerOP
typedef utility::pointer::shared_ptr< RigidChunkClaimer const >	RigidChunkClaimerCOP
typedef utility::pointer::weak_ptr< RigidChunkClaimer >	RigidChunkClaimerAP
typedef utility::pointer::weak_ptr< RigidChunkClaimer const >	RigidChunkClaimerCAP
typedef utility::pointer::shared_ptr< SequenceClaimer >	SequenceClaimerOP
typedef utility::pointer::shared_ptr< SequenceClaimer const >	SequenceClaimerCOP
typedef utility::pointer::weak_ptr< SequenceClaimer >	SequenceClaimerAP
typedef utility::pointer::weak_ptr< SequenceClaimer const >	SequenceClaimerCAP
typedef utility::pointer::shared_ptr< SequenceNumberResolver >	SequenceNumberResolverOP
typedef utility::pointer::shared_ptr< SequenceNumberResolver const >	SequenceNumberResolverCOP
typedef utility::pointer::weak_ptr< SequenceNumberResolver >	SequenceNumberResolverAP
typedef utility::pointer::weak_ptr< SequenceNumberResolver const >	SequenceNumberResolverCAP
typedef utility::pointer::shared_ptr< StartStructClaimer >	StartStructClaimerOP
typedef utility::pointer::shared_ptr< StartStructClaimer const >	StartStructClaimerCOP
typedef utility::pointer::weak_ptr< StartStructClaimer >	StartStructClaimerAP
typedef utility::pointer::weak_ptr< StartStructClaimer const >	StartStructClaimerCAP
typedef utility::pointer::shared_ptr< SymmetryClaimer >	SymmetryClaimerOP
typedef utility::pointer::shared_ptr< SymmetryClaimer const >	SymmetryClaimerCOP
typedef utility::pointer::weak_ptr< SymmetryClaimer >	SymmetryClaimerAP
typedef utility::pointer::weak_ptr< SymmetryClaimer const >	SymmetryClaimerCAP
typedef utility::pointer::shared_ptr< TemplateFragmentClaimer >	TemplateFragmentClaimerOP
typedef utility::pointer::shared_ptr< TemplateFragmentClaimer const >	TemplateFragmentClaimerCOP
typedef utility::pointer::weak_ptr< TemplateFragmentClaimer >	TemplateFragmentClaimerAP
typedef utility::pointer::weak_ptr< TemplateFragmentClaimer const >	TemplateFragmentClaimerCAP
typedef utility::pointer::shared_ptr< TemplateJumpClaimer >	TemplateJumpClaimerOP
typedef utility::pointer::shared_ptr< TemplateJumpClaimer const >	TemplateJumpClaimerCOP
typedef utility::pointer::weak_ptr< TemplateJumpClaimer >	TemplateJumpClaimerAP
typedef utility::pointer::weak_ptr< TemplateJumpClaimer const >	TemplateJumpClaimerCAP
typedef utility::pointer::shared_ptr< TMHTopologySamplerClaimer >	TMHTopologySamplerClaimerOP
typedef utility::pointer::shared_ptr< TMHTopologySamplerClaimer const >	TMHTopologySamplerClaimerCOP
typedef utility::pointer::weak_ptr< TMHTopologySamplerClaimer >	TMHTopologySamplerClaimerAP
typedef utility::pointer::weak_ptr< TMHTopologySamplerClaimer const >	TMHTopologySamplerClaimerCAP
typedef utility::pointer::shared_ptr< TopologyBroker >	TopologyBrokerOP
typedef utility::pointer::shared_ptr< TopologyBroker const >	TopologyBrokerCOP
typedef utility::pointer::weak_ptr< TopologyBroker >	TopologyBrokerAP
typedef utility::pointer::weak_ptr< TopologyBroker const >	TopologyBrokerCAP
typedef utility::pointer::shared_ptr< TopologyClaimer >	TopologyClaimerOP
typedef utility::pointer::shared_ptr< TopologyClaimer const >	TopologyClaimerCOP
typedef utility::pointer::weak_ptr< TopologyClaimer >	TopologyClaimerAP
typedef utility::pointer::weak_ptr< TopologyClaimer const >	TopologyClaimerCAP

Functions
std::ostream &	operator<< (std::ostream &os, ClaimerMessage const &cm)
static basic::Tracer	TR ("protocols.moves.RigidBodyMover")
static basic::Tracer	TRBM ("protocols.moves.RigidBodyMover")
protocols::loops::Loops	generate_rigid_from_alignment (pose::Pose query_pose, core::sequence::SequenceAlignment const &align, core::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, core::Size pos1, core::Size pos2)
bool	connects_rigid_regions (loops::Loops const &rigid, core::Size pos1, core::Size pos2)
bool	compare_sequence_claim_priority (claims::SequenceClaimOP const &a, claims::SequenceClaimOP const &b)
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, utility::vector1< FragmentContainer > &fragment_list)
void	add_claims_from_file (TopologyBroker &broker, std::string const &file, CmdLineData &cmdline_data, utility::vector1< FragmentContainer > &fragment_list)
void	add_cmdline_claims (TopologyBroker &, bool do_I_need_frags=true)
	read broker::setup flag and add all claims to Broker More...

Typedef Documentation

AsymFoldandDockClaimerAP

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

AsymFoldandDockClaimerCAP

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

AsymFoldandDockClaimerCOP

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

AsymFoldandDockClaimerOP

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

BasicJumpClaimerAP

typedef utility::pointer::weak_ptr< BasicJumpClaimer > protocols::topology_broker::BasicJumpClaimerAP

BasicJumpClaimerCAP

typedef utility::pointer::weak_ptr< BasicJumpClaimer const > protocols::topology_broker::BasicJumpClaimerCAP

BasicJumpClaimerCOP

typedef utility::pointer::shared_ptr< BasicJumpClaimer const > protocols::topology_broker::BasicJumpClaimerCOP

BasicJumpClaimerOP

typedef utility::pointer::shared_ptr< BasicJumpClaimer > protocols::topology_broker::BasicJumpClaimerOP

ClaimerMessageAP

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

ClaimerMessageCAP

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

ClaimerMessageCOP

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

ClaimerMessageOP

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

ConstraintClaimerAP

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

ConstraintClaimerCAP

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

ConstraintClaimerCOP

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

ConstraintClaimerOP

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

ConstraintEvaluatorWrapperAP

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

ConstraintEvaluatorWrapperCAP

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

ConstraintEvaluatorWrapperCOP

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

ConstraintEvaluatorWrapperOP

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

CutBiasClaimerAP

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

CutBiasClaimerCAP

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

CutBiasClaimerCOP

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

CutBiasClaimerOP

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

DensityScoringClaimerAP

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

DensityScoringClaimerCAP

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

DensityScoringClaimerCOP

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

DensityScoringClaimerOP

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

DisulfJumpClaimerAP

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

DisulfJumpClaimerCAP

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

DisulfJumpClaimerCOP

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

DisulfJumpClaimerOP

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

FibrilModelingClaimerAP

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

FibrilModelingClaimerCAP

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

FibrilModelingClaimerCOP

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

FibrilModelingClaimerOP

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

FoldandDockClaimerAP

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

FoldandDockClaimerCAP

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

FoldandDockClaimerCOP

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

FoldandDockClaimerOP

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

FragmentClaimerAP

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

FragmentClaimerCAP

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

FragmentClaimerCOP

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

FragmentClaimerOP

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

FragmentJumpClaimerAP

typedef utility::pointer::weak_ptr< FragmentJumpClaimer > protocols::topology_broker::FragmentJumpClaimerAP

FragmentJumpClaimerCAP

typedef utility::pointer::weak_ptr< FragmentJumpClaimer const > protocols::topology_broker::FragmentJumpClaimerCAP

FragmentJumpClaimerCOP

typedef utility::pointer::shared_ptr< FragmentJumpClaimer const > protocols::topology_broker::FragmentJumpClaimerCOP

FragmentJumpClaimerOP

typedef utility::pointer::shared_ptr< FragmentJumpClaimer > protocols::topology_broker::FragmentJumpClaimerOP

LoopFragmentClaimerAP

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

LoopFragmentClaimerCAP

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

LoopFragmentClaimerCOP

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

LoopFragmentClaimerOP

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

MembraneTopologyClaimerAP

typedef utility::pointer::weak_ptr< MembraneTopologyClaimer > protocols::topology_broker::MembraneTopologyClaimerAP

MembraneTopologyClaimerCAP

typedef utility::pointer::weak_ptr< MembraneTopologyClaimer const > protocols::topology_broker::MembraneTopologyClaimerCAP

MembraneTopologyClaimerCOP

typedef utility::pointer::shared_ptr< MembraneTopologyClaimer const > protocols::topology_broker::MembraneTopologyClaimerCOP

MembraneTopologyClaimerOP

typedef utility::pointer::shared_ptr< MembraneTopologyClaimer > protocols::topology_broker::MembraneTopologyClaimerOP

MetalloClaimerAP

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

MetalloClaimerCAP

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

MetalloClaimerCOP

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

MetalloClaimerOP

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

PcsEnergyControllerAP

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

PcsEnergyControllerCAP

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

PcsEnergyControllerCOP

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

PcsEnergyControllerOP

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

PseudocontactShiftEnergyController_Ts1AP

typedef utility::pointer::weak_ptr< PseudocontactShiftEnergyController_Ts1 > protocols::topology_broker::PseudocontactShiftEnergyController_Ts1AP

PseudocontactShiftEnergyController_Ts1CAP

typedef utility::pointer::weak_ptr< PseudocontactShiftEnergyController_Ts1 const > protocols::topology_broker::PseudocontactShiftEnergyController_Ts1CAP

PseudocontactShiftEnergyController_Ts1COP

typedef utility::pointer::shared_ptr< PseudocontactShiftEnergyController_Ts1 const > protocols::topology_broker::PseudocontactShiftEnergyController_Ts1COP

PseudocontactShiftEnergyController_Ts1OP

typedef utility::pointer::shared_ptr< PseudocontactShiftEnergyController_Ts1 > protocols::topology_broker::PseudocontactShiftEnergyController_Ts1OP

PseudocontactShiftEnergyController_Ts2AP

typedef utility::pointer::weak_ptr< PseudocontactShiftEnergyController_Ts2 > protocols::topology_broker::PseudocontactShiftEnergyController_Ts2AP

PseudocontactShiftEnergyController_Ts2CAP

typedef utility::pointer::weak_ptr< PseudocontactShiftEnergyController_Ts2 const > protocols::topology_broker::PseudocontactShiftEnergyController_Ts2CAP

PseudocontactShiftEnergyController_Ts2COP

typedef utility::pointer::shared_ptr< PseudocontactShiftEnergyController_Ts2 const > protocols::topology_broker::PseudocontactShiftEnergyController_Ts2COP

PseudocontactShiftEnergyController_Ts2OP

typedef utility::pointer::shared_ptr< PseudocontactShiftEnergyController_Ts2 > protocols::topology_broker::PseudocontactShiftEnergyController_Ts2OP

PseudocontactShiftEnergyController_Ts3AP

typedef utility::pointer::weak_ptr< PseudocontactShiftEnergyController_Ts3 > protocols::topology_broker::PseudocontactShiftEnergyController_Ts3AP

PseudocontactShiftEnergyController_Ts3CAP

typedef utility::pointer::weak_ptr< PseudocontactShiftEnergyController_Ts3 const > protocols::topology_broker::PseudocontactShiftEnergyController_Ts3CAP

PseudocontactShiftEnergyController_Ts3COP

typedef utility::pointer::shared_ptr< PseudocontactShiftEnergyController_Ts3 const > protocols::topology_broker::PseudocontactShiftEnergyController_Ts3COP

PseudocontactShiftEnergyController_Ts3OP

typedef utility::pointer::shared_ptr< PseudocontactShiftEnergyController_Ts3 > protocols::topology_broker::PseudocontactShiftEnergyController_Ts3OP

PseudocontactShiftEnergyController_Ts4AP

typedef utility::pointer::weak_ptr< PseudocontactShiftEnergyController_Ts4 > protocols::topology_broker::PseudocontactShiftEnergyController_Ts4AP

PseudocontactShiftEnergyController_Ts4CAP

typedef utility::pointer::weak_ptr< PseudocontactShiftEnergyController_Ts4 const > protocols::topology_broker::PseudocontactShiftEnergyController_Ts4CAP

PseudocontactShiftEnergyController_Ts4COP

typedef utility::pointer::shared_ptr< PseudocontactShiftEnergyController_Ts4 const > protocols::topology_broker::PseudocontactShiftEnergyController_Ts4COP

PseudocontactShiftEnergyController_Ts4OP

typedef utility::pointer::shared_ptr< PseudocontactShiftEnergyController_Ts4 > protocols::topology_broker::PseudocontactShiftEnergyController_Ts4OP

PseudocontactShiftEnergyControllerAP

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

PseudocontactShiftEnergyControllerCAP

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

PseudocontactShiftEnergyControllerCOP

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

PseudocontactShiftEnergyControllerOP

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

RigidBodyRandomTMHMoverCOP

typedef utility::pointer::shared_ptr<RigidBodyRandomTMHMover const> protocols::topology_broker::RigidBodyRandomTMHMoverCOP

RigidBodyRandomTMHMoverOP

typedef utility::pointer::shared_ptr<RigidBodyRandomTMHMover> protocols::topology_broker::RigidBodyRandomTMHMoverOP

RigidChunkClaimerAP

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

RigidChunkClaimerCAP

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

RigidChunkClaimerCOP

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

RigidChunkClaimerOP

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

SequenceClaimerAP

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

SequenceClaimerCAP

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

SequenceClaimerCOP

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

SequenceClaimerOP

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

SequenceNumberResolverAP

typedef utility::pointer::weak_ptr< SequenceNumberResolver > protocols::topology_broker::SequenceNumberResolverAP

SequenceNumberResolverCAP

typedef utility::pointer::weak_ptr< SequenceNumberResolver const > protocols::topology_broker::SequenceNumberResolverCAP

SequenceNumberResolverCOP

typedef utility::pointer::shared_ptr< SequenceNumberResolver const > protocols::topology_broker::SequenceNumberResolverCOP

SequenceNumberResolverOP

typedef utility::pointer::shared_ptr< SequenceNumberResolver > protocols::topology_broker::SequenceNumberResolverOP

StartStructClaimerAP

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

StartStructClaimerCAP

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

StartStructClaimerCOP

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

StartStructClaimerOP

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

SymmetryClaimerAP

typedef utility::pointer::weak_ptr< SymmetryClaimer > protocols::topology_broker::SymmetryClaimerAP

SymmetryClaimerCAP

typedef utility::pointer::weak_ptr< SymmetryClaimer const > protocols::topology_broker::SymmetryClaimerCAP

SymmetryClaimerCOP

typedef utility::pointer::shared_ptr< SymmetryClaimer const > protocols::topology_broker::SymmetryClaimerCOP

SymmetryClaimerOP

typedef utility::pointer::shared_ptr< SymmetryClaimer > protocols::topology_broker::SymmetryClaimerOP

TemplateFragmentClaimerAP

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

TemplateFragmentClaimerCAP

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

TemplateFragmentClaimerCOP

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

TemplateFragmentClaimerOP

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

TemplateJumpClaimerAP

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

TemplateJumpClaimerCAP

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

TemplateJumpClaimerCOP

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

TemplateJumpClaimerOP

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

TMHTopologySamplerClaimerAP

typedef utility::pointer::weak_ptr< TMHTopologySamplerClaimer > protocols::topology_broker::TMHTopologySamplerClaimerAP

TMHTopologySamplerClaimerCAP

typedef utility::pointer::weak_ptr< TMHTopologySamplerClaimer const > protocols::topology_broker::TMHTopologySamplerClaimerCAP

TMHTopologySamplerClaimerCOP

typedef utility::pointer::shared_ptr< TMHTopologySamplerClaimer const > protocols::topology_broker::TMHTopologySamplerClaimerCOP

TMHTopologySamplerClaimerOP

typedef utility::pointer::shared_ptr< TMHTopologySamplerClaimer > protocols::topology_broker::TMHTopologySamplerClaimerOP

TopologyBrokerAP

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

TopologyBrokerCAP

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

TopologyBrokerCOP

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

TopologyBrokerOP

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

TopologyClaimerAP

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

TopologyClaimerCAP

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

TopologyClaimerCOP

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

TopologyClaimerOP

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

Function Documentation

add_claims_from_file()

void protocols::topology_broker::add_claims_from_file	(	TopologyBroker &	broker,
		std::string const &	file,
		CmdLineData &	cmdline_data,
		utility::vector1< FragmentContainer > &	fragment_list
	)

References add_claims_from_stream().

Referenced by add_cmdline_claims().

add_claims_from_stream()

void protocols::topology_broker::add_claims_from_stream	(	TopologyBroker &	broker,
		std::istream &	is,
		CmdLineData &	cmdline_data,
		utility::vector1< FragmentContainer > &	fragment_list
	)

References protocols::topology_broker::ConstraintClaimer::_static_type_name(), protocols::topology_broker::TopologyBroker::add(), protocols::topology_broker::CmdLineData::b_has_constraint_claimer, read_frags(), tr(), and protocols::topology_broker::TopologyBroker::use_job_pose().

Referenced by add_claims_from_file().

add_cmdline_claims()

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

References protocols::topology_broker::TopologyBroker::add(), add_claims_from_file(), protocols::topology_broker::CmdLineData::b_has_constraint_claimer, core::chemical::CENTROID, protocols::abinitio::filename(), protocols::topology_broker::TopologyBroker::has_sequence_claimer(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), 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().

compare_sequence_claim_priority()

bool protocols::topology_broker::compare_sequence_claim_priority	(	claims::SequenceClaimOP const &	a,
		claims::SequenceClaimOP const &	b
	)

References core::pose::motif::a(), and protocols::match::upstream::b.

Referenced by protocols::topology_broker::TopologyBroker::initialize_sequence().

connects_rigid_regions()

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

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().

copy_internal_coords()

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

References 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::size(), and tr().

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

fix_internal_coords_of_siblings()

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

References core::kinematics::AtomTree::atom(), core::conformation::Residue::atom_index(), core::conformation::Residue::atom_name(), core::conformation::Conformation::atom_tree(), core::id::AtomID::atomno(), core::pose::Pose::conformation(), core::kinematics::AtomTree::dof(), core::kinematics::AtomTree::has(), core::kinematics::tree::Atom::parent(), core::chemical::rings::PHI, core::pose::Pose::residue(), core::id::AtomID::rsd(), core::conformation::Conformation::set_bond_angle(), core::conformation::Conformation::set_dof(), core::pose::Pose::size(), tr(), and core::pose::Pose::xyz().

Referenced by fix_mainchain_connect().

fix_mainchain_connect()

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

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_atom(), core::conformation::Residue::mainchain_torsion(), core::conformation::Residue::n_mainchain_atoms(), 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().

generate_rigid_from_alignment()

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

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

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

is_not_neighbor_to_rigid()

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

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

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

operator<<()

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

operator>>()

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

inline

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

read_frags()

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

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().

TR()

static basic::Tracer protocols::topology_broker::TR ( "protocols.moves.RigidBodyMover"  )

static

Referenced by protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), protocols::topology_broker::RigidBodyRandomTMHMover::apply(), protocols::topology_broker::MembraneTopologyClaimer::generate_claims(), and protocols::topology_broker::RigidBodyRandomTMHMover::RigidBodyRandomTMHMover().

TRBM()

static basic::Tracer protocols::topology_broker::TRBM ( "protocols.moves.RigidBodyMover"  )

static