protocols::topology_broker Namespace Reference

Namespaces
	claims
	weights

Classes
class	AsymFoldandDockClaimer
class	BasicJumpClaimer
class	ClaimerMessage
struct	CmdLineData
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_FailedBroking
class	EXCN_FilterFailed
class	EXCN_Input
class	EXCN_TopologyBroker
class	EXCN_Unknown
class	FibrilModelingClaimer
class	FoldandDockClaimer
class	FragmentClaimer
class	FragmentContainer
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 More...
class	SequenceClaimer
class	SequenceNumberResolver
class	StartStructClaimer
class	SuggestValueMessage
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
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...

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Function Documentation

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(), utility::io::izstream::good(), utility::excn::EXCN_BadInput::msg(), and utility::io::izstream::open().

Referenced by add_cmdline_claims().

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, protocols::topology_broker::TopologyClaimerFactory::get_instance(), getline(), protocols::topology_broker::TopologyClaimerFactory::newTopologyClaimer(), option, 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

References protocols::topology_broker::TopologyBroker::add(), add_claims_from_file(), core::chemical::CENTROID, filename(), protocols::topology_broker::TopologyBroker::has_sequence_claimer(), option, basic::options::option, core::import_pose::pose_from_pdb(), core::sequence::read_fasta_file(), core::fragment::read_std_frags_from_cmd(), utility::options::FileVectorOption::size(), tr(), and user.

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

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

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

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

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

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
	)

References numeric::angle_radians(), 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::pose::Pose::residue(), core::id::AtomID::rsd(), runtime_assert, 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
	)

References core::chemical::ResidueType::atom_index(), core::conformation::Residue::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(), runtime_assert, 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
	)

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
	)

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
	)

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

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

inline

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

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

References getline(), core::fragment::FragmentIO::read_data(), runtime_assert, 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().

static thread_local 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().

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

static