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protocols::forge::build Namespace Reference

Namespaces

 BuildInstructionState
 
 SegmentInsertConnectionScheme
 

Classes

class  Bridge
 connect two contiguous but disjoint sections of a Pose into one continuous section More...
 
class  BuildInstruction
 tracks modifications to be made and is capable of making residue length changes on a Pose More...
 
class  BuildManager
 a container for managing BuildInstructions More...
 
class  ConnectRight
 instruction to connect one Pose onto the right side of another More...
 
class  GrowLeft
 instruction to create an n-side extension More...
 
class  GrowRight
 instruction to create a c-side extension More...
 
struct  Interval
 simple struct defining a closed interval of residues [left, right] where left <= right More...
 
class  RelativeConnectRight
 version of ConnectRight instruction that depends upon results from another BuildInstruction More...
 
struct  RelativeSequencePosition
 computes a position wrt values in given BuildInstruction More...
 
struct  CountFromLeft
 count starting from interval().left in a BuildInstruction More...
 
class  SegmentInsert
 insert an external segment flanked by new regions More...
 
class  SegmentRebuild
 instruction to rebuild a segment More...
 
class  SegmentSwap
 instruction to swap a segment with an external segment More...
 

Typedefs

typedef utility::pointer::shared_ptr< BridgeBridgeOP
 owning pointer for Bridge More...
 
typedef utility::pointer::shared_ptr< Bridge const > BridgeCOP
 owning pointer for const Bridge More...
 
typedef utility::pointer::weak_ptr< BridgeBridgeAP
 access pointer for Bridge More...
 
typedef utility::pointer::weak_ptr< Bridge const > BridgeCAP
 access pointer for const Bridge More...
 
typedef utility::pointer::shared_ptr< BuildInstructionBuildInstructionOP
 owning pointer for BuildInstruction More...
 
typedef utility::pointer::shared_ptr< BuildInstruction const > BuildInstructionCOP
 owning pointer for const BuildInstruction More...
 
typedef utility::pointer::weak_ptr< BuildInstructionBuildInstructionAP
 access pointer for BuildInstruction More...
 
typedef utility::pointer::weak_ptr< BuildInstruction const > BuildInstructionCAP
 access pointer for const BuildInstruction More...
 
typedef utility::pointer::shared_ptr< BuildManagerBuildManagerOP
 owning pointer for BuildManager More...
 
typedef utility::pointer::shared_ptr< BuildManager const > BuildManagerCOP
 owning pointer for const BuildManager More...
 
typedef utility::pointer::weak_ptr< BuildManagerBuildManagerAP
 access pointer for BuildManager More...
 
typedef utility::pointer::weak_ptr< BuildManager const > BuildManagerCAP
 access pointer for const BuildManager More...
 
typedef utility::pointer::shared_ptr< ConnectRightConnectRightOP
 owning pointer for ConnectRight More...
 
typedef utility::pointer::shared_ptr< ConnectRight const > ConnectRightCOP
 owning pointer for const ConnectRight More...
 
typedef utility::pointer::weak_ptr< ConnectRightConnectRightAP
 access pointer for ConnectRight More...
 
typedef utility::pointer::weak_ptr< ConnectRight const > ConnectRightCAP
 access pointer for const ConnectRight More...
 
typedef utility::pointer::shared_ptr< GrowLeftGrowLeftOP
 owning pointer for GrowLeft More...
 
typedef utility::pointer::shared_ptr< GrowLeft const > GrowLeftCOP
 owning pointer for const GrowLeft More...
 
typedef utility::pointer::weak_ptr< GrowLeftGrowLeftAP
 access pointer for GrowLeft More...
 
typedef utility::pointer::weak_ptr< GrowLeft const > GrowLeftCAP
 access pointer for const GrowLeft More...
 
typedef utility::pointer::shared_ptr< GrowRightGrowRightOP
 owning pointer for GrowRight More...
 
typedef utility::pointer::shared_ptr< GrowRight const > GrowRightCOP
 owning pointer for const GrowRight More...
 
typedef utility::pointer::weak_ptr< GrowRightGrowRightAP
 access pointer for GrowRight More...
 
typedef utility::pointer::weak_ptr< GrowRight const > GrowRightCAP
 access pointer for const GrowRight More...
 
typedef utility::pointer::shared_ptr< RelativeConnectRightRelativeConnectRightOP
 owning pointer for RelativeConnectRight More...
 
typedef utility::pointer::shared_ptr< RelativeConnectRight const > RelativeConnectRightCOP
 owning pointer for const RelativeConnectRight More...
 
typedef utility::pointer::weak_ptr< RelativeConnectRightRelativeConnectRightAP
 access pointer for RelativeConnectRight More...
 
typedef utility::pointer::weak_ptr< RelativeConnectRight const > RelativeConnectRightCAP
 access pointer for const RelativeConnectRight More...
 
typedef utility::pointer::shared_ptr< RelativeSequencePositionRelativeSequencePositionOP
 owning pointer for RelativeSequencePosition More...
 
typedef utility::pointer::shared_ptr< RelativeSequencePosition const > RelativeSequencePositionCOP
 owning pointer for const RelativeSequencePosition More...
 
typedef utility::pointer::weak_ptr< RelativeSequencePositionRelativeSequencePositionAP
 access pointer for RelativeSequencePosition More...
 
typedef utility::pointer::weak_ptr< RelativeSequencePosition const > RelativeSequencePositionCAP
 access pointer for const RelativeSequencePosition More...
 
typedef utility::pointer::shared_ptr< CountFromLeftCountFromLeftOP
 owning pointer for CountFromLeft More...
 
typedef utility::pointer::shared_ptr< CountFromLeft const > CountFromLeftCOP
 owning pointer for const CountFromLeft More...
 
typedef utility::pointer::weak_ptr< CountFromLeftCountFromLeftAP
 access pointer for CountFromLeft More...
 
typedef utility::pointer::weak_ptr< CountFromLeft const > CountFromLeftCAP
 access pointer for const CountFromLeft More...
 
typedef utility::pointer::shared_ptr< SegmentInsertSegmentInsertOP
 owning pointer for SegmentInsert More...
 
typedef utility::pointer::shared_ptr< SegmentInsert const > SegmentInsertCOP
 owning pointer for const SegmentInsert More...
 
typedef utility::pointer::weak_ptr< SegmentInsertSegmentInsertAP
 access pointer for SegmentInsert More...
 
typedef utility::pointer::weak_ptr< SegmentInsert const > SegmentInsertCAP
 access pointer for const SegmentInsert More...
 
typedef utility::pointer::shared_ptr< SegmentRebuildSegmentRebuildOP
 owning pointer for SegmentRebuild More...
 
typedef utility::pointer::shared_ptr< SegmentRebuild const > SegmentRebuildCOP
 owning pointer for const SegmentRebuild More...
 
typedef utility::pointer::weak_ptr< SegmentRebuildSegmentRebuildAP
 access pointer for SegmentRebuild More...
 
typedef utility::pointer::weak_ptr< SegmentRebuild const > SegmentRebuildCAP
 access pointer for const SegmentRebuild More...
 
typedef utility::pointer::shared_ptr< SegmentSwapSegmentSwapOP
 owning pointer for SegmentSwap More...
 
typedef utility::pointer::shared_ptr< SegmentSwap const > SegmentSwapCOP
 owning pointer for const SegmentSwap More...
 
typedef utility::pointer::weak_ptr< SegmentSwapSegmentSwapAP
 access pointer for SegmentSwap More...
 
typedef utility::pointer::weak_ptr< SegmentSwap const > SegmentSwapCAP
 access pointer for const SegmentSwap More...
 

Functions

static basic::Tracer TR ("protocols.forge.build.BuildInstruction")
 
static basic::Tracer TR ("protocols.forge.build.BuildManager")
 
static basic::Tracer TR ("protocols.forge.build.SegmentInsert")
 

Typedef Documentation

◆ BridgeAP

typedef utility::pointer::weak_ptr< Bridge > protocols::forge::build::BridgeAP

access pointer for Bridge

◆ BridgeCAP

typedef utility::pointer::weak_ptr< Bridge const > protocols::forge::build::BridgeCAP

access pointer for const Bridge

◆ BridgeCOP

typedef utility::pointer::shared_ptr< Bridge const > protocols::forge::build::BridgeCOP

owning pointer for const Bridge

◆ BridgeOP

typedef utility::pointer::shared_ptr< Bridge > protocols::forge::build::BridgeOP

owning pointer for Bridge

◆ BuildInstructionAP

typedef utility::pointer::weak_ptr< BuildInstruction > protocols::forge::build::BuildInstructionAP

access pointer for BuildInstruction

◆ BuildInstructionCAP

typedef utility::pointer::weak_ptr< BuildInstruction const > protocols::forge::build::BuildInstructionCAP

access pointer for const BuildInstruction

◆ BuildInstructionCOP

typedef utility::pointer::shared_ptr< BuildInstruction const > protocols::forge::build::BuildInstructionCOP

owning pointer for const BuildInstruction

◆ BuildInstructionOP

typedef utility::pointer::shared_ptr< BuildInstruction > protocols::forge::build::BuildInstructionOP

owning pointer for BuildInstruction

◆ BuildManagerAP

typedef utility::pointer::weak_ptr< BuildManager > protocols::forge::build::BuildManagerAP

access pointer for BuildManager

◆ BuildManagerCAP

typedef utility::pointer::weak_ptr< BuildManager const > protocols::forge::build::BuildManagerCAP

access pointer for const BuildManager

◆ BuildManagerCOP

typedef utility::pointer::shared_ptr< BuildManager const > protocols::forge::build::BuildManagerCOP

owning pointer for const BuildManager

◆ BuildManagerOP

typedef utility::pointer::shared_ptr< BuildManager > protocols::forge::build::BuildManagerOP

owning pointer for BuildManager

◆ ConnectRightAP

typedef utility::pointer::weak_ptr< ConnectRight > protocols::forge::build::ConnectRightAP

access pointer for ConnectRight

◆ ConnectRightCAP

typedef utility::pointer::weak_ptr< ConnectRight const > protocols::forge::build::ConnectRightCAP

access pointer for const ConnectRight

◆ ConnectRightCOP

typedef utility::pointer::shared_ptr< ConnectRight const > protocols::forge::build::ConnectRightCOP

owning pointer for const ConnectRight

◆ ConnectRightOP

typedef utility::pointer::shared_ptr< ConnectRight > protocols::forge::build::ConnectRightOP

owning pointer for ConnectRight

◆ CountFromLeftAP

typedef utility::pointer::weak_ptr< CountFromLeft > protocols::forge::build::CountFromLeftAP

access pointer for CountFromLeft

◆ CountFromLeftCAP

typedef utility::pointer::weak_ptr< CountFromLeft const > protocols::forge::build::CountFromLeftCAP

access pointer for const CountFromLeft

◆ CountFromLeftCOP

typedef utility::pointer::shared_ptr< CountFromLeft const > protocols::forge::build::CountFromLeftCOP

owning pointer for const CountFromLeft

◆ CountFromLeftOP

typedef utility::pointer::shared_ptr< CountFromLeft > protocols::forge::build::CountFromLeftOP

owning pointer for CountFromLeft

◆ GrowLeftAP

typedef utility::pointer::weak_ptr< GrowLeft > protocols::forge::build::GrowLeftAP

access pointer for GrowLeft

◆ GrowLeftCAP

typedef utility::pointer::weak_ptr< GrowLeft const > protocols::forge::build::GrowLeftCAP

access pointer for const GrowLeft

◆ GrowLeftCOP

typedef utility::pointer::shared_ptr< GrowLeft const > protocols::forge::build::GrowLeftCOP

owning pointer for const GrowLeft

◆ GrowLeftOP

typedef utility::pointer::shared_ptr< GrowLeft > protocols::forge::build::GrowLeftOP

owning pointer for GrowLeft

◆ GrowRightAP

typedef utility::pointer::weak_ptr< GrowRight > protocols::forge::build::GrowRightAP

access pointer for GrowRight

◆ GrowRightCAP

typedef utility::pointer::weak_ptr< GrowRight const > protocols::forge::build::GrowRightCAP

access pointer for const GrowRight

◆ GrowRightCOP

typedef utility::pointer::shared_ptr< GrowRight const > protocols::forge::build::GrowRightCOP

owning pointer for const GrowRight

◆ GrowRightOP

typedef utility::pointer::shared_ptr< GrowRight > protocols::forge::build::GrowRightOP

owning pointer for GrowRight

◆ RelativeConnectRightAP

access pointer for RelativeConnectRight

◆ RelativeConnectRightCAP

typedef utility::pointer::weak_ptr< RelativeConnectRight const > protocols::forge::build::RelativeConnectRightCAP

access pointer for const RelativeConnectRight

◆ RelativeConnectRightCOP

typedef utility::pointer::shared_ptr< RelativeConnectRight const > protocols::forge::build::RelativeConnectRightCOP

owning pointer for const RelativeConnectRight

◆ RelativeConnectRightOP

owning pointer for RelativeConnectRight

◆ RelativeSequencePositionAP

access pointer for RelativeSequencePosition

◆ RelativeSequencePositionCAP

access pointer for const RelativeSequencePosition

◆ RelativeSequencePositionCOP

owning pointer for const RelativeSequencePosition

◆ RelativeSequencePositionOP

owning pointer for RelativeSequencePosition

◆ SegmentInsertAP

typedef utility::pointer::weak_ptr< SegmentInsert > protocols::forge::build::SegmentInsertAP

access pointer for SegmentInsert

◆ SegmentInsertCAP

typedef utility::pointer::weak_ptr< SegmentInsert const > protocols::forge::build::SegmentInsertCAP

access pointer for const SegmentInsert

◆ SegmentInsertCOP

typedef utility::pointer::shared_ptr< SegmentInsert const > protocols::forge::build::SegmentInsertCOP

owning pointer for const SegmentInsert

◆ SegmentInsertOP

typedef utility::pointer::shared_ptr< SegmentInsert > protocols::forge::build::SegmentInsertOP

owning pointer for SegmentInsert

◆ SegmentRebuildAP

typedef utility::pointer::weak_ptr< SegmentRebuild > protocols::forge::build::SegmentRebuildAP

access pointer for SegmentRebuild

◆ SegmentRebuildCAP

typedef utility::pointer::weak_ptr< SegmentRebuild const > protocols::forge::build::SegmentRebuildCAP

access pointer for const SegmentRebuild

◆ SegmentRebuildCOP

typedef utility::pointer::shared_ptr< SegmentRebuild const > protocols::forge::build::SegmentRebuildCOP

owning pointer for const SegmentRebuild

◆ SegmentRebuildOP

typedef utility::pointer::shared_ptr< SegmentRebuild > protocols::forge::build::SegmentRebuildOP

owning pointer for SegmentRebuild

◆ SegmentSwapAP

typedef utility::pointer::weak_ptr< SegmentSwap > protocols::forge::build::SegmentSwapAP

access pointer for SegmentSwap

◆ SegmentSwapCAP

typedef utility::pointer::weak_ptr< SegmentSwap const > protocols::forge::build::SegmentSwapCAP

access pointer for const SegmentSwap

◆ SegmentSwapCOP

typedef utility::pointer::shared_ptr< SegmentSwap const > protocols::forge::build::SegmentSwapCOP

owning pointer for const SegmentSwap

◆ SegmentSwapOP

typedef utility::pointer::shared_ptr< SegmentSwap > protocols::forge::build::SegmentSwapOP

owning pointer for SegmentSwap

Function Documentation

◆ TR() [1/3]

static basic::Tracer protocols::forge::build::TR ( "protocols.forge.build.BuildInstruction"  )
static

◆ TR() [2/3]

static basic::Tracer protocols::forge::build::TR ( "protocols.forge.build.BuildManager"  )
static

◆ TR() [3/3]

static basic::Tracer protocols::forge::build::TR ( "protocols.forge.build.SegmentInsert"  )
static