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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...
 
struct  CountFromLeft
 count starting from interval().left in a BuildInstruction 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...
 
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
< Bridge
BridgeOP
 owning pointer for Bridge More...
 
typedef
utility::pointer::shared_ptr
< Bridge const > 
BridgeCOP
 owning pointer for const Bridge More...
 
typedef
utility::pointer::weak_ptr
< Bridge
BridgeAP
 access pointer for Bridge More...
 
typedef
utility::pointer::weak_ptr
< Bridge const > 
BridgeCAP
 access pointer for const Bridge More...
 
typedef
utility::pointer::shared_ptr
< BuildInstruction
BuildInstructionOP
 owning pointer for BuildInstruction More...
 
typedef
utility::pointer::shared_ptr
< BuildInstruction const > 
BuildInstructionCOP
 owning pointer for const BuildInstruction More...
 
typedef
utility::pointer::weak_ptr
< BuildInstruction
BuildInstructionAP
 access pointer for BuildInstruction More...
 
typedef
utility::pointer::weak_ptr
< BuildInstruction const > 
BuildInstructionCAP
 access pointer for const BuildInstruction More...
 
typedef
utility::pointer::shared_ptr
< BuildManager
BuildManagerOP
 owning pointer for BuildManager More...
 
typedef
utility::pointer::shared_ptr
< BuildManager const > 
BuildManagerCOP
 owning pointer for const BuildManager More...
 
typedef
utility::pointer::weak_ptr
< BuildManager
BuildManagerAP
 access pointer for BuildManager More...
 
typedef
utility::pointer::weak_ptr
< BuildManager const > 
BuildManagerCAP
 access pointer for const BuildManager More...
 
typedef
utility::pointer::shared_ptr
< ConnectRight
ConnectRightOP
 owning pointer for ConnectRight More...
 
typedef
utility::pointer::shared_ptr
< ConnectRight const > 
ConnectRightCOP
 owning pointer for const ConnectRight More...
 
typedef
utility::pointer::weak_ptr
< ConnectRight
ConnectRightAP
 access pointer for ConnectRight More...
 
typedef
utility::pointer::weak_ptr
< ConnectRight const > 
ConnectRightCAP
 access pointer for const ConnectRight More...
 
typedef
utility::pointer::shared_ptr
< GrowLeft
GrowLeftOP
 owning pointer for GrowLeft More...
 
typedef
utility::pointer::shared_ptr
< GrowLeft const > 
GrowLeftCOP
 owning pointer for const GrowLeft More...
 
typedef
utility::pointer::weak_ptr
< GrowLeft
GrowLeftAP
 access pointer for GrowLeft More...
 
typedef
utility::pointer::weak_ptr
< GrowLeft const > 
GrowLeftCAP
 access pointer for const GrowLeft More...
 
typedef
utility::pointer::shared_ptr
< GrowRight
GrowRightOP
 owning pointer for GrowRight More...
 
typedef
utility::pointer::shared_ptr
< GrowRight const > 
GrowRightCOP
 owning pointer for const GrowRight More...
 
typedef
utility::pointer::weak_ptr
< GrowRight
GrowRightAP
 access pointer for GrowRight More...
 
typedef
utility::pointer::weak_ptr
< GrowRight const > 
GrowRightCAP
 access pointer for const GrowRight More...
 
typedef
utility::pointer::shared_ptr
< RelativeConnectRight
RelativeConnectRightOP
 owning pointer for RelativeConnectRight More...
 
typedef
utility::pointer::shared_ptr
< RelativeConnectRight const > 
RelativeConnectRightCOP
 owning pointer for const RelativeConnectRight More...
 
typedef
utility::pointer::weak_ptr
< RelativeConnectRight
RelativeConnectRightAP
 access pointer for RelativeConnectRight More...
 
typedef
utility::pointer::weak_ptr
< RelativeConnectRight const > 
RelativeConnectRightCAP
 access pointer for const RelativeConnectRight More...
 
typedef
utility::pointer::shared_ptr
< RelativeSequencePosition
RelativeSequencePositionOP
 owning pointer for RelativeSequencePosition More...
 
typedef
utility::pointer::shared_ptr
< RelativeSequencePosition
const > 
RelativeSequencePositionCOP
 owning pointer for const RelativeSequencePosition More...
 
typedef
utility::pointer::weak_ptr
< RelativeSequencePosition
RelativeSequencePositionAP
 access pointer for RelativeSequencePosition More...
 
typedef
utility::pointer::weak_ptr
< RelativeSequencePosition
const > 
RelativeSequencePositionCAP
 access pointer for const RelativeSequencePosition More...
 
typedef
utility::pointer::shared_ptr
< CountFromLeft
CountFromLeftOP
 owning pointer for CountFromLeft More...
 
typedef
utility::pointer::shared_ptr
< CountFromLeft const > 
CountFromLeftCOP
 owning pointer for const CountFromLeft More...
 
typedef
utility::pointer::weak_ptr
< CountFromLeft
CountFromLeftAP
 access pointer for CountFromLeft More...
 
typedef
utility::pointer::weak_ptr
< CountFromLeft const > 
CountFromLeftCAP
 access pointer for const CountFromLeft More...
 
typedef
utility::pointer::shared_ptr
< SegmentInsert
SegmentInsertOP
 owning pointer for SegmentInsert More...
 
typedef
utility::pointer::shared_ptr
< SegmentInsert const > 
SegmentInsertCOP
 owning pointer for const SegmentInsert More...
 
typedef
utility::pointer::weak_ptr
< SegmentInsert
SegmentInsertAP
 access pointer for SegmentInsert More...
 
typedef
utility::pointer::weak_ptr
< SegmentInsert const > 
SegmentInsertCAP
 access pointer for const SegmentInsert More...
 
typedef
utility::pointer::shared_ptr
< SegmentRebuild
SegmentRebuildOP
 owning pointer for SegmentRebuild More...
 
typedef
utility::pointer::shared_ptr
< SegmentRebuild const > 
SegmentRebuildCOP
 owning pointer for const SegmentRebuild More...
 
typedef
utility::pointer::weak_ptr
< SegmentRebuild
SegmentRebuildAP
 access pointer for SegmentRebuild More...
 
typedef
utility::pointer::weak_ptr
< SegmentRebuild const > 
SegmentRebuildCAP
 access pointer for const SegmentRebuild More...
 
typedef
utility::pointer::shared_ptr
< SegmentSwap
SegmentSwapOP
 owning pointer for SegmentSwap More...
 
typedef
utility::pointer::shared_ptr
< SegmentSwap const > 
SegmentSwapCOP
 owning pointer for const SegmentSwap More...
 
typedef
utility::pointer::weak_ptr
< SegmentSwap
SegmentSwapAP
 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

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

access pointer for Bridge

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

access pointer for const Bridge

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

owning pointer for const Bridge

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

owning pointer for Bridge

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

access pointer for BuildInstruction

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

access pointer for const BuildInstruction

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

owning pointer for const BuildInstruction

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

owning pointer for BuildInstruction

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

access pointer for BuildManager

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

access pointer for const BuildManager

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

owning pointer for const BuildManager

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

owning pointer for BuildManager

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

access pointer for ConnectRight

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

access pointer for const ConnectRight

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

owning pointer for const ConnectRight

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

owning pointer for ConnectRight

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

access pointer for CountFromLeft

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

access pointer for const CountFromLeft

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

owning pointer for const CountFromLeft

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

owning pointer for CountFromLeft

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

access pointer for GrowLeft

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

access pointer for const GrowLeft

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

owning pointer for const GrowLeft

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

owning pointer for GrowLeft

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

access pointer for GrowRight

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

access pointer for const GrowRight

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

owning pointer for const GrowRight

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

owning pointer for GrowRight

access pointer for RelativeConnectRight

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

access pointer for const RelativeConnectRight

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

owning pointer for const RelativeConnectRight

owning pointer for RelativeConnectRight

access pointer for RelativeSequencePosition

access pointer for const RelativeSequencePosition

owning pointer for const RelativeSequencePosition

owning pointer for RelativeSequencePosition

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

access pointer for SegmentInsert

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

access pointer for const SegmentInsert

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

owning pointer for const SegmentInsert

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

owning pointer for SegmentInsert

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

access pointer for SegmentRebuild

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

access pointer for const SegmentRebuild

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

owning pointer for const SegmentRebuild

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

owning pointer for SegmentRebuild

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

access pointer for SegmentSwap

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

access pointer for const SegmentSwap

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

owning pointer for const SegmentSwap

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

owning pointer for SegmentSwap

Function Documentation

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