Namespaces
	util

Classes
class	NoRepackDisulfides
	prevent disulfides from being repacked; assume disulfides info in Pose is up-to-date More...

class	NoRepackDisulfidesCreator

class	OperateOnCertainResidues

class	OperateOnCertainResiduesCreator

class	OptCysHG
	run optH on non-disulfided bonded CYS only; meant to relieve any clashes caused by swapping of CYD->CYS after calling Conformation::detect_disulfides() More...

class	OptCysHGCreator

class	OptH
	run optH; disallowed positions may be set to prevent optimization for those residues More...

class	OptHCreator

class	ReplicateTask

class	ReplicateTaskCreator

class	ResFilter

class	ResFilterCreator
	The ResFilterCreator class's responsibilities are to create on demand a new ResFilter class. The ResFilterCreator must register itself with the ResFilterFactory at load time (before main() begins) so that the ResFilterFactory is ready to start creating ResFilters by the time any protocol requests one. More...

class	AnyResFilterCreator

class	AllResFilterCreator

class	NoResFilterCreator

class	ResidueTypeFilterCreator

class	ResidueHasPropertyCreator

class	ResidueLacksPropertyCreator

class	ResidueName3IsCreator

class	ResidueName3IsntCreator

class	ResidueIndexIsCreator

class	ResidueIndexIsntCreator

class	ResiduePDBIndexIsCreator

class	ResiduePDBIndexIsntCreator

class	ChainIsCreator

class	ChainIsntCreator

class	ResFilterFactory

class	ResFilterRegistrator
	This templated class will register an instance of an ResFilterCreator (class T) with the ResFilterFactory. It will ensure that no ResFilter creator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place. More...

class	ResFilterComposition

class	AnyResFilter

class	AllResFilter

class	NoResFilter

class	ResidueTypeFilter

class	ResidueHasProperty

class	ResidueLacksProperty

class	ResidueName3Is

class	ResidueName3Isnt

class	ResidueIndexIs

class	ResidueIndexIsnt

class	ResiduePDBIndexIs

class	ResiduePDBIndexIsnt

class	ChainIs

class	ChainIsnt

class	ResLvlTaskOperation

class	ResLvlTaskOperationCreator
	The ResLvlTaskOperationCreator class's responsibilities are to create on demand a new ResLvlTaskOperation class. The ResLvlTaskOperationCreator must register itself with the ResLvlTaskOperationFactory at load time (before main() begins) so that the ResLvlTaskOperationFactory is ready to start creating ResLvlTaskOperations by the time any protocol requests one. More...

class	RestrictToRepackingRLTCreator

class	RestrictAbsentCanonicalAASRLTCreator

class	DisallowIfNonnativeRLTCreator

class	PreventRepackingRLTCreator

class	AddBehaviorRLTCreator

class	ResLvlTaskOperationFactory

class	ResLvlTaskOperationRegistrator
	This templated class will register an instance of an ResLvlTaskOperationCreator (class T) with the ResLvlTaskOperationFactory. It will ensure that no ResLvlTaskOperation creator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place. More...

class	RestrictToRepackingRLT

class	RestrictAbsentCanonicalAASRLT

class	DisallowIfNonnativeRLT

class	PreventRepackingRLT

class	AddBehaviorRLT

class	DockingNoRepack1

class	DockingNoRepack2

class	RestrictToInterface

class	TaskOperation

class	TaskOperationCreator
	The TaskOperationCreator class's responsibilities are to create on demand a new TaskOperation class. The TaskOperationCreator must register itself with the TaskOperationFactory at load time (before main() begins) so that the TaskOperationFactory is ready to start creating TaskOperations by the time any protocol requests one. More...

class	RestrictYSDesignCreator

class	PreventRepackingCreator

class	PreserveCBetaCreator

class	AppendRotamerSetCreator

class	AppendResidueRotamerSetCreator

class	AppendRotamerCreator

class	SetRotamerCouplingsCreator

class	SetRotamerLinksCreator

class	ReadResfileCreator

class	ReadResfileAndObeyLengthEventsCreator

class	IncludeCurrentCreator

class	InitializeExtraRotsFromCommandlineCreator

class	InitializeFromCommandlineCreator

class	ExtraRotamersGenericCreator

class	RotamerExplosionCreator

class	RestrictAbsentCanonicalAASCreator

class	RestrictResidueToRepackingCreator

class	RestrictToRepackingCreator

class	DisallowIfNonnativeCreator

class	ExtraRotamersCreator

class	ExtraChiCutoffCreator

class	TaskOperationFactory

class	TaskOperationRegistrator
	This templated class will register an instance of an TaskOperationCreator (class T) with the TaskOperationFactory. It will ensure that no TaskOperation creator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place. More...

class	RestrictToRepacking

class	RestrictResidueToRepacking
	RestrictResidueToRepacking. More...

class	RestrictAbsentCanonicalAAS

class	DisallowIfNonnative
	DisallowIfNonnative allows you to define what residues are NOT allowed in packing unless that residue is present in the input. Behaves like RestrictAbsentCanonicalAAS and NOTAA except will allow a resitricted residue at a position if it is there to begin with at the time of Task creation. Will do all residues unless otherwise defined by selection syntax below. More...

class	RotamerExplosion
	rotamer explosion for a residue More...

class	InitializeFromCommandline

class	InitializeExtraRotsFromCommandline

class	IncludeCurrent

class	ExtraRotamersGeneric

class	ReadResfile

class	ReadResfileAndObeyLengthEvents
	written by flo, feb 2011 class that can apply a resfile to a pose that had its length changed at some point in a protocol. A LengthEventCollector must be set in the pose's observer cache for this to work properly More...

class	SetRotamerCouplings

class	SetRotamerLinks

class	AppendRotamer
	when a PackerTask is created by the Factory, the RotamerOperation will be given to it More...

class	AppendRotamerSet
	when a PackerTask is created by the Factory, the RotamerSetOperation will be given to it More...

class	AppendResidueRotamerSet
	Apply rotamerSetOperation to only the rotamerSet for the given residue. More...

class	PreserveCBeta

class	PreventRepacking
	PreventRepacking allows you to prevent repacking (NATRO behavior) through the Factory. Useful if you do not know the residue numbers when the resfile is created. Note that this is unlike RestrictToRepacking; you have to specify which residues. If PreventRepacking worked on the entire Task you'd have a do-nothing task. More...

class	RestrictYSDesign
	RestrictYSDesign restricts positions to a binary Tyr/Ser alphabet. More...

class	ExtraRotamers
	ExtraRotamer for a residue. You know, -ex1, -ex2, all that. More...

class	ExtraChiCutoff
	ExtraChiCutoff (correponding to flag "-extrachi_cutoff <float>" ) More...

Typedefs
typedef utility::pointer::owning_ptr < NoRepackDisulfides >	NoRepackDisulfidesOP
	NoRepackDisulfides owning pointer. More...

typedef utility::pointer::owning_ptr < NoRepackDisulfides const >	NoRepackDisulfidesCOP
	NoRepackDisulfides const owning pointer. More...

typedef utility::pointer::access_ptr < NoRepackDisulfides >	NoRepackDisulfidesAP
	NoRepackDisulfides owning pointer. More...

typedef utility::pointer::access_ptr < NoRepackDisulfides const >	NoRepackDisulfidesCAP
	NoRepackDisulfides const owning pointer. More...

typedef utility::pointer::owning_ptr < OperateOnCertainResidues >	OperateOnCertainResiduesOP

typedef utility::pointer::owning_ptr < OperateOnCertainResidues >	OperateOnCertainResiduesCOP

typedef utility::pointer::owning_ptr < OptCysHG >	OptCysHGOP
	OptCysHG owning pointer. More...

typedef utility::pointer::owning_ptr < OptCysHG const >	OptCysHGCOP
	OptCysHG const owning pointer. More...

typedef utility::pointer::access_ptr < OptCysHG >	OptCysHGAP
	OptCysHG owning pointer. More...

typedef utility::pointer::access_ptr < OptCysHG const >	OptCysHGCAP
	OptCysHG const owning pointer. More...

typedef utility::pointer::owning_ptr < OptH >	OptHOP
	OptH owning pointer. More...

typedef utility::pointer::owning_ptr < OptH const >	OptHCOP
	OptH const owning pointer. More...

typedef utility::pointer::access_ptr < OptH >	OptHAP
	OptH owning pointer. More...

typedef utility::pointer::access_ptr < OptH const >	OptHCAP
	OptH const owning pointer. More...

typedef utility::pointer::owning_ptr < ReplicateTask >	ReplicateTaskOP
	ReplicateTask owning pointer. More...

typedef utility::pointer::owning_ptr < ReplicateTask const >	ReplicateTaskCOP
	ReplicateTask const owning pointer. More...

typedef utility::pointer::access_ptr < ReplicateTask >	ReplicateTaskAP
	ReplicateTask owning pointer. More...

typedef utility::pointer::access_ptr < ReplicateTask const >	ReplicateTaskCAP
	ReplicateTask const owning pointer. More...

typedef utility::pointer::owning_ptr < ResFilter >	ResFilterOP

typedef utility::pointer::owning_ptr < ResFilter >	ResFilterCOP

typedef utility::pointer::owning_ptr < ResFilterCreator >	ResFilterCreatorOP

typedef utility::pointer::owning_ptr < ResFilterCreator const >	ResFilterCreatorCOP

typedef utility::pointer::owning_ptr < ResFilterFactory >	ResFilterFactoryOP

typedef utility::pointer::owning_ptr < ResFilterFactory const >	ResFilterFactoryCOP

typedef utility::pointer::owning_ptr < ResidueHasProperty >	ResidueHasPropertyOP

typedef utility::pointer::owning_ptr < ResidueLacksProperty >	ResidueLacksPropertyOP

typedef utility::pointer::owning_ptr < ResidueName3Is >	ResidueName3IsOP

typedef utility::pointer::owning_ptr < ResidueName3Isnt >	ResidueName3IsntOP

typedef utility::pointer::owning_ptr < ResidueIndexIs >	ResidueIndexIsOP

typedef utility::pointer::owning_ptr < ResidueIndexIsnt >	ResidueIndexIsntOP

typedef utility::pointer::owning_ptr < ResiduePDBIndexIs >	ResiduePDBIndexIsOP

typedef utility::pointer::owning_ptr < ResiduePDBIndexIsnt >	ResiduePDBIndexIsntOP

typedef utility::pointer::owning_ptr < ChainIs >	ChainIsOP

typedef utility::pointer::owning_ptr < ChainIsnt >	ChainIsntOP

typedef utility::pointer::owning_ptr < ResLvlTaskOperation >	ResLvlTaskOperationOP

typedef utility::pointer::owning_ptr < ResLvlTaskOperation >	ResLvlTaskOperationCOP

typedef utility::pointer::owning_ptr < ResLvlTaskOperationCreator >	ResLvlTaskOperationCreatorOP

typedef utility::pointer::owning_ptr < ResLvlTaskOperationCreator const >	ResLvlTaskOperationCreatorCOP

typedef utility::pointer::owning_ptr < ResLvlTaskOperationFactory >	ResLvlTaskOperationFactoryOP

typedef utility::pointer::owning_ptr < ResLvlTaskOperationFactory const >	ResLvlTaskOperationFactoryCOP

typedef utility::pointer::owning_ptr < RestrictToRepackingRLT >	RestrictToRepackingRLTOP

typedef utility::pointer::owning_ptr < RestrictAbsentCanonicalAASRLT >	RestrictAbsentCanonicalAASRLTOP

typedef utility::pointer::owning_ptr < DisallowIfNonnativeRLT >	DisallowIfNonnativeRLTOP

typedef utility::pointer::owning_ptr < PreventRepackingRLT >	PreventRepackingRLTOP

typedef utility::pointer::owning_ptr < AddBehaviorRLT >	AddBehaviorRLTOP

typedef utility::pointer::owning_ptr < TaskOperation >	TaskOperationOP

typedef utility::pointer::owning_ptr < TaskOperation >	TaskOperationCOP

typedef boost::shared_ptr < TaskOperation >	TaskOperationSP

typedef utility::pointer::owning_ptr < TaskOperationCreator >	TaskOperationCreatorOP

typedef utility::pointer::owning_ptr < TaskOperationCreator const >	TaskOperationCreatorCOP

typedef utility::pointer::owning_ptr < TaskOperationFactory >	TaskOperationFactoryOP

typedef utility::pointer::owning_ptr < TaskOperationFactory const >	TaskOperationFactoryCOP

typedef utility::pointer::owning_ptr < RestrictToRepacking >	RestrictToRepackingOP

typedef utility::pointer::owning_ptr < RestrictResidueToRepacking >	RestrictResidueToRepackingOP

typedef utility::pointer::owning_ptr < RestrictAbsentCanonicalAAS >	RestrictAbsentCanonicalAASOP

typedef utility::pointer::owning_ptr < DisallowIfNonnative >	DisallowIfNonnativeOP

typedef utility::pointer::owning_ptr < InitializeFromCommandline >	InitializeFromCommandlineOP

typedef utility::pointer::owning_ptr < ReadResfile >	ReadResfileOP

typedef utility::pointer::owning_ptr < SetRotamerCouplings >	SetRotamerCouplingsOP

typedef utility::pointer::owning_ptr < AppendRotamer >	AppendRotamerOP

typedef utility::pointer::owning_ptr < AppendRotamerSet >	AppendRotamerSetOP

typedef utility::pointer::owning_ptr < PreserveCBeta >	PreserveCBetaOP

typedef utility::pointer::owning_ptr < PreventRepacking >	PreventRepackingOP

typedef utility::pointer::owning_ptr < IncludeCurrent >	IncludeCurrentOP

typedef utility::pointer::owning_ptr < RotamerExplosion >	RotamerExplosionOP

typedef utility::pointer::owning_ptr < ExtraChiCutoff >	ExtraChiCutoffOP

Functions
static basic::Tracer	TR ("core.pack.task.operation.NoRepackDisulfides")

static basic::Tracer	TR ("core.pack.task.operation.OperateOnCertainResidues", t_info)

static basic::Tracer	TR ("core.pack.task.operation.ResFilters")

static basic::Tracer	TR ("core.pack.task.operation.TaskOperation")

static basic::Tracer	TR ("core.pack.task.operation.TaskOperationFactory")

static basic::Tracer	TR ("core.pack.task.operation.TaskOperations", t_info)