Rosetta 3.4
Namespaces | Classes | Typedefs | Functions
core::pack::task::operation Namespace Reference

Namespaces

namespace  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  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  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.
typedef
utility::pointer::owning_ptr
< NoRepackDisulfides const > 
NoRepackDisulfidesCOP
 NoRepackDisulfides const owning pointer.
typedef
utility::pointer::access_ptr
< NoRepackDisulfides
NoRepackDisulfidesAP
 NoRepackDisulfides owning pointer.
typedef
utility::pointer::access_ptr
< NoRepackDisulfides const > 
NoRepackDisulfidesCAP
 NoRepackDisulfides const owning pointer.
typedef
utility::pointer::owning_ptr
< OperateOnCertainResidues
OperateOnCertainResiduesOP
typedef
utility::pointer::owning_ptr
< OperateOnCertainResidues
OperateOnCertainResiduesCOP
typedef
utility::pointer::owning_ptr
< OptCysHG
OptCysHGOP
 OptCysHG owning pointer.
typedef
utility::pointer::owning_ptr
< OptCysHG const > 
OptCysHGCOP
 OptCysHG const owning pointer.
typedef
utility::pointer::access_ptr
< OptCysHG
OptCysHGAP
 OptCysHG owning pointer.
typedef
utility::pointer::access_ptr
< OptCysHG const > 
OptCysHGCAP
 OptCysHG const owning pointer.
typedef
utility::pointer::owning_ptr
< OptH
OptHOP
 OptH owning pointer.
typedef
utility::pointer::owning_ptr
< OptH const > 
OptHCOP
 OptH const owning pointer.
typedef
utility::pointer::access_ptr
< OptH
OptHAP
 OptH owning pointer.
typedef
utility::pointer::access_ptr
< OptH const > 
OptHCAP
 OptH const owning pointer.
typedef
utility::pointer::owning_ptr
< ReplicateTask
ReplicateTaskOP
 ReplicateTask owning pointer.
typedef
utility::pointer::owning_ptr
< ReplicateTask const > 
ReplicateTaskCOP
 ReplicateTask const owning pointer.
typedef
utility::pointer::access_ptr
< ReplicateTask
ReplicateTaskAP
 ReplicateTask owning pointer.
typedef
utility::pointer::access_ptr
< ReplicateTask const > 
ReplicateTaskCAP
 ReplicateTask const owning pointer.
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
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)

Typedef Documentation

NoRepackDisulfides owning pointer.

NoRepackDisulfides const owning pointer.

NoRepackDisulfides const owning pointer.

NoRepackDisulfides owning pointer.

OptCysHG owning pointer.

OptCysHG const owning pointer.

OptCysHG const owning pointer.

OptCysHG owning pointer.

OptH owning pointer.

OptH const owning pointer.

OptH const owning pointer.

OptH owning pointer.

ReplicateTask owning pointer.

ReplicateTask const owning pointer.

ReplicateTask const owning pointer.

ReplicateTask owning pointer.


Function Documentation

static basic::Tracer core::pack::task::operation::TR ( "core.pack.task.operation.NoRepackDisulfides"  ) [static]
static basic::Tracer core::pack::task::operation::TR ( "core.pack.task.operation.TaskOperations"  ,
t_info   
) [static]
static basic::Tracer core::pack::task::operation::TR ( "core.pack.task.operation.TaskOperationFactory"  ) [static]
static basic::Tracer core::pack::task::operation::TR ( "core.pack.task.operation.TaskOperation"  ) [static]
static basic::Tracer core::pack::task::operation::TR ( "core.pack.task.operation.ResFilters"  ) [static]
static basic::Tracer core::pack::task::operation::TR ( "core.pack.task.operation.OperateOnCertainResidues"  ,
t_info   
) [static]
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