Rosetta
Classes | Typedefs | Enumerations | Functions
protocols::task_operations Namespace Reference

Classes

class  AlignedThreadOperation
 
class  AlignedThreadOperationCreator
 
class  ConservativeDesignOperation
 A TaskOperation that sets the allowed amino acids of designable residues to the native amino acid's conservative mutations. More...
 
class  ConservativeDesignOperationCreator
 
class  CrystalContactsOperation
 
class  CrystalContactsOperationCreator
 
class  DatabaseThread
 
class  DatabaseThreadCreator
 
class  DesignAroundOperation
 
class  DesignAroundOperationCreator
 
class  DsspDesignOperation
 TaskOperation that can be used to restrict AAs allowed at each position based on DSSP-assigned secondary structure. More...
 
class  DsspDesignOperationCreator
 
class  ImportUnboundRotamersOperation
 
class  ImportUnboundRotamersOperationCreator
 
class  InteractingRotamerExplosion
 : taskop to oversample rotamers that make good interactions with a (set of) specified target residue(s) similar to Rosetta 2.x rotamer explosion More...
 
class  InteractingRotamerExplosionCreator
 
class  JointSequenceOperation
 
class  JointSequenceOperationCreator
 
class  LimitAromaChi2_RotamerSetOperation
 
class  LimitAromaChi2Operation
 
class  LimitAromaChi2OperationCreator
 
class  LinkResidues
 
class  LinkResiduesCreator
 
class  ModifyAnnealer
 
class  ModifyAnnealerCreator
 
class  MutationSetDesignOperation
 Sample a set of mutations each time packer is generated. A MutationSet is a simple map of resnum:aa. Each apply will sample a set either at random, or with a set of weights. More...
 
class  pHVariantTaskOperation
 During repacking, allow interchangeability of protonated and deprotonated variants. More...
 
class  pHVariantTaskOperationCreator
 
class  PreventChainFromRepackingOperation
 
class  PreventChainFromRepackingOperationCreator
 
class  PreventResiduesFromRepackingOperation
 
class  PreventResiduesFromRepackingOperationCreator
 
class  ProteinCore
 
class  ProteinCoreFilterCreator
 
class  ProteinInterfaceDesignOperation
 
class  ProteinInterfaceDesignOperationCreator
 
class  PruneBuriedUnsats_RotamerSetsOperation
 
class  PruneBuriedUnsatsOperation
 
class  PruneBuriedUnsatsOperationCreator
 
class  ReadResfileFromDB
 
class  ReadResfileFromDBCreator
 
class  ResfileCommandOperation
 Applies the equivalent of a resfile line (without the resnums) to residues specified in a residue selector. More...
 
class  ResfileCommandOperationCreator
 
class  ResidueProbDesignOperation
 A TaskOperation that allows amino acids at designable positions through a set of aa probabilities (aa profile). More...
 
class  ResidueProbDesignOperationCreator
 
class  RestrictAAsFromProbabilities
 A class to restrict designable amino acids depending on the probabilities from a PerResidueProbabilitiesMetric. More...
 
class  RestrictAAsFromProbabilitiesCreator
 
class  RestrictByCalculatorsOperation
 
class  RestrictByCalculatorsOperationCreator
 
class  RestrictChainToRepackingOperation
 
class  RestrictChainToRepackingOperationCreator
 
class  RestrictIdentitiesAtAlignedPositionsOperation
 
class  RestrictIdentitiesAtAlignedPositionsOperationCreator
 
class  RestrictIdentitiesOperation
 
class  RestrictIdentitiesOperationCreator
 
class  RestrictInterGroupVectorOperation
 
class  RestrictInterGroupVectorOperationCreator
 
class  RestrictNativeResiduesOperation
 
class  RestrictNativeResiduesOperationCreator
 
class  RestrictNonSurfaceToRepackingOperation
 
class  RestrictNonSurfaceToRepackingOperationCreator
 
class  RestrictOperationsBase
 
class  RestrictResiduesToRepackingOperation
 
class  RestrictResiduesToRepackingOperationCreator
 
class  RestrictToAlignedSegmentsOperation
 
class  RestrictToAlignedSegmentsOperationCreator
 
class  RestrictToCDRH3Loop
 
class  RestrictToCDRH3LoopCreator
 
class  RestrictToInterfaceOperation
 
class  RestrictToInterfaceOperationCreator
 
class  RestrictToInterfaceVectorOperation
 
class  RestrictToInterfaceVectorOperationCreator
 
class  RestrictToMoveMapChiOperation
 A TaskOperation that accepts a movemap and restricts chi that are false to either packing or design. Does not turn anything on, just like the rest of the RestrictTo operations. More...
 
class  RestrictToNeighborhoodOperation
 
class  RestrictToNeighborhoodOperationCreator
 
class  RestrictToTerminiOperation
 
class  RestrictToTerminiOperationCreator
 
class  RetrieveStoredTaskOperation
 
class  RetrieveStoredTaskOperationCreator
 
class  SelectByDeltaScoreOperation
 
class  SelectByDeltaScoreOperationCreator
 
class  SelectByDensityFitOperation
 
class  SelectByDensityFitOperationCreator
 
class  SelectBySASAOperation
 
class  SelectBySASAOperationCreator
 
class  SelectResiduesWithinChainOperation
 
class  SelectResiduesWithinChainOperationCreator
 
class  SeqprofConsensusOperation
 
class  RestrictConservedLowDdgOperation
 a Task operation that will check whether the amino acid at a position is conserved in the sequence profile and has an unfavorable ddG when mutated to ala. all positions that match this criterion will get set to repacking. More...
 
class  SeqprofConsensusOperationCreator
 
class  RestrictConservedLowDdgOperationCreator
 
class  SequenceMotifTaskOperation
 A TaskOp that takes a regex-like pattern and turns it into a set of design residues. The string should identify what to do for each position. More...
 
class  SequenceMotifTaskOperationCreator
 
class  SetIGTypeOperation
 
class  SetIGTypeOperationCreator
 
class  STMStoredTask
 
class  StoreCombinedStoredTasksMover
 mover that can be used to save or restore a task at an arbitrary point during a rosetta scripts protocol. other task operations, movers, or filters can be set up to access tasks saved by this mover during their apply calls. More...
 
class  StoreCombinedStoredTasksMoverCreator
 
class  StoreCompoundTaskMover
 
class  StoreCompoundTaskMoverCreator
 
class  StoreTaskMover
 mover that can be used to save or restore a task at an arbitrary point during a rosetta scripts protocol. other task operations, movers, or filters can be set up to access tasks saved by this mover during their apply calls. More...
 
class  StoreTaskMoverCreator
 
class  ThreadSequenceOperation
 
class  ThreadSequenceOperationCreator
 

Typedefs

typedef utility::pointer::shared_ptr< AlignedThreadOperation > AlignedThreadOperationOP
 
typedef utility::pointer::shared_ptr< AlignedThreadOperation const > AlignedThreadOperationCOP
 
typedef utility::pointer::shared_ptr< ConservativeDesignOperation > ConservativeDesignOperationOP
 
typedef utility::pointer::shared_ptr< ConservativeDesignOperation const > ConservativeDesignOperationCOP
 
typedef utility::pointer::shared_ptr< CrystalContactsOperation > CrystalContactsOperationOP
 
typedef utility::pointer::shared_ptr< CrystalContactsOperation const > CrystalContactsOperationCOP
 
typedef utility::pointer::shared_ptr< DatabaseThread > DatabaseThreadOP
 
typedef utility::pointer::shared_ptr< DatabaseThread const > DatabaseThreadCOP
 
typedef utility::pointer::shared_ptr< DesignAroundOperation > DesignAroundOperationOP
 
typedef utility::pointer::shared_ptr< DesignAroundOperation const > DesignAroundOperationCOP
 
typedef utility::pointer::shared_ptr< DsspDesignOperation > DsspDesignOperationOP
 
typedef utility::pointer::shared_ptr< ImportUnboundRotamersOperation > ImportUnboundRotamersOperationOP
 
typedef utility::pointer::shared_ptr< ImportUnboundRotamersOperation const > ImportUnboundRotamersOperationCOP
 
typedef utility::pointer::shared_ptr< InteractingRotamerOperation > InteractingRotamerOperationOP
 
typedef utility::pointer::shared_ptr< InteractingRotamerOperation const > InteractingRotamerOperationCOP
 
typedef utility::pointer::shared_ptr< JointSequenceOperation > JointSequenceOperationOP
 
typedef utility::pointer::shared_ptr< LimitAromaChi2_RotamerSetOperation > LimitAromaChi2_RotamerSetOperationOP
 
typedef utility::pointer::shared_ptr< LimitAromaChi2_RotamerSetOperation const > LimitAromaChi2_RotamerSetOperationCOP
 
typedef utility::pointer::shared_ptr< LimitAromaChi2Operation > LimitAromaChi2OperationOP
 
typedef utility::pointer::shared_ptr< LimitAromaChi2Operation const > LimitAromaChi2OperationCOP
 
typedef utility::pointer::shared_ptr< LinkResidues > LinkResiduesOP
 
typedef utility::pointer::shared_ptr< LinkResidues const > LinkResiduesCOP
 
typedef utility::pointer::shared_ptr< ModifyAnnealer > ModifyAnnealerOP
 
typedef utility::pointer::shared_ptr< ModifyAnnealer const > ModifyAnnealerCOP
 
typedef utility::pointer::shared_ptr< MutationSetDesignOperation > MutationSetDesignOperationOP
 
typedef utility::pointer::shared_ptr< MutationSetDesignOperation const > MutationSetDesignOperationCOP
 
typedef std::map< core::Size, core::chemical::AA > MutationSet
 
typedef utility::pointer::shared_ptr< pHVariantTaskOperation > pHVariantTaskOperationOP
 
typedef utility::pointer::shared_ptr< pHVariantTaskOperation const > pHVariantTaskOperationCOP
 
typedef utility::pointer::shared_ptr< PreventChainFromRepackingOperation > PreventChainFromRepackingOperationOP
 
typedef utility::pointer::shared_ptr< PreventChainFromRepackingOperation const > PreventChainFromRepackingOperationCOP
 
typedef utility::pointer::shared_ptr< PreventResiduesFromRepackingOperation > PreventResiduesFromRepackingOperationOP
 
typedef utility::pointer::shared_ptr< PreventResiduesFromRepackingOperation const > PreventResiduesFromRepackingOperationCOP
 
typedef utility::pointer::shared_ptr< ProteinInterfaceDesignOperation > ProteinInterfaceDesignOperationOP
 
typedef utility::pointer::shared_ptr< ProteinInterfaceDesignOperation const > ProteinInterfaceDesignOperationCOP
 
typedef utility::pointer::shared_ptr< PruneBuriedUnsats_RotamerSetsOperation > PruneBuriedUnsats_RotamerSetsOperationOP
 
typedef utility::pointer::shared_ptr< PruneBuriedUnsats_RotamerSetsOperation const > PruneBuriedUnsats_RotamerSetsOperationCOP
 
typedef utility::pointer::shared_ptr< PruneBuriedUnsatsOperation > PruneBuriedUnsatsOperationOP
 
typedef utility::pointer::shared_ptr< PruneBuriedUnsatsOperation const > PruneBuriedUnsatsOperationCOP
 
typedef utility::pointer::shared_ptr< ReadResfileFromDB > ReadResfileFromDBOP
 
typedef utility::pointer::shared_ptr< ResfileCommandOperation > ResfileCommandOperationOP
 
typedef utility::pointer::shared_ptr< ResfileCommandOperation const > ResfileCommandOperationCOP
 
typedef std::map< core::chemical::AA, Real > AAProbabilities
 
typedef std::map< core::Size, AAProbabilities > PerResidueAAProbSet
 
typedef utility::pointer::shared_ptr< ResidueProbDesignOperation > ResidueProbDesignOperationOP
 
typedef utility::pointer::shared_ptr< ResidueProbDesignOperation const > ResidueProbDesignOperationCOP
 
using RestrictAAsFromProbabilitiesOP = utility::pointer::shared_ptr< RestrictAAsFromProbabilities >
 
using RestrictAAsFromProbabilitiesCOP = utility::pointer::shared_ptr< RestrictAAsFromProbabilities const >
 
typedef utility::pointer::shared_ptr< RestrictByCalculatorsOperation > RestrictByCalculatorsOperationOP
 
typedef utility::pointer::shared_ptr< RestrictByCalculatorsOperation const > RestrictByCalculatorsOperationCOP
 
typedef utility::pointer::shared_ptr< RestrictChainToRepackingOperation > RestrictChainToRepackingOperationOP
 
typedef utility::pointer::shared_ptr< RestrictChainToRepackingOperation const > RestrictChainToRepackingOperationCOP
 
typedef utility::pointer::shared_ptr< RestrictIdentitiesAtAlignedPositionsOperation > RestrictIdentitiesAtAlignedPositionsOperationOP
 
typedef utility::pointer::shared_ptr< RestrictIdentitiesAtAlignedPositionsOperation const > RestrictIdentitiesAtAlignedPositionsOperationCOP
 
typedef utility::pointer::shared_ptr< RestrictIdentitiesOperation > RestrictIdentitiesOperationOP
 
typedef utility::pointer::shared_ptr< RestrictIdentitiesOperation const > RestrictIdentitiesOperationCOP
 
typedef utility::pointer::shared_ptr< RestrictInterGroupVectorOperation > RestrictInterGroupVectorOperationOP
 
typedef utility::pointer::shared_ptr< RestrictInterGroupVectorOperation const > RestrictInterGroupVectorOperationCOP
 
typedef utility::pointer::shared_ptr< RestrictNativeResiduesOperation > RestrictNativeResiduesOperationOP
 
typedef utility::pointer::shared_ptr< RestrictNonSurfaceToRepackingOperation > RestrictNonSurfaceToRepackingOperationOP
 
typedef utility::pointer::shared_ptr< RestrictOperationsBase > RestrictOperationsBaseOP
 
typedef utility::pointer::shared_ptr< RestrictOperationsBase const > RestrictOperationsBaseCOP
 
typedef utility::pointer::shared_ptr< RestrictResiduesToRepackingOperation > RestrictResiduesToRepackingOperationOP
 
typedef utility::pointer::shared_ptr< RestrictResiduesToRepackingOperation const > RestrictResiduesToRepackingOperationCOP
 
typedef utility::pointer::shared_ptr< RestrictToAlignedSegmentsOperation > RestrictToAlignedSegmentsOperationOP
 
typedef utility::pointer::shared_ptr< RestrictToAlignedSegmentsOperation const > RestrictToAlignedSegmentsOperationCOP
 
typedef utility::pointer::shared_ptr< RestrictToCDRH3Loop > RestrictToCDRH3LoopOP
 
typedef utility::pointer::shared_ptr< RestrictToInterfaceOperation > RestrictToInterfaceOperationOP
 
typedef utility::pointer::shared_ptr< RestrictToInterfaceOperation const > RestrictToInterfaceOperationCOP
 
typedef utility::pointer::shared_ptr< RestrictToInterfaceVectorOperation > RestrictToInterfaceVectorOperationOP
 
typedef utility::pointer::shared_ptr< RestrictToInterfaceVectorOperation const > RestrictToInterfaceVectorOperationCOP
 
typedef utility::pointer::shared_ptr< RestrictToMoveMapChiOperation > RestrictToMoveMapChiOperationOP
 
typedef utility::pointer::shared_ptr< RestrictToNeighborhoodOperation > RestrictToNeighborhoodOperationOP
 
typedef utility::pointer::shared_ptr< RestrictToNeighborhoodOperation const > RestrictToNeighborhoodOperationCOP
 
typedef utility::pointer::shared_ptr< RestrictToTerminiOperation > RestrictToTerminiOperationOP
 
typedef utility::pointer::shared_ptr< RestrictToTerminiOperation const > RestrictToTerminiOperationCOP
 
typedef utility::pointer::shared_ptr< RetrieveStoredTaskOperation > RetrieveStoredTaskOperationOP
 
typedef utility::pointer::shared_ptr< RetrieveStoredTaskOperation const > RetrieveStoredTaskOperationCOP
 
typedef utility::pointer::shared_ptr< SelectByDeltaScoreOperation > SelectByDeltaScoreOperationOP
 
typedef utility::pointer::shared_ptr< SelectByDensityFitOperation > SelectByDensityFitOperationOP
 
typedef utility::pointer::shared_ptr< SelectByDensityFitOperation const > SelectByDensityFitOperationCOP
 
typedef utility::pointer::shared_ptr< SelectBySASAOperation > SelectBySASAOperationOP
 
typedef utility::pointer::shared_ptr< SelectBySASAOperation const > SelectBySASAOperationCOP
 
typedef utility::pointer::shared_ptr< SelectResiduesWithinChainOperation > SelectResiduesWithinChainOperationOP
 
typedef utility::pointer::shared_ptr< SelectResiduesWithinChainOperation const > SelectResiduesWithinChainOperationCOP
 
typedef utility::pointer::shared_ptr< SeqprofConsensusOperation > SeqprofConsensusOperationOP
 
typedef utility::pointer::shared_ptr< RestrictConservedLowDdgOperation > RestrictConservedLowDdgOperationOP
 
typedef utility::pointer::shared_ptr< SequenceMotifTaskOperation > SequenceMotifTaskOperationOP
 
typedef utility::pointer::shared_ptr< SequenceMotifTaskOperation const > SequenceMotifTaskOperationCOP
 
typedef utility::pointer::shared_ptr< SetIGTypeOperation > SetIGTypeOperationOP
 
typedef utility::pointer::shared_ptr< SetIGTypeOperation const > SetIGTypeOperationCOP
 
typedef utility::pointer::shared_ptr< STMStoredTask > STMStoredTaskOP
 
typedef utility::pointer::shared_ptr< STMStoredTask const > STMStoredTaskCOP
 
typedef utility::pointer::shared_ptr< StoreCombinedStoredTasksMover > StoreCombinedStoredTasksMoverOP
 
typedef utility::pointer::shared_ptr< StoreCombinedStoredTasksMover const > StoreCombinedStoredTasksMoverCOP
 
typedef utility::pointer::shared_ptr< StoreCompoundTaskMover > StoreCompoundTaskMoverOP
 
typedef utility::pointer::shared_ptr< StoreCompoundTaskMover const > StoreCompoundTaskMoverCOP
 
typedef utility::pointer::shared_ptr< StoreTaskMover > StoreTaskMoverOP
 
typedef utility::pointer::shared_ptr< StoreTaskMover const > StoreTaskMoverCOP
 
typedef utility::pointer::shared_ptr< ThreadSequenceOperation > ThreadSequenceOperationOP
 
typedef utility::pointer::shared_ptr< ThreadSequenceOperation const > ThreadSequenceOperationCOP
 

Enumerations

enum  boolean_operations {
  AND =1 , OR , XOR , NOR ,
  NAND , ORNOT , ANDNOT , NOT
}
 

Functions

std::string dsspdo_subelement_ct_name (std::string const &name)
 
std::string dsspdo_group_name ()
 
std::string linkres_subelement_ctname (std::string const &name)
 
std::string linkres_subelement_group ()
 
static basic::Tracer TR ("protocols.toolbox.task_operations.ReadResfileFromDB")
 
std::string rtas_subelement_ct_naming_function (std::string const &name)
 
static basic::Tracer TR ("protocols.task_operations.STMStoredTask")
 

Typedef Documentation

◆ AAProbabilities

typedef std::map< core::chemical::AA, Real > protocols::task_operations::AAProbabilities

◆ AlignedThreadOperationCOP

typedef utility::pointer::shared_ptr< AlignedThreadOperation const > protocols::task_operations::AlignedThreadOperationCOP

◆ AlignedThreadOperationOP

typedef utility::pointer::shared_ptr< AlignedThreadOperation > protocols::task_operations::AlignedThreadOperationOP

◆ ConservativeDesignOperationCOP

typedef utility::pointer::shared_ptr< ConservativeDesignOperation const > protocols::task_operations::ConservativeDesignOperationCOP

◆ ConservativeDesignOperationOP

typedef utility::pointer::shared_ptr< ConservativeDesignOperation > protocols::task_operations::ConservativeDesignOperationOP

◆ CrystalContactsOperationCOP

typedef utility::pointer::shared_ptr< CrystalContactsOperation const > protocols::task_operations::CrystalContactsOperationCOP

◆ CrystalContactsOperationOP

typedef utility::pointer::shared_ptr< CrystalContactsOperation > protocols::task_operations::CrystalContactsOperationOP

◆ DatabaseThreadCOP

typedef utility::pointer::shared_ptr< DatabaseThread const > protocols::task_operations::DatabaseThreadCOP

◆ DatabaseThreadOP

typedef utility::pointer::shared_ptr< DatabaseThread > protocols::task_operations::DatabaseThreadOP

◆ DesignAroundOperationCOP

typedef utility::pointer::shared_ptr< DesignAroundOperation const > protocols::task_operations::DesignAroundOperationCOP

◆ DesignAroundOperationOP

typedef utility::pointer::shared_ptr< DesignAroundOperation > protocols::task_operations::DesignAroundOperationOP

◆ DsspDesignOperationOP

typedef utility::pointer::shared_ptr< DsspDesignOperation > protocols::task_operations::DsspDesignOperationOP

◆ ImportUnboundRotamersOperationCOP

typedef utility::pointer::shared_ptr< ImportUnboundRotamersOperation const > protocols::task_operations::ImportUnboundRotamersOperationCOP

◆ ImportUnboundRotamersOperationOP

typedef utility::pointer::shared_ptr< ImportUnboundRotamersOperation > protocols::task_operations::ImportUnboundRotamersOperationOP

◆ InteractingRotamerOperationCOP

typedef utility::pointer::shared_ptr< InteractingRotamerOperation const > protocols::task_operations::InteractingRotamerOperationCOP

◆ InteractingRotamerOperationOP

typedef utility::pointer::shared_ptr< InteractingRotamerOperation > protocols::task_operations::InteractingRotamerOperationOP

◆ JointSequenceOperationOP

typedef utility::pointer::shared_ptr< JointSequenceOperation > protocols::task_operations::JointSequenceOperationOP

◆ LimitAromaChi2_RotamerSetOperationCOP

typedef utility::pointer::shared_ptr< LimitAromaChi2_RotamerSetOperation const > protocols::task_operations::LimitAromaChi2_RotamerSetOperationCOP

◆ LimitAromaChi2_RotamerSetOperationOP

typedef utility::pointer::shared_ptr< LimitAromaChi2_RotamerSetOperation > protocols::task_operations::LimitAromaChi2_RotamerSetOperationOP

◆ LimitAromaChi2OperationCOP

typedef utility::pointer::shared_ptr< LimitAromaChi2Operation const > protocols::task_operations::LimitAromaChi2OperationCOP

◆ LimitAromaChi2OperationOP

typedef utility::pointer::shared_ptr< LimitAromaChi2Operation > protocols::task_operations::LimitAromaChi2OperationOP

◆ LinkResiduesCOP

typedef utility::pointer::shared_ptr< LinkResidues const > protocols::task_operations::LinkResiduesCOP

◆ LinkResiduesOP

typedef utility::pointer::shared_ptr< LinkResidues > protocols::task_operations::LinkResiduesOP

◆ ModifyAnnealerCOP

typedef utility::pointer::shared_ptr< ModifyAnnealer const > protocols::task_operations::ModifyAnnealerCOP

◆ ModifyAnnealerOP

typedef utility::pointer::shared_ptr< ModifyAnnealer > protocols::task_operations::ModifyAnnealerOP

◆ MutationSet

typedef std::map<core::Size, core::chemical::AA> protocols::task_operations::MutationSet

◆ MutationSetDesignOperationCOP

typedef utility::pointer::shared_ptr< MutationSetDesignOperation const > protocols::task_operations::MutationSetDesignOperationCOP

◆ MutationSetDesignOperationOP

typedef utility::pointer::shared_ptr< MutationSetDesignOperation > protocols::task_operations::MutationSetDesignOperationOP

◆ PerResidueAAProbSet

typedef std::map< core::Size, AAProbabilities > protocols::task_operations::PerResidueAAProbSet

◆ pHVariantTaskOperationCOP

typedef utility::pointer::shared_ptr< pHVariantTaskOperation const > protocols::task_operations::pHVariantTaskOperationCOP

◆ pHVariantTaskOperationOP

typedef utility::pointer::shared_ptr< pHVariantTaskOperation > protocols::task_operations::pHVariantTaskOperationOP

◆ PreventChainFromRepackingOperationCOP

typedef utility::pointer::shared_ptr< PreventChainFromRepackingOperation const > protocols::task_operations::PreventChainFromRepackingOperationCOP

◆ PreventChainFromRepackingOperationOP

typedef utility::pointer::shared_ptr< PreventChainFromRepackingOperation > protocols::task_operations::PreventChainFromRepackingOperationOP

◆ PreventResiduesFromRepackingOperationCOP

typedef utility::pointer::shared_ptr< PreventResiduesFromRepackingOperation const > protocols::task_operations::PreventResiduesFromRepackingOperationCOP

◆ PreventResiduesFromRepackingOperationOP

typedef utility::pointer::shared_ptr< PreventResiduesFromRepackingOperation > protocols::task_operations::PreventResiduesFromRepackingOperationOP

◆ ProteinInterfaceDesignOperationCOP

typedef utility::pointer::shared_ptr< ProteinInterfaceDesignOperation const > protocols::task_operations::ProteinInterfaceDesignOperationCOP

◆ ProteinInterfaceDesignOperationOP

typedef utility::pointer::shared_ptr< ProteinInterfaceDesignOperation > protocols::task_operations::ProteinInterfaceDesignOperationOP

◆ PruneBuriedUnsats_RotamerSetsOperationCOP

typedef utility::pointer::shared_ptr< PruneBuriedUnsats_RotamerSetsOperation const > protocols::task_operations::PruneBuriedUnsats_RotamerSetsOperationCOP

◆ PruneBuriedUnsats_RotamerSetsOperationOP

typedef utility::pointer::shared_ptr< PruneBuriedUnsats_RotamerSetsOperation > protocols::task_operations::PruneBuriedUnsats_RotamerSetsOperationOP

◆ PruneBuriedUnsatsOperationCOP

typedef utility::pointer::shared_ptr< PruneBuriedUnsatsOperation const > protocols::task_operations::PruneBuriedUnsatsOperationCOP

◆ PruneBuriedUnsatsOperationOP

typedef utility::pointer::shared_ptr< PruneBuriedUnsatsOperation > protocols::task_operations::PruneBuriedUnsatsOperationOP

◆ ReadResfileFromDBOP

typedef utility::pointer::shared_ptr< ReadResfileFromDB > protocols::task_operations::ReadResfileFromDBOP

◆ ResfileCommandOperationCOP

typedef utility::pointer::shared_ptr< ResfileCommandOperation const > protocols::task_operations::ResfileCommandOperationCOP

◆ ResfileCommandOperationOP

typedef utility::pointer::shared_ptr< ResfileCommandOperation > protocols::task_operations::ResfileCommandOperationOP

◆ ResidueProbDesignOperationCOP

typedef utility::pointer::shared_ptr< ResidueProbDesignOperation const > protocols::task_operations::ResidueProbDesignOperationCOP

◆ ResidueProbDesignOperationOP

typedef utility::pointer::shared_ptr< ResidueProbDesignOperation > protocols::task_operations::ResidueProbDesignOperationOP

◆ RestrictAAsFromProbabilitiesCOP

using protocols::task_operations::RestrictAAsFromProbabilitiesCOP = typedef utility::pointer::shared_ptr< RestrictAAsFromProbabilities const >

◆ RestrictAAsFromProbabilitiesOP

using protocols::task_operations::RestrictAAsFromProbabilitiesOP = typedef utility::pointer::shared_ptr< RestrictAAsFromProbabilities >

◆ RestrictByCalculatorsOperationCOP

typedef utility::pointer::shared_ptr< RestrictByCalculatorsOperation const > protocols::task_operations::RestrictByCalculatorsOperationCOP

◆ RestrictByCalculatorsOperationOP

typedef utility::pointer::shared_ptr< RestrictByCalculatorsOperation > protocols::task_operations::RestrictByCalculatorsOperationOP

◆ RestrictChainToRepackingOperationCOP

typedef utility::pointer::shared_ptr< RestrictChainToRepackingOperation const > protocols::task_operations::RestrictChainToRepackingOperationCOP

◆ RestrictChainToRepackingOperationOP

typedef utility::pointer::shared_ptr< RestrictChainToRepackingOperation > protocols::task_operations::RestrictChainToRepackingOperationOP

◆ RestrictConservedLowDdgOperationOP

typedef utility::pointer::shared_ptr< RestrictConservedLowDdgOperation > protocols::task_operations::RestrictConservedLowDdgOperationOP

◆ RestrictIdentitiesAtAlignedPositionsOperationCOP

typedef utility::pointer::shared_ptr< RestrictIdentitiesAtAlignedPositionsOperation const > protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperationCOP

◆ RestrictIdentitiesAtAlignedPositionsOperationOP

typedef utility::pointer::shared_ptr< RestrictIdentitiesAtAlignedPositionsOperation > protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperationOP

◆ RestrictIdentitiesOperationCOP

typedef utility::pointer::shared_ptr< RestrictIdentitiesOperation const > protocols::task_operations::RestrictIdentitiesOperationCOP

◆ RestrictIdentitiesOperationOP

typedef utility::pointer::shared_ptr< RestrictIdentitiesOperation > protocols::task_operations::RestrictIdentitiesOperationOP

◆ RestrictInterGroupVectorOperationCOP

typedef utility::pointer::shared_ptr< RestrictInterGroupVectorOperation const > protocols::task_operations::RestrictInterGroupVectorOperationCOP

◆ RestrictInterGroupVectorOperationOP

typedef utility::pointer::shared_ptr< RestrictInterGroupVectorOperation > protocols::task_operations::RestrictInterGroupVectorOperationOP

◆ RestrictNativeResiduesOperationOP

typedef utility::pointer::shared_ptr< RestrictNativeResiduesOperation > protocols::task_operations::RestrictNativeResiduesOperationOP

◆ RestrictNonSurfaceToRepackingOperationOP

typedef utility::pointer::shared_ptr< RestrictNonSurfaceToRepackingOperation > protocols::task_operations::RestrictNonSurfaceToRepackingOperationOP

◆ RestrictOperationsBaseCOP

typedef utility::pointer::shared_ptr< RestrictOperationsBase const > protocols::task_operations::RestrictOperationsBaseCOP

◆ RestrictOperationsBaseOP

typedef utility::pointer::shared_ptr< RestrictOperationsBase > protocols::task_operations::RestrictOperationsBaseOP

◆ RestrictResiduesToRepackingOperationCOP

typedef utility::pointer::shared_ptr< RestrictResiduesToRepackingOperation const > protocols::task_operations::RestrictResiduesToRepackingOperationCOP

◆ RestrictResiduesToRepackingOperationOP

typedef utility::pointer::shared_ptr< RestrictResiduesToRepackingOperation > protocols::task_operations::RestrictResiduesToRepackingOperationOP

◆ RestrictToAlignedSegmentsOperationCOP

typedef utility::pointer::shared_ptr< RestrictToAlignedSegmentsOperation const > protocols::task_operations::RestrictToAlignedSegmentsOperationCOP

◆ RestrictToAlignedSegmentsOperationOP

typedef utility::pointer::shared_ptr< RestrictToAlignedSegmentsOperation > protocols::task_operations::RestrictToAlignedSegmentsOperationOP

◆ RestrictToCDRH3LoopOP

typedef utility::pointer::shared_ptr< RestrictToCDRH3Loop > protocols::task_operations::RestrictToCDRH3LoopOP

◆ RestrictToInterfaceOperationCOP

typedef utility::pointer::shared_ptr< RestrictToInterfaceOperation const > protocols::task_operations::RestrictToInterfaceOperationCOP

◆ RestrictToInterfaceOperationOP

typedef utility::pointer::shared_ptr< RestrictToInterfaceOperation > protocols::task_operations::RestrictToInterfaceOperationOP

◆ RestrictToInterfaceVectorOperationCOP

typedef utility::pointer::shared_ptr< RestrictToInterfaceVectorOperation const > protocols::task_operations::RestrictToInterfaceVectorOperationCOP

◆ RestrictToInterfaceVectorOperationOP

typedef utility::pointer::shared_ptr< RestrictToInterfaceVectorOperation > protocols::task_operations::RestrictToInterfaceVectorOperationOP

◆ RestrictToMoveMapChiOperationOP

typedef utility::pointer::shared_ptr< RestrictToMoveMapChiOperation > protocols::task_operations::RestrictToMoveMapChiOperationOP

◆ RestrictToNeighborhoodOperationCOP

typedef utility::pointer::shared_ptr< RestrictToNeighborhoodOperation const > protocols::task_operations::RestrictToNeighborhoodOperationCOP

◆ RestrictToNeighborhoodOperationOP

typedef utility::pointer::shared_ptr< RestrictToNeighborhoodOperation > protocols::task_operations::RestrictToNeighborhoodOperationOP

◆ RestrictToTerminiOperationCOP

typedef utility::pointer::shared_ptr< RestrictToTerminiOperation const > protocols::task_operations::RestrictToTerminiOperationCOP

◆ RestrictToTerminiOperationOP

typedef utility::pointer::shared_ptr< RestrictToTerminiOperation > protocols::task_operations::RestrictToTerminiOperationOP

◆ RetrieveStoredTaskOperationCOP

typedef utility::pointer::shared_ptr< RetrieveStoredTaskOperation const > protocols::task_operations::RetrieveStoredTaskOperationCOP

◆ RetrieveStoredTaskOperationOP

typedef utility::pointer::shared_ptr< RetrieveStoredTaskOperation > protocols::task_operations::RetrieveStoredTaskOperationOP

◆ SelectByDeltaScoreOperationOP

typedef utility::pointer::shared_ptr< SelectByDeltaScoreOperation > protocols::task_operations::SelectByDeltaScoreOperationOP

◆ SelectByDensityFitOperationCOP

typedef utility::pointer::shared_ptr< SelectByDensityFitOperation const > protocols::task_operations::SelectByDensityFitOperationCOP

◆ SelectByDensityFitOperationOP

typedef utility::pointer::shared_ptr< SelectByDensityFitOperation > protocols::task_operations::SelectByDensityFitOperationOP

◆ SelectBySASAOperationCOP

typedef utility::pointer::shared_ptr< SelectBySASAOperation const > protocols::task_operations::SelectBySASAOperationCOP

◆ SelectBySASAOperationOP

typedef utility::pointer::shared_ptr< SelectBySASAOperation > protocols::task_operations::SelectBySASAOperationOP

◆ SelectResiduesWithinChainOperationCOP

typedef utility::pointer::shared_ptr< SelectResiduesWithinChainOperation const > protocols::task_operations::SelectResiduesWithinChainOperationCOP

◆ SelectResiduesWithinChainOperationOP

typedef utility::pointer::shared_ptr< SelectResiduesWithinChainOperation > protocols::task_operations::SelectResiduesWithinChainOperationOP

◆ SeqprofConsensusOperationOP

typedef utility::pointer::shared_ptr< SeqprofConsensusOperation > protocols::task_operations::SeqprofConsensusOperationOP

◆ SequenceMotifTaskOperationCOP

typedef utility::pointer::shared_ptr< SequenceMotifTaskOperation const > protocols::task_operations::SequenceMotifTaskOperationCOP

◆ SequenceMotifTaskOperationOP

typedef utility::pointer::shared_ptr< SequenceMotifTaskOperation > protocols::task_operations::SequenceMotifTaskOperationOP

◆ SetIGTypeOperationCOP

typedef utility::pointer::shared_ptr< SetIGTypeOperation const > protocols::task_operations::SetIGTypeOperationCOP

◆ SetIGTypeOperationOP

typedef utility::pointer::shared_ptr< SetIGTypeOperation > protocols::task_operations::SetIGTypeOperationOP

◆ STMStoredTaskCOP

typedef utility::pointer::shared_ptr< STMStoredTask const > protocols::task_operations::STMStoredTaskCOP

◆ STMStoredTaskOP

typedef utility::pointer::shared_ptr< STMStoredTask > protocols::task_operations::STMStoredTaskOP

◆ StoreCombinedStoredTasksMoverCOP

typedef utility::pointer::shared_ptr< StoreCombinedStoredTasksMover const > protocols::task_operations::StoreCombinedStoredTasksMoverCOP

◆ StoreCombinedStoredTasksMoverOP

typedef utility::pointer::shared_ptr< StoreCombinedStoredTasksMover > protocols::task_operations::StoreCombinedStoredTasksMoverOP

◆ StoreCompoundTaskMoverCOP

typedef utility::pointer::shared_ptr< StoreCompoundTaskMover const > protocols::task_operations::StoreCompoundTaskMoverCOP

◆ StoreCompoundTaskMoverOP

typedef utility::pointer::shared_ptr< StoreCompoundTaskMover > protocols::task_operations::StoreCompoundTaskMoverOP

◆ StoreTaskMoverCOP

typedef utility::pointer::shared_ptr< StoreTaskMover const > protocols::task_operations::StoreTaskMoverCOP

◆ StoreTaskMoverOP

typedef utility::pointer::shared_ptr< StoreTaskMover > protocols::task_operations::StoreTaskMoverOP

◆ ThreadSequenceOperationCOP

typedef utility::pointer::shared_ptr< ThreadSequenceOperation const > protocols::task_operations::ThreadSequenceOperationCOP

◆ ThreadSequenceOperationOP

typedef utility::pointer::shared_ptr< ThreadSequenceOperation > protocols::task_operations::ThreadSequenceOperationOP

Enumeration Type Documentation

◆ boolean_operations

enum protocols::task_operations::boolean_operations
Enumerator
AND 
OR 
XOR 
NOR 
NAND 
ORNOT 
ANDNOT 
NOT 

Function Documentation

◆ dsspdo_group_name()

std::string protocols::task_operations::dsspdo_group_name ( )

◆ dsspdo_subelement_ct_name()

std::string protocols::task_operations::dsspdo_subelement_ct_name ( std::string const &  name)

Referenced by protocols::task_operations::DsspDesignOperation::provide_xml_schema().

◆ linkres_subelement_ctname()

std::string protocols::task_operations::linkres_subelement_ctname ( std::string const &  name)

Referenced by protocols::task_operations::LinkResidues::provide_xml_schema().

◆ linkres_subelement_group()

std::string protocols::task_operations::linkres_subelement_group ( )

◆ rtas_subelement_ct_naming_function()

std::string protocols::task_operations::rtas_subelement_ct_naming_function ( std::string const &  name)

Referenced by protocols::task_operations::RestrictToAlignedSegmentsOperation::provide_xml_schema().

◆ TR() [1/2]

static basic::Tracer protocols::task_operations::TR ( "protocols.task_operations.STMStoredTask"  )
static

◆ TR() [2/2]

static basic::Tracer protocols::task_operations::TR ( "protocols.toolbox.task_operations.ReadResfileFromDB"  )
static

Referenced by protocols::task_operations::JointSequenceOperation::add_pose(), protocols::task_operations::PruneBuriedUnsats_RotamerSetsOperation::alter_rotamer_sets(), protocols::task_operations::StoreCombinedStoredTasksMover::apply(), protocols::task_operations::AlignedThreadOperation::apply(), protocols::task_operations::CrystalContactsOperation::apply(), protocols::task_operations::DatabaseThread::apply(), protocols::task_operations::LinkResidues::apply(), protocols::task_operations::ProteinInterfaceDesignOperation::apply(), protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::apply(), protocols::task_operations::RestrictIdentitiesOperation::apply(), protocols::task_operations::RestrictResiduesToRepackingOperation::apply(), protocols::task_operations::RestrictToAlignedSegmentsOperation::apply(), protocols::task_operations::RestrictToInterfaceVectorOperation::apply(), protocols::task_operations::SelectByDeltaScoreOperation::apply(), protocols::task_operations::SelectByDensityFitOperation::apply(), protocols::task_operations::SelectBySASAOperation::apply(), protocols::task_operations::SelectResiduesWithinChainOperation::apply(), protocols::task_operations::ReadResfileFromDB::apply(), protocols::task_operations::ResidueProbDesignOperation::apply(), protocols::task_operations::RestrictAAsFromProbabilities::apply(), protocols::task_operations::SequenceMotifTaskOperation::apply(), protocols::task_operations::DsspDesignOperation::apply(), protocols::task_operations::JointSequenceOperation::apply(), protocols::task_operations::RestrictNativeResiduesOperation::apply(), protocols::task_operations::StoreCompoundTaskMover::CompoundDesignableTask(), protocols::task_operations::StoreCompoundTaskMover::CompoundPackableTask(), protocols::task_operations::RestrictAAsFromProbabilities::disable_AAs(), protocols::task_operations::DatabaseThread::find_length(), protocols::task_operations::CrystalContactsOperation::is_crystal_contact(), protocols::task_operations::ConservativeDesignOperation::load_data_from_db(), protocols::task_operations::RestrictToInterfaceOperation::make_calculator(), protocols::task_operations::RestrictToNeighborhoodOperation::make_calculator(), protocols::task_operations::StoreCompoundTaskMover::parse_my_tag(), protocols::task_operations::DsspDesignOperation::parse_tag(), protocols::task_operations::JointSequenceOperation::parse_tag(), protocols::task_operations::LinkResidues::parse_tag(), protocols::task_operations::RestrictNativeResiduesOperation::parse_tag(), protocols::task_operations::RestrictToInterfaceVectorOperation::parse_tag(), protocols::task_operations::ProteinCore::parse_tag(), protocols::task_operations::AlignedThreadOperation::parse_tag(), protocols::task_operations::DesignAroundOperation::parse_tag(), protocols::task_operations::PreventResiduesFromRepackingOperation::parse_tag(), protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::parse_tag(), protocols::task_operations::RestrictIdentitiesOperation::parse_tag(), protocols::task_operations::RestrictResiduesToRepackingOperation::parse_tag(), protocols::task_operations::SelectResiduesWithinChainOperation::parse_tag(), protocols::task_operations::ThreadSequenceOperation::parse_tag(), protocols::task_operations::DatabaseThread::pick_sequence_from_database(), protocols::task_operations::ResidueProbDesignOperation::set_aa_probabilities_from_file(), protocols::task_operations::DsspDesignOperation::set_default_sse_residues(), protocols::task_operations::RestrictAAsFromProbabilities::set_use_cached_data(), and protocols::task_operations::ConservativeDesignOperation::skip_resid().

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