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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  RestrictByCalculatorsOperation
 
class  RestrictByCalculatorsOperationCreator
 
class  RestrictChainToRepackingOperation
 
class  RestrictChainToRepackingOperationCreator
 
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  RestrictConservedLowDdgOperationCreator
 
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  SeqprofConsensusOperationCreator
 
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
 
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

typedef utility::pointer::shared_ptr< DatabaseThread const > protocols::task_operations::DatabaseThreadCOP
typedef utility::pointer::shared_ptr< DatabaseThread > protocols::task_operations::DatabaseThreadOP
typedef utility::pointer::shared_ptr< DesignAroundOperation const > protocols::task_operations::DesignAroundOperationCOP
typedef utility::pointer::shared_ptr< InteractingRotamerOperation const > protocols::task_operations::InteractingRotamerOperationCOP
typedef utility::pointer::shared_ptr< InteractingRotamerOperation > protocols::task_operations::InteractingRotamerOperationOP
typedef utility::pointer::shared_ptr< LinkResidues const > protocols::task_operations::LinkResiduesCOP
typedef utility::pointer::shared_ptr< LinkResidues > protocols::task_operations::LinkResiduesOP
typedef utility::pointer::shared_ptr< ModifyAnnealer const > protocols::task_operations::ModifyAnnealerCOP
typedef utility::pointer::shared_ptr< ModifyAnnealer > protocols::task_operations::ModifyAnnealerOP
typedef utility::pointer::shared_ptr< ReadResfileFromDB > protocols::task_operations::ReadResfileFromDBOP
typedef utility::pointer::shared_ptr< SelectBySASAOperation const > protocols::task_operations::SelectBySASAOperationCOP
typedef utility::pointer::shared_ptr< SetIGTypeOperation const > protocols::task_operations::SetIGTypeOperationCOP
typedef utility::pointer::shared_ptr< STMStoredTask const > protocols::task_operations::STMStoredTaskCOP
typedef utility::pointer::shared_ptr< STMStoredTask > protocols::task_operations::STMStoredTaskOP
typedef utility::pointer::shared_ptr< StoreTaskMover const > protocols::task_operations::StoreTaskMoverCOP
typedef utility::pointer::shared_ptr< StoreTaskMover > protocols::task_operations::StoreTaskMoverOP

Enumeration Type Documentation

Enumerator
AND 
OR 
XOR 
NOR 
NAND 
ORNOT 
ANDNOT 
NOT 

Function Documentation

std::string protocols::task_operations::dsspdo_group_name ( )
std::string protocols::task_operations::dsspdo_subelement_ct_name ( std::string const &  name)
std::string protocols::task_operations::linkres_subelement_ctname ( std::string const &  name)
std::string protocols::task_operations::linkres_subelement_group ( )
std::string protocols::task_operations::rtas_subelement_ct_naming_function ( std::string const &  name)
static basic::Tracer protocols::task_operations::TR ( "protocols.task_operations.STMStoredTask"  )
static
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::SelectBySASAOperation::apply(), protocols::task_operations::SelectByDensityFitOperation::apply(), protocols::task_operations::SelectByDeltaScoreOperation::apply(), protocols::task_operations::DatabaseThread::apply(), protocols::task_operations::SelectResiduesWithinChainOperation::apply(), protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::apply(), protocols::task_operations::RestrictToAlignedSegmentsOperation::apply(), protocols::task_operations::AlignedThreadOperation::apply(), protocols::task_operations::CrystalContactsOperation::apply(), protocols::task_operations::RestrictIdentitiesOperation::apply(), protocols::task_operations::RestrictResiduesToRepackingOperation::apply(), protocols::task_operations::ReadResfileFromDB::apply(), protocols::task_operations::LinkResidues::apply(), protocols::task_operations::ResidueProbDesignOperation::apply(), protocols::task_operations::RestrictNativeResiduesOperation::apply(), protocols::task_operations::SequenceMotifTaskOperation::apply(), protocols::task_operations::ProteinInterfaceDesignOperation::apply(), protocols::task_operations::JointSequenceOperation::apply(), protocols::task_operations::RestrictToInterfaceVectorOperation::apply(), protocols::task_operations::DsspDesignOperation::apply(), protocols::task_operations::StoreCompoundTaskMover::CompoundDesignableTask(), protocols::task_operations::StoreCompoundTaskMover::CompoundPackableTask(), 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::ProteinCore::parse_tag(), protocols::task_operations::SelectResiduesWithinChainOperation::parse_tag(), protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::parse_tag(), protocols::task_operations::AlignedThreadOperation::parse_tag(), protocols::task_operations::ThreadSequenceOperation::parse_tag(), protocols::task_operations::RestrictIdentitiesOperation::parse_tag(), protocols::task_operations::PreventResiduesFromRepackingOperation::parse_tag(), protocols::task_operations::DesignAroundOperation::parse_tag(), protocols::task_operations::RestrictNativeResiduesOperation::parse_tag(), protocols::task_operations::RestrictResiduesToRepackingOperation::parse_tag(), protocols::task_operations::LinkResidues::parse_tag(), protocols::task_operations::JointSequenceOperation::parse_tag(), protocols::task_operations::RestrictToInterfaceVectorOperation::parse_tag(), protocols::task_operations::DsspDesignOperation::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(), and protocols::task_operations::ConservativeDesignOperation::skip_resid().