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core::pack::task::operation::TaskOperation Class Referenceabstract

#include <TaskOperation.hh>

Inherits VirtualBase.

Inherited by core::pack::task::operation::AppendResidueRotamerSet, core::pack::task::operation::AppendRotamer, core::pack::task::operation::AppendRotamerSet, core::pack::task::operation::ClashBasedRepackShell, core::pack::task::operation::DesignRestrictions, core::pack::task::operation::DisallowIfNonnative, core::pack::task::operation::EnableMultiCoolAnnealer, core::pack::task::operation::EnableSmartAnnealer, core::pack::task::operation::ExtraChiCutoff, core::pack::task::operation::ExtraRotamers, core::pack::task::operation::ExtraRotamersGeneric, core::pack::task::operation::FillAUTOTaskOperation, core::pack::task::operation::IncludeCurrent, core::pack::task::operation::InitializeExtraRotsFromCommandline, core::pack::task::operation::InitializeFromCommandline, core::pack::task::operation::InitializeFromOptionCollection, core::pack::task::operation::KeepSequenceSymmetry, core::pack::task::operation::NoRepackDisulfides, core::pack::task::operation::OperateOnCertainResidues, core::pack::task::operation::OperateOnResidueSubset, core::pack::task::operation::OptCysHG, core::pack::task::operation::OptH, core::pack::task::operation::PreserveCBeta, core::pack::task::operation::PreventRepacking, core::pack::task::operation::ProhibitResidueProperties, core::pack::task::operation::ProhibitSpecifiedBaseResidueTypes, core::pack::task::operation::ReadResfile, core::pack::task::operation::ReplicateTask, core::pack::task::operation::RestrictAbsentCanonicalAAS, core::pack::task::operation::RestrictInteractionGraphThreadsOperation, core::pack::task::operation::RestrictResidueToRepacking, core::pack::task::operation::RestrictToRepacking, core::pack::task::operation::RestrictToResidueProperties, core::pack::task::operation::RestrictToSpecifiedBaseResidueTypes, core::pack::task::operation::RestrictYSDesign, core::pack::task::operation::RotamerExplosion, core::pack::task::operation::SetRotamerCouplings, core::pack::task::operation::SetRotamerLinks, core::pack::task::operation::UseMultiCoolAnnealer, protocols::antibody::task_operations::AddCDRProfileSetsOperation, protocols::antibody::task_operations::AddCDRProfilesOperation, protocols::antibody::task_operations::DisableAntibodyRegionOperation, protocols::antibody::task_operations::DisableCDRsOperation, protocols::antibody::task_operations::RestrictToCDRsAndNeighbors, protocols::denovo_design::task_operations::ConsensusLoopDesignOperation, protocols::dna::RestrictDesignToProteinDNAInterface, protocols::dna::WatsonCrickRotamerCouplings, protocols::enzdes::AddLigandMotifRotamers, protocols::enzdes::AddRigidBodyLigandConfs, protocols::enzdes::DetectProteinLigandInterface, protocols::enzdes::ProteinLigandInterfaceUpweighter, protocols::enzdes::SetCatalyticResPackBehavior, protocols::flxbb::CombinedTaskOperation, protocols::flxbb::LayerDesignOperation, protocols::forge::remodel::RemodelRotamerLinks, protocols::hbnet::ConstrainHBondNetwork, protocols::hotspot_hashing::AddSearchPatternRotSetOp, protocols::legacy_sewing::LegacyReadNativeRotamersFile, protocols::matdes::BuildingBlockInterfaceOperation, protocols::optimize_weights::ScaleAnnealerTemperatureOperation, protocols::pack_interface::ProteinProteinInterfaceUpweighter, protocols::simple_task_operations::DockingNoRepack1, protocols::simple_task_operations::DockingNoRepack2, protocols::simple_task_operations::InterfaceTaskOperation, protocols::simple_task_operations::RestrictToLoops, protocols::splice::SampleRotamersFromPDB, protocols::symmetric_docking::SymRestrictTaskForDocking, protocols::task_operations::ConservativeDesignOperation, protocols::task_operations::CrystalContactsOperation, protocols::task_operations::DsspDesignOperation, protocols::task_operations::ImportUnboundRotamersOperation, protocols::task_operations::InteractingRotamerExplosion, protocols::task_operations::JointSequenceOperation, protocols::task_operations::LimitAromaChi2Operation, protocols::task_operations::LinkResidues, protocols::task_operations::ModifyAnnealer, protocols::task_operations::MutationSetDesignOperation, protocols::task_operations::pHVariantTaskOperation, protocols::task_operations::PruneBuriedUnsatsOperation, protocols::task_operations::ReadResfileFromDB, protocols::task_operations::ResfileCommandOperation, protocols::task_operations::ResidueProbDesignOperation, protocols::task_operations::RestrictIdentitiesOperation, protocols::task_operations::RestrictInterGroupVectorOperation, protocols::task_operations::RestrictNativeResiduesOperation, protocols::task_operations::RestrictNonSurfaceToRepackingOperation, protocols::task_operations::RestrictOperationsBase, protocols::task_operations::RestrictToCDRH3Loop, protocols::task_operations::RestrictToMoveMapChiOperation, protocols::task_operations::RestrictToTerminiOperation, protocols::task_operations::RetrieveStoredTaskOperation, protocols::task_operations::SelectByDeltaScoreOperation, protocols::task_operations::SelectByDensityFitOperation, protocols::task_operations::SelectBySASAOperation, protocols::task_operations::SeqprofConsensusOperation, protocols::task_operations::SequenceMotifTaskOperation, and protocols::task_operations::SetIGTypeOperation.

Public Types

typedef utility::tag::TagCOP TagCOP
 
typedef basic::datacache::DataMap DataMap
 
typedef pose::Pose Pose
 

Public Member Functions

 ~TaskOperation () override
 
virtual TaskOperationOP clone () const =0
 Create another task operation of the type matching the most-derived version of the class. More...
 
virtual void apply (Pose const &, PackerTask &) const =0
 Change a packer task in some way. The input pose is the one to which the input task will be later applied. More...
 
virtual void parse_tag (TagCOP, DataMap &)
 Used to parse an xml-like tag to load parameters and properties. More...
 
virtual bool task_operation_provides_citation_info () const
 Does this task operation provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool task_operation_is_unpublished () const
 Does this task_operation indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Member Typedef Documentation

typedef basic::datacache::DataMap core::pack::task::operation::TaskOperation::DataMap

Constructor & Destructor Documentation

core::pack::task::operation::TaskOperation::~TaskOperation ( )
overridedefault

Member Function Documentation

virtual void core::pack::task::operation::TaskOperation::apply ( Pose const &  ,
PackerTask  
) const
pure virtual

Change a packer task in some way. The input pose is the one to which the input task will be later applied.

Implemented in core::pack::task::operation::ExtraChiCutoff, core::pack::task::operation::ExtraRotamers, core::pack::task::operation::RestrictYSDesign, core::pack::task::operation::PreventRepacking, core::pack::task::operation::PreserveCBeta, core::pack::task::operation::AppendResidueRotamerSet, core::pack::task::operation::AppendRotamerSet, core::pack::task::operation::AppendRotamer, core::pack::task::operation::SetRotamerLinks, core::pack::task::operation::SetRotamerCouplings, core::pack::task::operation::ReadResfileAndObeyLengthEvents, core::pack::task::operation::ReadResfile, core::pack::task::operation::ExtraRotamersGeneric, core::pack::task::operation::IncludeCurrent, core::pack::task::operation::InitializeExtraRotsFromCommandline, core::pack::task::operation::InitializeFromOptionCollection, core::pack::task::operation::UseMultiCoolAnnealer, core::pack::task::operation::InitializeFromCommandline, core::pack::task::operation::RotamerExplosion, protocols::flxbb::CombinedTaskOperation, core::pack::task::operation::DisallowIfNonnative, protocols::enzdes::AddLigandMotifRotamers, core::pack::task::operation::RestrictAbsentCanonicalAAS, protocols::enzdes::AddRigidBodyLigandConfs, core::pack::task::operation::RestrictResidueToRepacking, protocols::flxbb::LayerDesignOperation, core::pack::task::operation::RestrictToRepacking, protocols::enzdes::ProteinLigandInterfaceUpweighter, protocols::denovo_design::task_operations::ConsensusLoopDesignOperation, protocols::splice::SampleRotamersFromPDB, protocols::task_operations::LimitAromaChi2Operation, core::pack::task::operation::ProhibitResidueProperties, protocols::optimize_weights::ScaleAnnealerTemperatureOperation, protocols::task_operations::RestrictConservedLowDdgOperation, protocols::simple_task_operations::RestrictToInterface, core::pack::task::operation::RestrictToResidueProperties, protocols::task_operations::PruneBuriedUnsatsOperation, core::pack::task::operation::DesignRestrictions, protocols::task_operations::DsspDesignOperation, core::pack::task::operation::ProhibitSpecifiedBaseResidueTypes, protocols::antibody::task_operations::AddCDRProfilesOperation, protocols::simple_task_operations::DockingNoRepack2, protocols::enzdes::DetectProteinLigandInterface, protocols::antibody::task_operations::RestrictToCDRsAndNeighbors, protocols::legacy_sewing::LegacyReadRepeatNativeRotamersFile, protocols::task_operations::RestrictInterGroupVectorOperation, protocols::antibody::task_operations::AddCDRProfileSetsOperation, protocols::task_operations::RestrictToInterfaceVectorOperation, protocols::task_operations::RestrictToMoveMapChiOperation, protocols::hotspot_hashing::AddSearchPatternRotSetOp, protocols::simple_task_operations::DockingNoRepack1, protocols::task_operations::ImportUnboundRotamersOperation, protocols::antibody::task_operations::DisableCDRsOperation, protocols::task_operations::SeqprofConsensusOperation, core::pack::task::operation::ClashBasedRepackShell, core::pack::task::operation::OptH, protocols::antibody::task_operations::DisableAntibodyRegionOperation, core::pack::task::operation::RestrictToSpecifiedBaseResidueTypes, core::pack::task::operation::OptCysHG, core::pack::task::operation::RestrictInteractionGraphThreadsOperation, core::pack::task::operation::NoRepackDisulfides, protocols::task_operations::JointSequenceOperation, protocols::task_operations::ProteinInterfaceDesignOperation, protocols::task_operations::RestrictToNeighborhoodOperation, core::pack::task::operation::OperateOnResidueSubset, protocols::task_operations::SequenceMotifTaskOperation, protocols::simple_task_operations::RestrictToLoops, protocols::task_operations::RestrictNativeResiduesOperation, core::pack::task::operation::OperateOnCertainResidues, protocols::task_operations::MutationSetDesignOperation, protocols::task_operations::ResidueProbDesignOperation, protocols::simple_task_operations::RestrictToLoopsAndNeighbors, protocols::task_operations::LinkResidues, protocols::task_operations::ResfileCommandOperation, protocols::task_operations::RestrictToTerminiOperation, core::pack::task::operation::ReplicateTask, protocols::splice::DesignInterfacesOperation, protocols::task_operations::DesignAroundOperation, protocols::task_operations::PreventResiduesFromRepackingOperation, protocols::task_operations::ReadResfileFromDB, protocols::task_operations::RestrictResiduesToRepackingOperation, protocols::task_operations::RestrictIdentitiesOperation, protocols::enzdes::SetCatalyticResPackBehavior, protocols::matdes::BuildingBlockInterfaceOperation, protocols::task_operations::ConservativeDesignOperation, protocols::task_operations::ThreadSequenceOperation, core::pack::task::operation::EnableMultiCoolAnnealer, core::pack::task::operation::EnableSmartAnnealer, protocols::pack_interface::ProteinProteinInterfaceUpweighter, protocols::task_operations::CrystalContactsOperation, protocols::task_operations::RestrictToInterfaceOperation, core::pack::task::operation::FillAUTOTaskOperation, core::pack::task::operation::KeepSequenceSymmetry, protocols::task_operations::pHVariantTaskOperation, protocols::task_operations::PreventChainFromRepackingOperation, protocols::hbnet::ConstrainHBondNetwork, protocols::task_operations::AlignedThreadOperation, protocols::task_operations::InteractingRotamerExplosion, protocols::task_operations::RestrictToAlignedSegmentsOperation, protocols::task_operations::RestrictToCDRH3Loop, protocols::dna::RestrictDesignToProteinDNAInterface, protocols::task_operations::RestrictByCalculatorsOperation, protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation, protocols::task_operations::RestrictNonSurfaceToRepackingOperation, protocols::task_operations::RestrictChainToRepackingOperation, protocols::task_operations::RetrieveStoredTaskOperation, protocols::task_operations::SelectResiduesWithinChainOperation, protocols::legacy_sewing::LegacyReadNativeRotamersFile, protocols::splice::FindEndpointsOperation, protocols::task_operations::DatabaseThread, protocols::task_operations::ModifyAnnealer, protocols::task_operations::SelectByDeltaScoreOperation, protocols::task_operations::SetIGTypeOperation, protocols::task_operations::SelectByDensityFitOperation, protocols::task_operations::SelectBySASAOperation, protocols::symmetric_docking::SymRestrictTaskForDocking, protocols::task_operations::RestrictOperationsBase, protocols::dna::WatsonCrickRotamerCouplings, and protocols::forge::remodel::RemodelRotamerLinks.

virtual TaskOperationOP core::pack::task::operation::TaskOperation::clone ( ) const
pure virtual

Create another task operation of the type matching the most-derived version of the class.

Implemented in core::pack::task::operation::ExtraChiCutoff, core::pack::task::operation::ExtraRotamers, core::pack::task::operation::RestrictYSDesign, core::pack::task::operation::PreventRepacking, core::pack::task::operation::PreserveCBeta, core::pack::task::operation::AppendResidueRotamerSet, core::pack::task::operation::AppendRotamerSet, core::pack::task::operation::AppendRotamer, core::pack::task::operation::SetRotamerLinks, core::pack::task::operation::SetRotamerCouplings, core::pack::task::operation::ReadResfileAndObeyLengthEvents, core::pack::task::operation::ReadResfile, core::pack::task::operation::ExtraRotamersGeneric, core::pack::task::operation::IncludeCurrent, core::pack::task::operation::InitializeExtraRotsFromCommandline, core::pack::task::operation::InitializeFromOptionCollection, core::pack::task::operation::UseMultiCoolAnnealer, core::pack::task::operation::InitializeFromCommandline, core::pack::task::operation::RotamerExplosion, protocols::flxbb::CombinedTaskOperation, core::pack::task::operation::DisallowIfNonnative, protocols::enzdes::AddLigandMotifRotamers, core::pack::task::operation::RestrictAbsentCanonicalAAS, core::pack::task::operation::RestrictResidueToRepacking, protocols::enzdes::AddRigidBodyLigandConfs, core::pack::task::operation::RestrictToRepacking, protocols::denovo_design::task_operations::ConsensusLoopDesignOperation, protocols::enzdes::ProteinLigandInterfaceUpweighter, protocols::splice::SampleRotamersFromPDB, core::pack::task::operation::ProhibitResidueProperties, protocols::optimize_weights::ScaleAnnealerTemperatureOperation, protocols::task_operations::ResidueProbDesignOperation, protocols::simple_task_operations::RestrictToInterface, protocols::task_operations::RestrictConservedLowDdgOperation, core::pack::task::operation::RestrictToResidueProperties, protocols::task_operations::LimitAromaChi2Operation, protocols::task_operations::MutationSetDesignOperation, protocols::flxbb::LayerDesignOperation, protocols::task_operations::PruneBuriedUnsatsOperation, core::pack::task::operation::ProhibitSpecifiedBaseResidueTypes, protocols::task_operations::ConservativeDesignOperation, core::pack::task::operation::DesignRestrictions, protocols::simple_task_operations::DockingNoRepack2, protocols::enzdes::DetectProteinLigandInterface, protocols::legacy_sewing::LegacyReadRepeatNativeRotamersFile, protocols::antibody::task_operations::AddCDRProfilesOperation, protocols::task_operations::RestrictToInterfaceVectorOperation, protocols::task_operations::RestrictToMoveMapChiOperation, protocols::hotspot_hashing::AddSearchPatternRotSetOp, protocols::simple_task_operations::DockingNoRepack1, protocols::antibody::task_operations::RestrictToCDRsAndNeighbors, protocols::task_operations::DsspDesignOperation, protocols::task_operations::RestrictInterGroupVectorOperation, protocols::task_operations::ImportUnboundRotamersOperation, core::pack::task::operation::ClashBasedRepackShell, core::pack::task::operation::RestrictToSpecifiedBaseResidueTypes, core::pack::task::operation::OptH, protocols::antibody::task_operations::AddCDRProfileSetsOperation, protocols::task_operations::SeqprofConsensusOperation, core::pack::task::operation::OperateOnResidueSubset, core::pack::task::operation::OptCysHG, protocols::task_operations::ProteinInterfaceDesignOperation, protocols::task_operations::RestrictToNeighborhoodOperation, core::pack::task::operation::NoRepackDisulfides, protocols::antibody::task_operations::DisableCDRsOperation, core::pack::task::operation::OperateOnCertainResidues, protocols::antibody::task_operations::DisableAntibodyRegionOperation, protocols::task_operations::JointSequenceOperation, protocols::task_operations::LinkResidues, protocols::task_operations::RestrictNativeResiduesOperation, protocols::task_operations::RestrictToTerminiOperation, core::pack::task::operation::ReplicateTask, core::pack::task::operation::RestrictInteractionGraphThreadsOperation, protocols::task_operations::DesignAroundOperation, protocols::task_operations::PreventResiduesFromRepackingOperation, protocols::task_operations::ReadResfileFromDB, protocols::task_operations::RestrictResiduesToRepackingOperation, protocols::splice::DesignInterfacesOperation, protocols::simple_task_operations::RestrictToLoopsAndNeighbors, protocols::task_operations::SequenceMotifTaskOperation, protocols::enzdes::SetCatalyticResPackBehavior, protocols::matdes::BuildingBlockInterfaceOperation, protocols::task_operations::CrystalContactsOperation, protocols::task_operations::InteractingRotamerExplosion, protocols::task_operations::RestrictToInterfaceOperation, protocols::hbnet::ConstrainHBondNetwork, protocols::pack_interface::ProteinProteinInterfaceUpweighter, protocols::simple_task_operations::RestrictToLoops, protocols::task_operations::PreventChainFromRepackingOperation, protocols::dna::RestrictDesignToProteinDNAInterface, protocols::task_operations::AlignedThreadOperation, protocols::task_operations::RestrictNonSurfaceToRepackingOperation, protocols::task_operations::RestrictToAlignedSegmentsOperation, protocols::task_operations::RestrictToCDRH3Loop, protocols::task_operations::ThreadSequenceOperation, protocols::task_operations::RestrictByCalculatorsOperation, protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation, protocols::task_operations::ResfileCommandOperation, protocols::task_operations::RestrictChainToRepackingOperation, protocols::task_operations::DatabaseThread, protocols::task_operations::RetrieveStoredTaskOperation, protocols::task_operations::SelectResiduesWithinChainOperation, protocols::legacy_sewing::LegacyReadNativeRotamersFile, protocols::task_operations::ModifyAnnealer, protocols::task_operations::RestrictIdentitiesOperation, protocols::task_operations::SelectByDeltaScoreOperation, protocols::splice::FindEndpointsOperation, protocols::task_operations::SetIGTypeOperation, core::pack::task::operation::EnableMultiCoolAnnealer, core::pack::task::operation::EnableSmartAnnealer, core::pack::task::operation::FillAUTOTaskOperation, core::pack::task::operation::KeepSequenceSymmetry, protocols::symmetric_docking::SymRestrictTaskForDocking, protocols::task_operations::SelectByDensityFitOperation, protocols::task_operations::SelectBySASAOperation, protocols::task_operations::pHVariantTaskOperation, protocols::task_operations::RestrictOperationsBase, protocols::dna::WatsonCrickRotamerCouplings, and protocols::forge::remodel::RemodelRotamerLinks.

void core::pack::task::operation::TaskOperation::parse_tag ( TagCOP  tag,
DataMap  
)
virtual

Used to parse an xml-like tag to load parameters and properties.

Reimplemented in core::pack::task::operation::ExtraChiCutoff, core::pack::task::operation::ExtraRotamers, core::pack::task::operation::PreventRepacking, core::pack::task::operation::ReadResfileAndObeyLengthEvents, core::pack::task::operation::ReadResfile, core::pack::task::operation::ExtraRotamersGeneric, core::pack::task::operation::InitializeFromOptionCollection, core::pack::task::operation::UseMultiCoolAnnealer, core::pack::task::operation::InitializeFromCommandline, core::pack::task::operation::RotamerExplosion, core::pack::task::operation::DisallowIfNonnative, core::pack::task::operation::RestrictAbsentCanonicalAAS, protocols::enzdes::AddLigandMotifRotamers, core::pack::task::operation::RestrictResidueToRepacking, protocols::enzdes::AddRigidBodyLigandConfs, protocols::denovo_design::task_operations::ConsensusLoopDesignOperation, core::pack::task::operation::RestrictToRepacking, protocols::flxbb::LayerDesignOperation, protocols::enzdes::ProteinLigandInterfaceUpweighter, protocols::splice::SampleRotamersFromPDB, protocols::task_operations::LimitAromaChi2Operation, core::pack::task::operation::ProhibitResidueProperties, protocols::simple_task_operations::RestrictToInterface, protocols::task_operations::RestrictConservedLowDdgOperation, core::pack::task::operation::RestrictToResidueProperties, protocols::task_operations::PruneBuriedUnsatsOperation, protocols::task_operations::DsspDesignOperation, core::pack::task::operation::ProhibitSpecifiedBaseResidueTypes, core::pack::task::operation::DesignRestrictions, protocols::enzdes::DetectProteinLigandInterface, protocols::task_operations::RestrictToInterfaceVectorOperation, core::pack::task::operation::OperateOnResidueSubset, protocols::antibody::task_operations::AddCDRProfilesOperation, protocols::task_operations::ImportUnboundRotamersOperation, protocols::antibody::task_operations::RestrictToCDRsAndNeighbors, core::pack::task::operation::OperateOnCertainResidues, protocols::hotspot_hashing::AddSearchPatternRotSetOp, core::pack::task::operation::ClashBasedRepackShell, core::pack::task::operation::RestrictToSpecifiedBaseResidueTypes, protocols::dna::RestrictDesignToProteinDNAInterface, protocols::task_operations::ReadResfileFromDB, protocols::antibody::task_operations::AddCDRProfileSetsOperation, protocols::task_operations::ProteinInterfaceDesignOperation, protocols::task_operations::SeqprofConsensusOperation, protocols::antibody::task_operations::DisableCDRsOperation, protocols::antibody::task_operations::DisableAntibodyRegionOperation, protocols::task_operations::JointSequenceOperation, protocols::task_operations::RestrictToTerminiOperation, protocols::task_operations::ResidueProbDesignOperation, protocols::task_operations::LinkResidues, protocols::task_operations::RestrictResiduesToRepackingOperation, core::pack::task::operation::RestrictInteractionGraphThreadsOperation, protocols::legacy_sewing::LegacyReadNativeRotamersFile, protocols::task_operations::RestrictNativeResiduesOperation, protocols::splice::DesignInterfacesOperation, protocols::task_operations::DesignAroundOperation, protocols::task_operations::PreventResiduesFromRepackingOperation, protocols::task_operations::ConservativeDesignOperation, protocols::enzdes::SetCatalyticResPackBehavior, protocols::matdes::BuildingBlockInterfaceOperation, protocols::task_operations::RestrictIdentitiesOperation, protocols::task_operations::ThreadSequenceOperation, protocols::pack_interface::ProteinProteinInterfaceUpweighter, protocols::task_operations::CrystalContactsOperation, protocols::task_operations::SequenceMotifTaskOperation, protocols::simple_task_operations::RestrictToLoopsAndNeighbors, protocols::task_operations::PreventChainFromRepackingOperation, protocols::task_operations::RestrictChainToRepackingOperation, protocols::hbnet::ConstrainHBondNetwork, protocols::task_operations::AlignedThreadOperation, protocols::task_operations::RestrictToAlignedSegmentsOperation, protocols::simple_task_operations::RestrictToLoops, protocols::task_operations::InteractingRotamerExplosion, protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation, protocols::task_operations::SelectResiduesWithinChainOperation, protocols::task_operations::RestrictNonSurfaceToRepackingOperation, protocols::task_operations::ResfileCommandOperation, protocols::splice::FindEndpointsOperation, protocols::task_operations::RetrieveStoredTaskOperation, protocols::task_operations::ModifyAnnealer, protocols::task_operations::SelectBySASAOperation, protocols::task_operations::DatabaseThread, protocols::task_operations::SelectByDeltaScoreOperation, protocols::task_operations::SetIGTypeOperation, core::pack::task::operation::EnableMultiCoolAnnealer, core::pack::task::operation::EnableSmartAnnealer, protocols::task_operations::SelectByDensityFitOperation, core::pack::task::operation::FillAUTOTaskOperation, core::pack::task::operation::KeepSequenceSymmetry, protocols::task_operations::pHVariantTaskOperation, protocols::dna::WatsonCrickRotamerCouplings, and protocols::forge::remodel::RemodelRotamerLinks.

References core::pack::task::operation::TR().

utility::vector1< basic::citation_manager::UnpublishedModuleInfoCOP > core::pack::task::operation::TaskOperation::provide_authorship_info_for_unpublished ( ) const
virtual

Provide a list of authors and their e-mail addresses, as strings.

Returns
A list of pairs of (author, e-mail address). Empty list if not unpublished.
Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)
utility::vector1< basic::citation_manager::CitationCollectionCOP > core::pack::task::operation::TaskOperation::provide_citation_info ( ) const
virtual

Provide the citation.

Returns
A vector of citation collections. This allows the task operation to provide citations for itself and for any modules that it invokes.

The default implementation of this function provides an empty vector. It may be overriden by task operations wishing to provide citation information.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)
bool core::pack::task::operation::TaskOperation::task_operation_is_unpublished ( ) const
virtual

Does this task_operation indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)?

Defaults to false. Derived classes may override this to provide authorship info. If set to true, the provide_authorship_info_for_unpublished() override should also be provided.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)
bool core::pack::task::operation::TaskOperation::task_operation_provides_citation_info ( ) const
virtual

Does this task operation provide information about how to cite it?

Defaults to false. Derived classes may override this to provide citation info. If set to true, the provide_citation_info() override should also be provided.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

The documentation for this class was generated from the following files: