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core::pack::task::operation Namespace Reference

Classes

class  AddBehaviorRLT
 
class  AddBehaviorRLTCreator
 
class  AllResFilter
 
class  AllResFilterCreator
 
class  AnyResFilter
 
class  AnyResFilterCreator
 
class  AppendResidueRotamerSet
 Apply rotamerSetOperation to only the rotamerSet for the given residue. More...
 
class  AppendResidueRotamerSetCreator
 
class  AppendRotamer
 when a PackerTask is created by the Factory, the RotamerOperation will be given to it More...
 
class  AppendRotamerCreator
 
class  AppendRotamerSet
 when a PackerTask is created by the Factory, the RotamerSetOperation will be given to it More...
 
class  AppendRotamerSetCreator
 
class  ChainIs
 
class  ChainIsCreator
 
class  ChainIsnt
 
class  ChainIsntCreator
 
class  ClashBasedRepackShell
 Create a shell of residues that can repack around a smaller group of residues being repacked or designed. More...
 
class  ClashBasedRepackShellCreator
 
class  DesignRestrictions
 Combine a set of ResidueSelectors and ResidueLevelTaskOperations concisely, using boolean logic to join selectors concisely. More...
 
class  DesignRestrictionsCreator
 
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  DisallowIfNonnativeCreator
 
class  DisallowIfNonnativeRLT
 
class  DisallowIfNonnativeRLTCreator
 
class  EnableMultiCoolAnnealer
 Task Operation for turning on the multi-cool annealer. More...
 
class  EnableMultiCoolAnnealerCreator
 
class  EnableSmartAnnealer
 Task Operation for turning on the multi-cool annealer. More...
 
class  EnableSmartAnnealerCreator
 
class  ExtraChiCutoff
 ExtraChiCutoff (correponding to flag "-extrachi_cutoff <float>" ) More...
 
class  ExtraChiCutoffCreator
 
class  ExtraChiCutoffRLT
 
class  ExtraChiCutoffRLTCreator
 
class  ExtraRotamers
 ExtraRotamer for a residue. You know, -ex1, -ex2, all that. More...
 
struct  ExtraRotamerSamplingData
 
class  ExtraRotamersCreator
 
class  ExtraRotamersGeneric
 
class  ExtraRotamersGenericCreator
 
class  ExtraRotamersGenericRLT
 
class  ExtraRotamersGenericRLTCreator
 
class  FillAUTOTaskOperation
 fills the AUTO behavior for all residues in Task. Useful if a protocol expects AUTO-style resfile, but no resfile present. More...
 
class  FillAUTOTaskOperationCreator
 
class  IncludeCurrent
 
class  IncludeCurrentCreator
 
class  IncludeCurrentRLT
 
class  IncludeCurrentRLTCreator
 
class  InitializeExtraRotsFromCommandline
 
class  InitializeExtraRotsFromCommandlineCreator
 
class  InitializeFromCommandline
 
class  InitializeFromCommandlineCreator
 
class  InitializeFromOptionCollection
 retrieves an OptionCollection from the DataMap. More...
 
class  InitializeFromOptionCollectionCreator
 
class  KeepSequenceSymmetry
 Task Operation for turning on the multi-cool annealer. More...
 
class  KeepSequenceSymmetryCreator
 
class  NoRepackDisulfides
 prevent disulfides from being repacked; assume disulfides info in Pose is up-to-date More...
 
class  NoRepackDisulfidesCreator
 
class  NoResFilter
 
class  NoResFilterCreator
 
class  OperateOnCertainResidues
 
class  OperateOnCertainResiduesCreator
 
class  OperateOnResidueSubset
 Class, much like the OperateOnCertainResidues task operation, to apply a particular residue-level task operation on the residues identified by a ResidueSelector (Or a pre-selected subset). More...
 
class  OperateOnResidueSubsetCreator
 
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  PreserveCBeta
 
class  PreserveCBetaCreator
 
class  PreserveCBetaRLT
 
class  PreserveCBetaRLTCreator
 
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  PreventRepackingCreator
 
class  PreventRepackingRLT
 
class  PreventRepackingRLTCreator
 
class  ProhibitResidueProperties
 Restrict the palette of ResidueTypes to those with the given properties. More...
 
class  ProhibitResiduePropertiesCreator
 
class  ProhibitSpecifiedBaseResidueTypes
 Prohibit the base ResidueTypes provided by name from the palette of ResidueTypes. More...
 
class  ProhibitSpecifiedBaseResidueTypesCreator
 
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  ReadResfileAndObeyLengthEventsCreator
 
class  ReadResfileCreator
 
class  ReplicateTask
 
class  ResFilter
 
class  ResFilterComposition
 
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  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  ResidueHasPropertyCreator
 
class  ResidueIndexIs
 
class  ResidueIndexIsCreator
 
class  ResidueIndexIsnt
 
class  ResidueIndexIsntCreator
 
class  ResidueLacksProperty
 
class  ResidueLacksPropertyCreator
 
class  ResidueName3Is
 
class  ResidueName3IsCreator
 
class  ResidueName3Isnt
 
class  ResidueName3IsntCreator
 
class  ResiduePDBIndexIs
 
class  ResiduePDBIndexIsCreator
 
class  ResiduePDBIndexIsnt
 
class  ResiduePDBIndexIsntCreator
 
class  ResiduePDBInfoHasLabel
 
class  ResiduePDBInfoHasLabelCreator
 
class  ResiduePDBInfoLacksLabel
 
class  ResiduePDBInfoLacksLabelCreator
 
class  ResidueTypeFilter
 
class  ResidueTypeFilterCreator
 
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  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  RestrictAbsentCanonicalAAS
 RestrictAbsentCanonicalAAS. More...
 
class  RestrictAbsentCanonicalAASCreator
 
class  RestrictAbsentCanonicalAASExceptNativeRLT
 
class  RestrictAbsentCanonicalAASExceptNativeRLTCreator
 
class  RestrictAbsentCanonicalAASRLT
 
class  RestrictAbsentCanonicalAASRLTCreator
 
class  RestrictInteractionGraphThreadsOperation
 A task operation that restricts the number of threads allowed for interaction graph computation. More...
 
class  RestrictInteractionGraphThreadsOperationCreator
 
class  RestrictResidueToRepacking
 RestrictResidueToRepacking. More...
 
class  RestrictResidueToRepackingCreator
 
class  RestrictToRepacking
 RestrictToRepacking. More...
 
class  RestrictToRepackingCreator
 
class  RestrictToRepackingRLT
 
class  RestrictToRepackingRLTCreator
 
class  RestrictToResidueProperties
 Restrict the palette of ResidueTypes to those with the given properties. More...
 
class  RestrictToResiduePropertiesCreator
 
class  RestrictToSpecifiedBaseResidueTypes
 Restrict the palette of ResidueTypes to the base ResidueTypes provided by name. More...
 
class  RestrictToSpecifiedBaseResidueTypesCreator
 
class  RestrictYSDesign
 RestrictYSDesign restricts positions to a binary Tyr/Ser alphabet. More...
 
class  RestrictYSDesignCreator
 
class  RotamerExplosion
 rotamer explosion for a residue More...
 
class  RotamerExplosionCreator
 
class  SetRotamerCouplings
 
class  SetRotamerCouplingsCreator
 
class  SetRotamerLinks
 
class  SetRotamerLinksCreator
 
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  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  UseMultiCoolAnnealer
 
class  UseMultiCoolAnnealerCreator
 

Typedefs

typedef
utility::pointer::shared_ptr
< ClashBasedRepackShell
ClashBasedRepackShellOP
 ClashBasedRepackShell owning pointer. More...
 
typedef
utility::pointer::shared_ptr
< ClashBasedRepackShell const > 
ClashBasedRepackShellCOP
 ClashBasedRepackShell const owning pointer. More...
 
typedef
utility::pointer::weak_ptr
< ClashBasedRepackShell
ClashBasedRepackShellAP
 ClashBasedRepackShell owning pointer. More...
 
typedef
utility::pointer::weak_ptr
< ClashBasedRepackShell const > 
ClashBasedRepackShellCAP
 ClashBasedRepackShell const owning pointer. More...
 
typedef
utility::pointer::shared_ptr
< DesignRestrictions
DesignRestrictionsOP
 
typedef
utility::pointer::shared_ptr
< DesignRestrictions const > 
DesignRestrictionsCOP
 
typedef
utility::pointer::shared_ptr
< EnableMultiCoolAnnealer
EnableMultiCoolAnnealerOP
 
typedef
utility::pointer::shared_ptr
< EnableMultiCoolAnnealer
const > 
EnableMultiCoolAnnealerCOP
 
using EnableSmartAnnealerOP = utility::pointer::shared_ptr< EnableSmartAnnealer >
 
using EnableSmartAnnealerCOP = utility::pointer::shared_ptr< EnableSmartAnnealer const >
 
typedef
utility::pointer::shared_ptr
< FillAUTOTaskOperation
FillAUTOTaskOperationOP
 
typedef
utility::pointer::shared_ptr
< FillAUTOTaskOperation const > 
FillAUTOTaskOperationCOP
 
using KeepSequenceSymmetryOP = utility::pointer::shared_ptr< KeepSequenceSymmetry >
 
using KeepSequenceSymmetryCOP = utility::pointer::shared_ptr< KeepSequenceSymmetry const >
 
typedef
utility::pointer::shared_ptr
< NoRepackDisulfides
NoRepackDisulfidesOP
 NoRepackDisulfides owning pointer. More...
 
typedef
utility::pointer::shared_ptr
< NoRepackDisulfides const > 
NoRepackDisulfidesCOP
 NoRepackDisulfides const owning pointer. More...
 
typedef
utility::pointer::weak_ptr
< NoRepackDisulfides
NoRepackDisulfidesAP
 NoRepackDisulfides owning pointer. More...
 
typedef
utility::pointer::weak_ptr
< NoRepackDisulfides const > 
NoRepackDisulfidesCAP
 NoRepackDisulfides const owning pointer. More...
 
typedef
utility::pointer::shared_ptr
< OperateOnCertainResidues
OperateOnCertainResiduesOP
 
typedef
utility::pointer::shared_ptr
< OperateOnCertainResidues
OperateOnCertainResiduesCOP
 
typedef
utility::pointer::shared_ptr
< OperateOnResidueSubset
OperateOnResidueSubsetOP
 
typedef
utility::pointer::shared_ptr
< OperateOnResidueSubset
OperateOnResidueSubsetCOP
 
typedef
utility::pointer::shared_ptr
< OptCysHG
OptCysHGOP
 OptCysHG owning pointer. More...
 
typedef
utility::pointer::shared_ptr
< OptCysHG const > 
OptCysHGCOP
 OptCysHG const owning pointer. More...
 
typedef
utility::pointer::weak_ptr
< OptCysHG
OptCysHGAP
 OptCysHG owning pointer. More...
 
typedef
utility::pointer::weak_ptr
< OptCysHG const > 
OptCysHGCAP
 OptCysHG const owning pointer. More...
 
typedef
utility::pointer::shared_ptr
< OptH
OptHOP
 OptH owning pointer. More...
 
typedef
utility::pointer::shared_ptr
< OptH const > 
OptHCOP
 OptH const owning pointer. More...
 
typedef
utility::pointer::weak_ptr
< OptH
OptHAP
 OptH owning pointer. More...
 
typedef
utility::pointer::weak_ptr
< OptH const > 
OptHCAP
 OptH const owning pointer. More...
 
typedef
utility::pointer::shared_ptr
< ReplicateTask
ReplicateTaskOP
 ReplicateTask owning pointer. More...
 
typedef
utility::pointer::shared_ptr
< ReplicateTask const > 
ReplicateTaskCOP
 ReplicateTask const owning pointer. More...
 
typedef
utility::pointer::weak_ptr
< ReplicateTask
ReplicateTaskAP
 ReplicateTask owning pointer. More...
 
typedef
utility::pointer::weak_ptr
< ReplicateTask const > 
ReplicateTaskCAP
 ReplicateTask const owning pointer. More...
 
typedef
utility::pointer::shared_ptr
< ResFilter
ResFilterOP
 
typedef
utility::pointer::shared_ptr
< ResFilter
ResFilterCOP
 
typedef
utility::pointer::shared_ptr
< ResFilterCreator
ResFilterCreatorOP
 
typedef
utility::pointer::shared_ptr
< ResFilterCreator const > 
ResFilterCreatorCOP
 
typedef
utility::pointer::shared_ptr
< ResFilterFactory
ResFilterFactoryOP
 
typedef
utility::pointer::shared_ptr
< ResFilterFactory const > 
ResFilterFactoryCOP
 
typedef
utility::pointer::shared_ptr
< ResidueHasProperty
ResidueHasPropertyOP
 
typedef
utility::pointer::shared_ptr
< ResiduePDBInfoHasLabel
ResiduePDBInfoHasLabelOP
 
typedef
utility::pointer::shared_ptr
< ResidueLacksProperty
ResidueLacksPropertyOP
 
typedef
utility::pointer::shared_ptr
< ResidueName3Is
ResidueName3IsOP
 
typedef
utility::pointer::shared_ptr
< ResidueName3Isnt
ResidueName3IsntOP
 
typedef
utility::pointer::shared_ptr
< ResidueIndexIs
ResidueIndexIsOP
 
typedef
utility::pointer::shared_ptr
< ResidueIndexIsnt
ResidueIndexIsntOP
 
typedef
utility::pointer::shared_ptr
< ResiduePDBIndexIs
ResiduePDBIndexIsOP
 
typedef
utility::pointer::shared_ptr
< ResiduePDBIndexIsnt
ResiduePDBIndexIsntOP
 
typedef
utility::pointer::shared_ptr
< ChainIs
ChainIsOP
 
typedef
utility::pointer::shared_ptr
< ChainIsnt
ChainIsntOP
 
typedef
utility::pointer::shared_ptr
< ResLvlTaskOperation
ResLvlTaskOperationOP
 
typedef
utility::pointer::shared_ptr
< ResLvlTaskOperation const > 
ResLvlTaskOperationCOP
 
typedef
utility::pointer::shared_ptr
< ResLvlTaskOperationCreator
ResLvlTaskOperationCreatorOP
 
typedef
utility::pointer::shared_ptr
< ResLvlTaskOperationCreator
const > 
ResLvlTaskOperationCreatorCOP
 
typedef
utility::pointer::shared_ptr
< ResLvlTaskOperationFactory
ResLvlTaskOperationFactoryOP
 
typedef
utility::pointer::shared_ptr
< ResLvlTaskOperationFactory
const > 
ResLvlTaskOperationFactoryCOP
 
typedef
utility::pointer::shared_ptr
< RestrictToRepackingRLT
RestrictToRepackingRLTOP
 
typedef
utility::pointer::shared_ptr
< RestrictAbsentCanonicalAASRLT
RestrictAbsentCanonicalAASRLTOP
 
typedef
utility::pointer::shared_ptr
< DisallowIfNonnativeRLT
DisallowIfNonnativeRLTOP
 
typedef
utility::pointer::shared_ptr
< PreventRepackingRLT
PreventRepackingRLTOP
 
typedef
utility::pointer::shared_ptr
< AddBehaviorRLT
AddBehaviorRLTOP
 
using RestrictInteractionGraphThreadsOperationOP = utility::pointer::shared_ptr< RestrictInteractionGraphThreadsOperation >
 
using RestrictInteractionGraphThreadsOperationCOP = utility::pointer::shared_ptr< RestrictInteractionGraphThreadsOperation const >
 
typedef
utility::pointer::shared_ptr
< TaskOperation
TaskOperationOP
 
typedef
utility::pointer::shared_ptr
< TaskOperation
TaskOperationCOP
 
typedef
utility::pointer::shared_ptr
< TaskOperationCreator
TaskOperationCreatorOP
 
typedef
utility::pointer::shared_ptr
< TaskOperationCreator const > 
TaskOperationCreatorCOP
 
typedef
utility::pointer::shared_ptr
< TaskOperationFactory
TaskOperationFactoryOP
 
typedef
utility::pointer::shared_ptr
< TaskOperationFactory const > 
TaskOperationFactoryCOP
 
typedef
utility::pointer::shared_ptr
< AppendResidueRotamerSet
AppendResidueRotamerSetOP
 
typedef
utility::pointer::shared_ptr
< AppendRotamer
AppendRotamerOP
 
typedef
utility::pointer::shared_ptr
< AppendRotamerSet
AppendRotamerSetOP
 
typedef
utility::pointer::shared_ptr
< DisallowIfNonnative
DisallowIfNonnativeOP
 
typedef
utility::pointer::shared_ptr
< ExtraChiCutoff
ExtraChiCutoffOP
 
typedef
utility::pointer::shared_ptr
< ExtraRotamers
ExtraRotamersOP
 
typedef
utility::pointer::shared_ptr
< ExtraRotamersGeneric
ExtraRotamersGenericOP
 
typedef
utility::pointer::shared_ptr
< IncludeCurrent
IncludeCurrentOP
 
typedef
utility::pointer::shared_ptr
< InitializeExtraRotsFromCommandline
InitializeExtraRotsFromCommandlineOP
 
typedef
utility::pointer::shared_ptr
< InitializeFromCommandline
InitializeFromCommandlineOP
 
typedef
utility::pointer::shared_ptr
< UseMultiCoolAnnealer
UseMultiCoolAnnealerOP
 
typedef
utility::pointer::shared_ptr
< PreserveCBeta
PreserveCBetaOP
 
typedef
utility::pointer::shared_ptr
< PreventRepacking
PreventRepackingOP
 
typedef
utility::pointer::shared_ptr
< ProhibitResidueProperties
ProhibitResiduePropertiesOP
 
typedef
utility::pointer::shared_ptr
< ProhibitSpecifiedBaseResidueTypes
ProhibitSpecifiedBaseResidueTypesOP
 
typedef
utility::pointer::shared_ptr
< ReadResfile
ReadResfileOP
 
typedef
utility::pointer::shared_ptr
< ReadResfileAndObeyLengthEvents
ReadResfileAndObeyLengthEventsOP
 
typedef
utility::pointer::shared_ptr
< RestrictAbsentCanonicalAAS
RestrictAbsentCanonicalAASOP
 
typedef
utility::pointer::shared_ptr
< RestrictResidueToRepacking
RestrictResidueToRepackingOP
 
typedef
utility::pointer::shared_ptr
< RestrictToRepacking
RestrictToRepackingOP
 
typedef
utility::pointer::shared_ptr
< RestrictToResidueProperties
RestrictToResiduePropertiesOP
 
typedef
utility::pointer::shared_ptr
< RestrictToSpecifiedBaseResidueTypes
RestrictToSpecifiedBaseResidueTypesOP
 
typedef
utility::pointer::shared_ptr
< RestrictYSDesign
RestrictYSDesignOP
 
typedef
utility::pointer::shared_ptr
< RotamerExplosion
RotamerExplosionOP
 
typedef
utility::pointer::shared_ptr
< SetRotamerCouplings
SetRotamerCouplingsOP
 
typedef
utility::pointer::shared_ptr
< SetRotamerLinks
SetRotamerLinksOP
 

Functions

static basic::Tracer TR ("core.pack.task.operation.ClashBasedRepackShell")
 
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.OperateOnResidueSubset", t_info)
 
std::string const & rlto_datamap_category ()
 
void parse_residue_level_task_operations (utility::tag::TagCOP const &tag, basic::datacache::DataMap &dm, std::list< core::pack::task::operation::ResLvlTaskOperationOP > &rltos)
 
void parse_residue_level_task_operations (utility::tag::TagCOP const &tag, basic::datacache::DataMap &dm, std::list< core::pack::task::operation::ResLvlTaskOperationCOP > &rltos)
 
void attributes_for_parse_residue_level_operations (utility::tag::AttributeList &attributes)
 
static basic::Tracer TR ("core.pack.task.operation.ResFilters")
 
static basic::Tracer TR ("core.pack.task.operation.ResLvlTaskOperations", basic::t_info)
 
std::string complex_type_name_for_task_op (std::string const &task_op_name)
 
std::string complex_type_name_for_res_lvl_task_op (std::string const &task_op_name)
 
std::string complex_type_name_for_res_filter (std::string const &res_filter_name)
 
void task_op_schema_empty (utility::tag::XMLSchemaDefinition &xsd, std::string const &task_op_name, std::string const &description)
 
void task_op_schema_w_attributes (utility::tag::XMLSchemaDefinition &xsd, std::string const &task_op_name, utility::tag::AttributeList const &attributes, std::string const &description)
 
void res_lvl_task_op_schema_empty (utility::tag::XMLSchemaDefinition &xsd, std::string const &task_op_name, std::string const &description)
 
void res_lvl_task_op_schema_w_attributes (utility::tag::XMLSchemaDefinition &xsd, std::string const &task_op_name, utility::tag::AttributeList const &attributes, std::string const &description)
 
void res_filter_schema_w_attributes (utility::tag::XMLSchemaDefinition &xsd, std::string const &res_filter_name, utility::tag::AttributeList const &attributes, std::string const &description)
 
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", basic::t_info)
 
void parse_rotamer_sampling_data (utility::tag::TagCOP tag, ExtraRotamerSamplingData &sampling_data)
 Initialize rotamer sampling data based on the options (attributes) in an input Tag. More...
 
void define_extra_rotamers_sampling_level_restriction (utility::tag::XMLSchemaDefinition &xsd)
 
AttributeList rotamer_sampling_data_xml_schema_attributes (XMLSchemaDefinition &xsd)
 
void set_rotamer_sampling_data_for_RLT (ExtraRotamerSamplingData const &sampling_data, ResidueLevelTask &res_task)
 
utility::tag::AttributeList rotamer_sampling_data_xml_schema_attributes (utility::tag::XMLSchemaDefinition &xsd)
 Return the list of XML schema attributes that are read by the parse_rotamer_sampling_data function. More...
 

Typedef Documentation

typedef utility::pointer::shared_ptr< AddBehaviorRLT > core::pack::task::operation::AddBehaviorRLTOP
typedef utility::pointer::shared_ptr< AppendRotamer > core::pack::task::operation::AppendRotamerOP
typedef utility::pointer::shared_ptr< AppendRotamerSet > core::pack::task::operation::AppendRotamerSetOP
typedef utility::pointer::shared_ptr< ChainIsnt > core::pack::task::operation::ChainIsntOP
typedef utility::pointer::shared_ptr< ChainIs > core::pack::task::operation::ChainIsOP

ClashBasedRepackShell owning pointer.

ClashBasedRepackShell const owning pointer.

ClashBasedRepackShell const owning pointer.

ClashBasedRepackShell owning pointer.

typedef utility::pointer::shared_ptr< DesignRestrictions const > core::pack::task::operation::DesignRestrictionsCOP
using core::pack::task::operation::EnableSmartAnnealerCOP = typedef utility::pointer::shared_ptr< EnableSmartAnnealer const >
using core::pack::task::operation::EnableSmartAnnealerOP = typedef utility::pointer::shared_ptr< EnableSmartAnnealer >
typedef utility::pointer::shared_ptr< ExtraChiCutoff > core::pack::task::operation::ExtraChiCutoffOP
typedef utility::pointer::shared_ptr< ExtraRotamers > core::pack::task::operation::ExtraRotamersOP
typedef utility::pointer::shared_ptr< IncludeCurrent > core::pack::task::operation::IncludeCurrentOP
using core::pack::task::operation::KeepSequenceSymmetryCOP = typedef utility::pointer::shared_ptr< KeepSequenceSymmetry const >
using core::pack::task::operation::KeepSequenceSymmetryOP = typedef utility::pointer::shared_ptr< KeepSequenceSymmetry >

NoRepackDisulfides owning pointer.

typedef utility::pointer::weak_ptr< NoRepackDisulfides const > core::pack::task::operation::NoRepackDisulfidesCAP

NoRepackDisulfides const owning pointer.

typedef utility::pointer::shared_ptr< NoRepackDisulfides const > core::pack::task::operation::NoRepackDisulfidesCOP

NoRepackDisulfides const owning pointer.

NoRepackDisulfides owning pointer.

typedef utility::pointer::weak_ptr< OptCysHG > core::pack::task::operation::OptCysHGAP

OptCysHG owning pointer.

typedef utility::pointer::weak_ptr< OptCysHG const > core::pack::task::operation::OptCysHGCAP

OptCysHG const owning pointer.

typedef utility::pointer::shared_ptr< OptCysHG const > core::pack::task::operation::OptCysHGCOP

OptCysHG const owning pointer.

typedef utility::pointer::shared_ptr< OptCysHG > core::pack::task::operation::OptCysHGOP

OptCysHG owning pointer.

typedef utility::pointer::weak_ptr< OptH > core::pack::task::operation::OptHAP

OptH owning pointer.

typedef utility::pointer::weak_ptr< OptH const > core::pack::task::operation::OptHCAP

OptH const owning pointer.

typedef utility::pointer::shared_ptr< OptH const > core::pack::task::operation::OptHCOP

OptH const owning pointer.

typedef utility::pointer::shared_ptr< OptH > core::pack::task::operation::OptHOP

OptH owning pointer.

typedef utility::pointer::shared_ptr< PreserveCBeta > core::pack::task::operation::PreserveCBetaOP
typedef utility::pointer::shared_ptr< PreventRepacking > core::pack::task::operation::PreventRepackingOP
typedef utility::pointer::shared_ptr< ReadResfile > core::pack::task::operation::ReadResfileOP
typedef utility::pointer::weak_ptr< ReplicateTask > core::pack::task::operation::ReplicateTaskAP

ReplicateTask owning pointer.

typedef utility::pointer::weak_ptr< ReplicateTask const > core::pack::task::operation::ReplicateTaskCAP

ReplicateTask const owning pointer.

typedef utility::pointer::shared_ptr< ReplicateTask const > core::pack::task::operation::ReplicateTaskCOP

ReplicateTask const owning pointer.

typedef utility::pointer::shared_ptr< ReplicateTask > core::pack::task::operation::ReplicateTaskOP

ReplicateTask owning pointer.

typedef utility::pointer::shared_ptr< ResFilter > core::pack::task::operation::ResFilterCOP
typedef utility::pointer::shared_ptr< ResFilterCreator const > core::pack::task::operation::ResFilterCreatorCOP
typedef utility::pointer::shared_ptr< ResFilterCreator > core::pack::task::operation::ResFilterCreatorOP
typedef utility::pointer::shared_ptr< ResFilterFactory const > core::pack::task::operation::ResFilterFactoryCOP
typedef utility::pointer::shared_ptr< ResFilterFactory > core::pack::task::operation::ResFilterFactoryOP
typedef utility::pointer::shared_ptr< ResFilter > core::pack::task::operation::ResFilterOP
typedef utility::pointer::shared_ptr< ResidueIndexIsnt > core::pack::task::operation::ResidueIndexIsntOP
typedef utility::pointer::shared_ptr< ResidueIndexIs > core::pack::task::operation::ResidueIndexIsOP
typedef utility::pointer::shared_ptr< ResidueName3Isnt > core::pack::task::operation::ResidueName3IsntOP
typedef utility::pointer::shared_ptr< ResidueName3Is > core::pack::task::operation::ResidueName3IsOP
typedef utility::pointer::shared_ptr< ResLvlTaskOperation const > core::pack::task::operation::ResLvlTaskOperationCOP
typedef utility::pointer::shared_ptr< RestrictYSDesign > core::pack::task::operation::RestrictYSDesignOP
typedef utility::pointer::shared_ptr< RotamerExplosion > core::pack::task::operation::RotamerExplosionOP
typedef utility::pointer::shared_ptr< SetRotamerLinks > core::pack::task::operation::SetRotamerLinksOP
typedef utility::pointer::shared_ptr< TaskOperation > core::pack::task::operation::TaskOperationCOP
typedef utility::pointer::shared_ptr< TaskOperationCreator const > core::pack::task::operation::TaskOperationCreatorCOP
typedef utility::pointer::shared_ptr< TaskOperationFactory const > core::pack::task::operation::TaskOperationFactoryCOP
typedef utility::pointer::shared_ptr< TaskOperation > core::pack::task::operation::TaskOperationOP

Function Documentation

void core::pack::task::operation::attributes_for_parse_residue_level_operations ( utility::tag::AttributeList &  attributes)
std::string core::pack::task::operation::complex_type_name_for_res_filter ( std::string const &  res_filter_name)
std::string core::pack::task::operation::complex_type_name_for_res_lvl_task_op ( std::string const &  task_op_name)
std::string core::pack::task::operation::complex_type_name_for_task_op ( std::string const &  task_op_name)
void core::pack::task::operation::define_extra_rotamers_sampling_level_restriction ( utility::tag::XMLSchemaDefinition &  xsd)
void core::pack::task::operation::parse_residue_level_task_operations ( utility::tag::TagCOP const &  tag,
basic::datacache::DataMap &  dm,
std::list< core::pack::task::operation::ResLvlTaskOperationOP > &  rltos 
)
void core::pack::task::operation::parse_residue_level_task_operations ( utility::tag::TagCOP const &  tag,
basic::datacache::DataMap &  dm,
std::list< core::pack::task::operation::ResLvlTaskOperationCOP > &  rltos 
)
void core::pack::task::operation::parse_rotamer_sampling_data ( utility::tag::TagCOP  tag,
ExtraRotamerSamplingData &  sampling_data 
)

Initialize rotamer sampling data based on the options (attributes) in an input Tag.

References core::pack::task::operation::ExtraRotamerSamplingData::ex1_, core::pack::task::operation::ExtraRotamerSamplingData::ex1_sample_level_, core::pack::task::operation::ExtraRotamerSamplingData::ex1aro_, core::pack::task::operation::ExtraRotamerSamplingData::ex1aro_exposed_, core::pack::task::operation::ExtraRotamerSamplingData::ex1aro_exposed_sample_level_, core::pack::task::operation::ExtraRotamerSamplingData::ex1aro_sample_level_, core::pack::task::operation::ExtraRotamerSamplingData::ex2_, core::pack::task::operation::ExtraRotamerSamplingData::ex2_sample_level_, core::pack::task::operation::ExtraRotamerSamplingData::ex2aro_, core::pack::task::operation::ExtraRotamerSamplingData::ex2aro_exposed_, core::pack::task::operation::ExtraRotamerSamplingData::ex2aro_exposed_sample_level_, core::pack::task::operation::ExtraRotamerSamplingData::ex2aro_sample_level_, core::pack::task::operation::ExtraRotamerSamplingData::ex3_, core::pack::task::operation::ExtraRotamerSamplingData::ex3_sample_level_, core::pack::task::operation::ExtraRotamerSamplingData::ex4_, core::pack::task::operation::ExtraRotamerSamplingData::ex4_sample_level_, core::pack::task::operation::ExtraRotamerSamplingData::exdna_sample_level_, core::pack::task::operation::ExtraRotamerSamplingData::extrachi_cutoff_, core::pack::task::EXTRACHI_CUTOFF_LIMIT, and core::pack::task::NO_EXTRA_CHI_SAMPLES.

Referenced by core::pack::task::operation::ExtraRotamersGenericRLT::parse_tag(), and core::pack::task::operation::ExtraRotamersGeneric::parse_tag().

void core::pack::task::operation::res_filter_schema_w_attributes ( utility::tag::XMLSchemaDefinition &  xsd,
std::string const &  res_filter_name,
utility::tag::AttributeList const &  attributes,
std::string const &  description 
)
void core::pack::task::operation::res_lvl_task_op_schema_empty ( utility::tag::XMLSchemaDefinition &  xsd,
std::string const &  task_op_name,
std::string const &  description 
)
void core::pack::task::operation::res_lvl_task_op_schema_w_attributes ( utility::tag::XMLSchemaDefinition &  xsd,
std::string const &  task_op_name,
utility::tag::AttributeList const &  attributes,
std::string const &  description 
)
std::string const & core::pack::task::operation::rlto_datamap_category ( )
utility::tag::AttributeList core::pack::task::operation::rotamer_sampling_data_xml_schema_attributes ( utility::tag::XMLSchemaDefinition &  xsd)

Return the list of XML schema attributes that are read by the parse_rotamer_sampling_data function.

AttributeList core::pack::task::operation::rotamer_sampling_data_xml_schema_attributes ( XMLSchemaDefinition &  xsd)
void core::pack::task::operation::set_rotamer_sampling_data_for_RLT ( ExtraRotamerSamplingData const &  sampling_data,
ResidueLevelTask &  res_task 
)

References core::pack::task::ResidueLevelTask::and_extrachi_cutoff(), core::pack::task::operation::ExtraRotamerSamplingData::ex1_, core::pack::task::operation::ExtraRotamerSamplingData::ex1_sample_level_, core::pack::task::operation::ExtraRotamerSamplingData::ex1aro_, core::pack::task::operation::ExtraRotamerSamplingData::ex1aro_exposed_, core::pack::task::operation::ExtraRotamerSamplingData::ex1aro_exposed_sample_level_, core::pack::task::operation::ExtraRotamerSamplingData::ex1aro_sample_level_, core::pack::task::operation::ExtraRotamerSamplingData::ex2_, core::pack::task::operation::ExtraRotamerSamplingData::ex2_sample_level_, core::pack::task::operation::ExtraRotamerSamplingData::ex2aro_, core::pack::task::operation::ExtraRotamerSamplingData::ex2aro_exposed_, core::pack::task::operation::ExtraRotamerSamplingData::ex2aro_exposed_sample_level_, core::pack::task::operation::ExtraRotamerSamplingData::ex2aro_sample_level_, core::pack::task::operation::ExtraRotamerSamplingData::ex3_, core::pack::task::operation::ExtraRotamerSamplingData::ex3_sample_level_, core::pack::task::operation::ExtraRotamerSamplingData::ex4_, core::pack::task::operation::ExtraRotamerSamplingData::ex4_sample_level_, core::pack::task::operation::ExtraRotamerSamplingData::exdna_sample_level_, core::pack::task::operation::ExtraRotamerSamplingData::extrachi_cutoff_, core::pack::task::ResidueLevelTask::or_ex1(), core::pack::task::ResidueLevelTask::or_ex1_sample_level(), core::pack::task::ResidueLevelTask::or_ex1aro(), core::pack::task::ResidueLevelTask::or_ex1aro_exposed(), core::pack::task::ResidueLevelTask::or_ex1aro_exposed_sample_level(), core::pack::task::ResidueLevelTask::or_ex1aro_sample_level(), core::pack::task::ResidueLevelTask::or_ex2(), core::pack::task::ResidueLevelTask::or_ex2_sample_level(), core::pack::task::ResidueLevelTask::or_ex2aro(), core::pack::task::ResidueLevelTask::or_ex2aro_exposed(), core::pack::task::ResidueLevelTask::or_ex2aro_exposed_sample_level(), core::pack::task::ResidueLevelTask::or_ex2aro_sample_level(), core::pack::task::ResidueLevelTask::or_ex3(), core::pack::task::ResidueLevelTask::or_ex3_sample_level(), core::pack::task::ResidueLevelTask::or_ex4(), core::pack::task::ResidueLevelTask::or_ex4_sample_level(), and core::pack::task::ResidueLevelTask::or_exdna_sample_level().

Referenced by core::pack::task::operation::ExtraRotamersGenericRLT::apply(), and core::pack::task::operation::ExtraRotamersGeneric::apply().

void core::pack::task::operation::task_op_schema_empty ( utility::tag::XMLSchemaDefinition &  xsd,
std::string const &  task_op_name,
std::string const &  description 
)

References complex_type_name_for_task_op().

Referenced by protocols::forge::remodel::RemodelRotamerLinks::provide_xml_schema(), protocols::dna::WatsonCrickRotamerCouplings::provide_xml_schema(), protocols::simple_task_operations::InterfaceTaskOperation::provide_xml_schema(), protocols::task_operations::RestrictByCalculatorsOperation::provide_xml_schema(), protocols::task_operations::RestrictToCDRH3Loop::provide_xml_schema(), protocols::task_operations::RestrictToInterfaceOperation::provide_xml_schema(), protocols::hbnet::ConstrainHBondNetwork::provide_xml_schema(), core::pack::task::operation::FillAUTOTaskOperation::provide_xml_schema(), protocols::task_operations::MutationSetDesignOperation::provide_xml_schema(), protocols::task_operations::RestrictToNeighborhoodOperation::provide_xml_schema(), core::pack::task::operation::NoRepackDisulfides::provide_xml_schema(), protocols::task_operations::RestrictInterGroupVectorOperation::provide_xml_schema(), core::pack::task::operation::OptCysHG::provide_xml_schema(), protocols::simple_task_operations::DockingNoRepack1::provide_xml_schema(), protocols::task_operations::ImportUnboundRotamersOperation::provide_xml_schema(), protocols::task_operations::RestrictToMoveMapChiOperation::provide_xml_schema(), core::pack::task::operation::OptH::provide_xml_schema(), protocols::simple_task_operations::DockingNoRepack2::provide_xml_schema(), core::pack::task::operation::RestrictToRepacking::provide_xml_schema(), protocols::enzdes::AddRigidBodyLigandConfs::provide_xml_schema(), protocols::enzdes::AddLigandMotifRotamers::provide_xml_schema(), core::pack::task::operation::InitializeFromCommandline::provide_xml_schema(), core::pack::task::operation::InitializeExtraRotsFromCommandline::provide_xml_schema(), core::pack::task::operation::IncludeCurrent::provide_xml_schema(), core::pack::task::operation::SetRotamerCouplings::provide_xml_schema(), core::pack::task::operation::SetRotamerLinks::provide_xml_schema(), core::pack::task::operation::AppendRotamer::provide_xml_schema(), core::pack::task::operation::AppendRotamerSet::provide_xml_schema(), core::pack::task::operation::AppendResidueRotamerSet::provide_xml_schema(), core::pack::task::operation::PreserveCBeta::provide_xml_schema(), and core::pack::task::operation::RestrictYSDesign::provide_xml_schema().

void core::pack::task::operation::task_op_schema_w_attributes ( utility::tag::XMLSchemaDefinition &  xsd,
std::string const &  task_op_name,
utility::tag::AttributeList const &  attributes,
std::string const &  description 
)

References complex_type_name_for_task_op().

Referenced by protocols::task_operations::SelectBySASAOperation::provide_xml_schema(), protocols::task_operations::SelectByDensityFitOperation::provide_xml_schema(), protocols::task_operations::SelectByDeltaScoreOperation::provide_xml_schema(), protocols::task_operations::SetIGTypeOperation::provide_xml_schema(), protocols::task_operations::ModifyAnnealer::provide_xml_schema(), protocols::task_operations::SelectResiduesWithinChainOperation::provide_xml_schema(), protocols::task_operations::RetrieveStoredTaskOperation::provide_xml_schema(), protocols::splice::FindEndpointsOperation::provide_xml_schema(), protocols::task_operations::RestrictNonSurfaceToRepackingOperation::provide_xml_schema(), protocols::task_operations::InteractingRotamerExplosion::provide_xml_schema(), protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::provide_xml_schema(), protocols::simple_task_operations::RestrictToLoops::provide_xml_schema(), protocols::task_operations::PreventChainFromRepackingOperation::provide_xml_schema(), protocols::task_operations::CrystalContactsOperation::provide_xml_schema(), protocols::pack_interface::ProteinProteinInterfaceUpweighter::provide_xml_schema(), protocols::enzdes::SetCatalyticResPackBehavior::provide_xml_schema(), protocols::matdes::BuildingBlockInterfaceOperation::provide_xml_schema(), protocols::task_operations::ThreadSequenceOperation::provide_xml_schema(), protocols::task_operations::ReadResfileFromDB::provide_xml_schema(), protocols::task_operations::RestrictChainToRepackingOperation::provide_xml_schema(), protocols::task_operations::RestrictIdentitiesOperation::provide_xml_schema(), protocols::task_operations::RestrictResiduesToRepackingOperation::provide_xml_schema(), core::pack::task::operation::KeepSequenceSymmetry::provide_xml_schema(), protocols::task_operations::pHVariantTaskOperation::provide_xml_schema(), core::pack::task::operation::EnableMultiCoolAnnealer::provide_xml_schema(), protocols::task_operations::ConservativeDesignOperation::provide_xml_schema(), protocols::task_operations::DesignAroundOperation::provide_xml_schema(), core::pack::task::operation::EnableSmartAnnealer::provide_xml_schema(), protocols::splice::DesignInterfacesOperation::provide_xml_schema(), protocols::task_operations::ProteinInterfaceDesignOperation::provide_xml_schema(), protocols::simple_task_operations::RestrictToLoopsAndNeighbors::provide_xml_schema(), protocols::task_operations::PreventResiduesFromRepackingOperation::provide_xml_schema(), protocols::legacy_sewing::LegacyReadNativeRotamersFile::provide_xml_schema(), protocols::task_operations::ResidueProbDesignOperation::provide_xml_schema(), protocols::task_operations::RestrictNativeResiduesOperation::provide_xml_schema(), protocols::task_operations::RestrictToTerminiOperation::provide_xml_schema(), protocols::task_operations::AlignedThreadOperation::provide_xml_schema(), protocols::dna::RestrictDesignToProteinDNAInterface::provide_xml_schema(), protocols::antibody::task_operations::AddCDRProfileSetsOperation::provide_xml_schema(), core::pack::task::operation::RestrictInteractionGraphThreadsOperation::provide_xml_schema(), protocols::task_operations::DatabaseThread::provide_xml_schema(), core::pack::task::operation::RestrictToSpecifiedBaseResidueTypes::provide_xml_schema(), core::pack::task::operation::ClashBasedRepackShell::provide_xml_schema(), protocols::task_operations::ResfileCommandOperation::provide_xml_schema(), protocols::task_operations::RestrictToInterfaceVectorOperation::provide_xml_schema(), protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::provide_xml_schema(), protocols::antibody::task_operations::DisableAntibodyRegionOperation::provide_xml_schema(), protocols::legacy_sewing::LegacyReadRepeatNativeRotamersFile::provide_xml_schema(), protocols::antibody::task_operations::AddCDRProfilesOperation::provide_xml_schema(), protocols::antibody::task_operations::DisableCDRsOperation::provide_xml_schema(), protocols::task_operations::JointSequenceOperation::provide_xml_schema(), protocols::task_operations::SequenceMotifTaskOperation::provide_xml_schema(), protocols::enzdes::DetectProteinLigandInterface::provide_xml_schema(), core::pack::task::operation::ProhibitSpecifiedBaseResidueTypes::provide_xml_schema(), protocols::task_operations::PruneBuriedUnsatsOperation::provide_xml_schema(), core::pack::task::operation::RestrictToResidueProperties::provide_xml_schema(), protocols::simple_task_operations::RestrictToInterface::provide_xml_schema(), core::pack::task::operation::ProhibitResidueProperties::provide_xml_schema(), protocols::task_operations::LimitAromaChi2Operation::provide_xml_schema(), protocols::enzdes::ProteinLigandInterfaceUpweighter::provide_xml_schema(), protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::provide_xml_schema(), core::pack::task::operation::RestrictResidueToRepacking::provide_xml_schema(), core::pack::task::operation::RestrictAbsentCanonicalAAS::provide_xml_schema(), core::pack::task::operation::DisallowIfNonnative::provide_xml_schema(), core::pack::task::operation::RotamerExplosion::provide_xml_schema(), core::pack::task::operation::UseMultiCoolAnnealer::provide_xml_schema(), core::pack::task::operation::InitializeFromOptionCollection::provide_xml_schema(), core::pack::task::operation::ExtraRotamersGeneric::provide_xml_schema(), core::pack::task::operation::ReadResfile::provide_xml_schema(), core::pack::task::operation::ReadResfileAndObeyLengthEvents::provide_xml_schema(), core::pack::task::operation::PreventRepacking::provide_xml_schema(), core::pack::task::operation::ExtraRotamers::provide_xml_schema(), and core::pack::task::operation::ExtraChiCutoff::provide_xml_schema().

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.ResLvlTaskOperations"  ,
basic::t_info   
)
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.TaskOperationFactory"  )
static
static basic::Tracer core::pack::task::operation::TR ( "core.pack.task.operation.ClashBasedRepackShell"  )
static
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.OperateOnCertainResidues"  ,
t_info   
)
static
static basic::Tracer core::pack::task::operation::TR ( "core.pack.task.operation.OperateOnResidueSubset"  ,
t_info   
)
static
static basic::Tracer core::pack::task::operation::TR ( "core.pack.task.operation.TaskOperations"  ,
basic::t_info   
)
static