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protocols::antibody::task_operations::RestrictToCDRsAndNeighbors Class Reference

Task Operation to restrict packing/design to specific CDRs and neighbors. See DisableAntibodyRegionOperation and DisableCDRsOperation further restrict TaskFactory. More...

#include <RestrictToCDRsAndNeighbors.hh>

Inheritance diagram for protocols::antibody::task_operations::RestrictToCDRsAndNeighbors:
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Public Member Functions

 RestrictToCDRsAndNeighbors ()
 Default Constructor. More...
 
 RestrictToCDRsAndNeighbors (AntibodyInfoCOP ab_info)
 Constructor with AntibodyInfo. More...
 
 RestrictToCDRsAndNeighbors (AntibodyInfoCOP ab_info, utility::vector1< bool > const &cdrs)
 Constructor specifying CDRs to restrict to. More...
 
 RestrictToCDRsAndNeighbors (AntibodyInfoCOP ab_info, utility::vector1< bool > const &cdrs, bool allow_cdr_design)
 Constructor with more options. More...
 
 RestrictToCDRsAndNeighbors (AntibodyInfoCOP ab_info, utility::vector1< bool > const &cdrs, bool allow_cdr_design, bool allow_neighbor_framework_design, bool allow_neighbor_antigen_design)
 Constructor with most options. More...
 
 RestrictToCDRsAndNeighbors (RestrictToCDRsAndNeighbors const &src)
 
 ~RestrictToCDRsAndNeighbors () override
 
core::pack::task::operation::TaskOperationOP clone () const override
 Create another task operation of the type matching the most-derived version of the class. More...
 
void parse_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
 Configure from a RosettaScripts XML tag. More...
 
void apply (core::pose::Pose const &pose, core::pack::task::PackerTask &task) const override
 Change a packer task in some way. The input pose is the one to which the input task will be later applied. More...
 
void set_cdrs (utility::vector1< bool > const &cdrs)
 
void set_cdr_only (CDRNameEnum cdr)
 
void set_neighbor_distance (core::Real neighbor_dis)
 Set the distance for the detection of neighbor residues. 6A default. More...
 
void set_allow_design_cdr (bool allow_cdr_design)
 Allow design of CDRs? More...
 
void set_allow_design_neighbor_framework (bool allow_framework_design)
 Allow design of neighbor framework residues? More...
 
void set_allow_design_neighbor_antigen (bool allow_antigen_design)
 Allow design of neighbor antigen residues? More...
 
void set_stem_size (core::Size stem_size)
 Set the size of the stem - the number of residues going into the framework. This will be included as part of the loop when determining neighbors. However, the residues of the stem itself count as part of the framework. More...
 
void set_defaults ()
 
- Public Member Functions inherited from core::pack::task::operation::TaskOperation
 ~TaskOperation () override
 
virtual void provide_citation_info (basic::citation_manager::CitationCollectionList &) const
 Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...
 

Static Public Member Functions

static std::string keyname ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 

Private Attributes

AntibodyInfoCOP ab_info_
 
utility::vector1< boolcdrs_
 
core::Real neighbor_dis_
 
bool design_cdrs_
 
bool design_antigen_
 
bool design_framework_
 
core::Size stem_size_
 
AntibodyNumberingSchemeEnum numbering_scheme_
 Needed for default and RS constructor. More...
 
CDRDefinitionEnum cdr_definition_
 

Additional Inherited Members

- Public Types inherited from core::pack::task::operation::TaskOperation
typedef utility::tag::TagCOP TagCOP
 
typedef basic::datacache::DataMap DataMap
 
typedef pose::Pose Pose
 

Detailed Description

Task Operation to restrict packing/design to specific CDRs and neighbors. See DisableAntibodyRegionOperation and DisableCDRsOperation further restrict TaskFactory.

See options for control of the design of CDRs, antigen, and framework. By default, restricts to all packing of all CDRs and neighbors. See options for control of which CDRs, including whether to only restrict design and control of whether we design neighbor antigen and/or framework residues.

Constructor & Destructor Documentation

protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::RestrictToCDRsAndNeighbors ( )

Default Constructor.

References set_defaults().

protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::RestrictToCDRsAndNeighbors ( AntibodyInfoCOP  ab_info)

Constructor with AntibodyInfo.

References set_defaults().

protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::RestrictToCDRsAndNeighbors ( AntibodyInfoCOP  ab_info,
utility::vector1< bool > const &  cdrs 
)

Constructor specifying CDRs to restrict to.

References set_cdrs(), and set_defaults().

protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::RestrictToCDRsAndNeighbors ( AntibodyInfoCOP  ab_info,
utility::vector1< bool > const &  cdrs,
bool  allow_cdr_design 
)

Constructor with more options.

References design_cdrs_, set_cdrs(), and set_defaults().

protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::RestrictToCDRsAndNeighbors ( AntibodyInfoCOP  ab_info,
utility::vector1< bool > const &  cdrs,
bool  allow_cdr_design,
bool  allow_neighbor_framework_design,
bool  allow_neighbor_antigen_design 
)

Constructor with most options.

References design_antigen_, design_cdrs_, design_framework_, set_cdrs(), and set_defaults().

protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::RestrictToCDRsAndNeighbors ( RestrictToCDRsAndNeighbors const &  src)

References ab_info_.

protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::~RestrictToCDRsAndNeighbors ( )
overridedefault

Member Function Documentation

void protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::apply ( core::pose::Pose const &  ,
core::pack::task::PackerTask  
) const
overridevirtual
TaskOperationOP protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::clone ( ) const
overridevirtual

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

Implements core::pack::task::operation::TaskOperation.

std::string protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::keyname ( )
static
void protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::parse_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &   
)
overridevirtual
void protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::set_allow_design_cdr ( bool  allow_cdr_design)

Allow design of CDRs?

References design_cdrs_.

void protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::set_allow_design_neighbor_antigen ( bool  allow_antigen_design)

Allow design of neighbor antigen residues?

References design_antigen_.

void protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::set_allow_design_neighbor_framework ( bool  allow_framework_design)

Allow design of neighbor framework residues?

References design_framework_.

void protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::set_cdr_only ( CDRNameEnum  cdr)
void protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::set_cdrs ( utility::vector1< bool > const &  cdrs)
void protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::set_defaults ( )
void protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::set_neighbor_distance ( core::Real  neighbor_dis)

Set the distance for the detection of neighbor residues. 6A default.

References neighbor_dis_.

void protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::set_stem_size ( core::Size  stem_size)

Set the size of the stem - the number of residues going into the framework. This will be included as part of the loop when determining neighbors. However, the residues of the stem itself count as part of the framework.

References stem_size_.

Member Data Documentation

AntibodyInfoCOP protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::ab_info_
private
CDRDefinitionEnum protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::cdr_definition_
private

Referenced by apply(), parse_tag(), and set_defaults().

utility::vector1<bool> protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::cdrs_
private
bool protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::design_antigen_
private
bool protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::design_cdrs_
private
bool protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::design_framework_
private
core::Real protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::neighbor_dis_
private
AntibodyNumberingSchemeEnum protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::numbering_scheme_
private

Needed for default and RS constructor.

Referenced by apply(), parse_tag(), and set_defaults().

core::Size protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::stem_size_
private

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