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:

[legend]

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< bool >	cdrs_

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

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

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

References ab_info_, protocols::antibody::antigen_region, core::pack::task::operation::RestrictResidueToRepacking::apply(), core::pack::task::operation::PreventRepacking::apply(), cdr_definition_, protocols::antibody::cdr_region, cdrs_, design_antigen_, design_cdrs_, design_framework_, protocols::antibody::framework_region, protocols::antibody::get_cdr_loops(), core::pack::task::operation::RestrictResidueToRepacking::include_residue(), core::pack::task::operation::PreventRepacking::include_residue(), neighbor_dis_, numbering_scheme_, protocols::loops::select_loop_residues(), core::pose::Pose::size(), and stem_size_.

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

Referenced by protocols::antibody::task_operations::RestrictToCDRsAndNeighborsCreator::keyname(), and provide_xml_schema().

void protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::parse_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &
	)

overridevirtual

Configure from a RosettaScripts XML tag.

Reimplemented from core::pack::task::operation::TaskOperation.

References cdr_definition_, protocols::antibody::AntibodyEnumManager::cdr_definition_string_to_enum(), cdrs_, design_antigen_, design_cdrs_, design_framework_, protocols::antibody::get_cdr_bool_from_tag(), neighbor_dis_, numbering_scheme_, protocols::antibody::AntibodyEnumManager::numbering_scheme_string_to_enum(), stem_size_, and protocols::antibody::TR().

void protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References protocols::antibody::attributes_for_get_cdr_bool_from_tag(), keyname(), and core::pack::task::operation::task_op_schema_w_attributes().

Referenced by protocols::antibody::task_operations::RestrictToCDRsAndNeighborsCreator::provide_xml_schema().

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 )

References protocols::antibody::CDRNameEnum_proto_total, and cdrs_.

void protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::set_cdrs ( utility::vector1< bool > const & cdrs )

References protocols::antibody::CDRNameEnum_proto_total, and cdrs_.

Referenced by RestrictToCDRsAndNeighbors().

void protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::set_defaults ( )

References cdr_definition_, protocols::antibody::AntibodyEnumManager::cdr_definition_string_to_enum(), cdrs_, design_antigen_, design_cdrs_, design_framework_, protocols::antibody::h4, protocols::antibody::l4, neighbor_dis_, numbering_scheme_, protocols::antibody::AntibodyEnumManager::numbering_scheme_string_to_enum(), and stem_size_.

Referenced by RestrictToCDRsAndNeighbors().

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

Referenced by apply(), and RestrictToCDRsAndNeighbors().

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

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

bool protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::design_antigen_

private

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

bool protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::design_cdrs_

private

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

bool protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::design_framework_

private

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

core::Real protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::neighbor_dis_

private

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

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

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

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

src/protocols/antibody/task_operations/RestrictToCDRsAndNeighbors.hh
src/protocols/antibody/task_operations/RestrictToCDRsAndNeighbors.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation