Add Cluster-based sets of mutations as a TaskOperation. Essentially samples full sequences of CDRs within a particular CDR cluster randomly each time the packer is called. Does this for each CDR. More...

#include <AddCDRProfileSetsOperation.hh>

Inheritance diagram for protocols::antibody::task_operations::AddCDRProfileSetsOperation:

[legend]

Public Member Functions
	AddCDRProfileSetsOperation ()

	AddCDRProfileSetsOperation (AntibodyInfoCOP ab_info)

	AddCDRProfileSetsOperation (AntibodyInfoCOP ab_info, utility::vector1< bool > const &cdrs)

	AddCDRProfileSetsOperation (AntibodyInfoCOP ab_info, utility::vector1< bool > const &cdrs, bool limit_only_to_length)

	AddCDRProfileSetsOperation (AddCDRProfileSetsOperation const &src)

	~AddCDRProfileSetsOperation () 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...

utility::vector1< bool >	pre_load_data (core::pose::Pose const &pose)
	Pre load the data according to options instead of at each apply. More...

void	set_cdr_only (CDRNameEnum cdr)
	Set a single CDR with which to use this task op on. Default is all of them. More...

void	set_cdrs (utility::vector1< bool > const &cdrs)
	Set the CDRs with which to use this task op on. Default is all of them. More...

void	set_limit_only_to_length (bool limit_only_to_length)
	Set the class to sample all CDR sequences within a particular length, instead of by cluster, which is the default. Default False. More...

void	set_defaults ()

void	set_force_north_paper_db (bool force_north_db)
	Force the use of the antibody database that houses only the North data. This is the db distributed with Rosetta. If a current one is present in the database, it will use that instead. Default False. More...

void	set_use_outliers (bool use_outliers)
	Use cluster outliers as defined using DihedralDistance and RMSD. Default false. More...

void	set_cutoff (core::Size cutoff)
	Set the cutoff. Will not add the profile set if the total is less than or equal to this number. Default is 10. More...

void	set_picking_rounds (core::Size rounds)
	Set the number of times a sequence each chosen. Increase this number to increase variability of design. Default 1 round. More...

void	set_include_native_type (bool use_native)
	Include the poses current residue type in the allowed amino acids. Default True. More...

void	set_ignore_light_chain (bool const ignore_light_chain=false)

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 void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

static std::string	keyname ()

Private Attributes
AntibodyInfoCOP	ab_info_

utility::vector1< bool >	cdrs_

bool	limit_only_to_length_

bool	force_north_paper_db_

bool	use_outliers_

core::Size	cutoff_

core::Size	picking_rounds_

bool	include_native_restype_

CDRDBSequenceSet	sequences_

bool	pre_loaded_data_

AntibodyNumberingSchemeEnum	numbering_scheme_
	Needed for default and RS constructor. More...

bool	ignore_light_chain_ = false

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

Add Cluster-based sets of mutations as a TaskOperation. Essentially samples full sequences of CDRs within a particular CDR cluster randomly each time the packer is called. Does this for each CDR.

See protocols/task_operations/MutationSetDesignOperation for more info. If a CDR has an unknown cluster or there are no data for that particular CDR, will skip that CDR.

CDR definitions used are North/Dunbrack as the clusters are defined using it.

Note that by default, a data cutoff of 10 is set. If the cluster has less than 10 sequences it will be skipped. Use the set_cutoff function to change this.

Constructor & Destructor Documentation

protocols::antibody::task_operations::AddCDRProfileSetsOperation::AddCDRProfileSetsOperation ( )

References set_defaults().

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

References set_defaults().

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

References cdrs_, and set_defaults().

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

References cdrs_, limit_only_to_length_, and set_defaults().

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

References ab_info_.

protocols::antibody::task_operations::AddCDRProfileSetsOperation::~AddCDRProfileSetsOperation ( )

overridedefault

Member Function Documentation

void protocols::antibody::task_operations::AddCDRProfileSetsOperation::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::task_operations::MutationSetDesignOperation::apply(), cdrs_, cutoff_, force_north_paper_db_, protocols::antibody::AntibodyDatabaseManager::ignore_light_chain(), ignore_light_chain_, protocols::task_operations::MutationSetDesignOperation::include_native_aa(), include_native_restype_, limit_only_to_length_, protocols::antibody::AntibodyDatabaseManager::load_cdr_sequences(), protocols::antibody::North, numbering_scheme_, picking_rounds_, pre_loaded_data_, sequences_, protocols::task_operations::MutationSetDesignOperation::set_mutation_sets(), protocols::antibody::AntibodyDatabaseManager::set_outlier_use(), protocols::task_operations::MutationSetDesignOperation::set_picking_rounds(), protocols::antibody::TR(), protocols::antibody::design::transform_sequence_to_mutation_set(), and use_outliers_.

TaskOperationOP protocols::antibody::task_operations::AddCDRProfileSetsOperation::clone ( ) const

overridevirtual

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

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

static std::string protocols::antibody::task_operations::AddCDRProfileSetsOperation::keyname ( )

inlinestatic

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

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

overridevirtual

Configure from a RosettaScripts XML tag.

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

References cdrs_, cutoff_, force_north_paper_db_, protocols::antibody::get_cdr_bool_from_tag(), include_native_restype_, limit_only_to_length_, numbering_scheme_, protocols::antibody::AntibodyEnumManager::numbering_scheme_string_to_enum(), picking_rounds_, protocols::antibody::TR(), and use_outliers_.

utility::vector1< bool > protocols::antibody::task_operations::AddCDRProfileSetsOperation::pre_load_data ( core::pose::Pose const & pose )

Pre load the data according to options instead of at each apply.

References ab_info_, cdrs_, cutoff_, force_north_paper_db_, protocols::antibody::h4, protocols::antibody::AntibodyDatabaseManager::ignore_light_chain(), ignore_light_chain_, protocols::antibody::l4, limit_only_to_length_, protocols::antibody::AntibodyDatabaseManager::load_cdr_sequences(), protocols::antibody::North, numbering_scheme_, pre_loaded_data_, sequences_, protocols::antibody::AntibodyDatabaseManager::set_outlier_use(), protocols::antibody::TR(), and use_outliers_.

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

static

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

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

void protocols::antibody::task_operations::AddCDRProfileSetsOperation::set_cdr_only ( CDRNameEnum cdr )

Set a single CDR with which to use this task op on. Default is all of them.

References cdrs_.

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

Set the CDRs with which to use this task op on. Default is all of them.

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

void protocols::antibody::task_operations::AddCDRProfileSetsOperation::set_cutoff ( core::Size cutoff )

Set the cutoff. Will not add the profile set if the total is less than or equal to this number. Default is 10.

References cutoff_.

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

References cdrs_, cutoff_, force_north_paper_db_, include_native_restype_, limit_only_to_length_, numbering_scheme_, protocols::antibody::AntibodyEnumManager::numbering_scheme_string_to_enum(), picking_rounds_, pre_loaded_data_, sequences_, and use_outliers_.

Referenced by AddCDRProfileSetsOperation().

void protocols::antibody::task_operations::AddCDRProfileSetsOperation::set_force_north_paper_db ( bool force_north_db )

Force the use of the antibody database that houses only the North data. This is the db distributed with Rosetta. If a current one is present in the database, it will use that instead. Default False.

References force_north_paper_db_.

void protocols::antibody::task_operations::AddCDRProfileSetsOperation::set_ignore_light_chain ( bool const ignore_light_chain = false )

inline

References ignore_light_chain_.

void protocols::antibody::task_operations::AddCDRProfileSetsOperation::set_include_native_type ( bool use_native )

Include the poses current residue type in the allowed amino acids. Default True.

References include_native_restype_.

void protocols::antibody::task_operations::AddCDRProfileSetsOperation::set_limit_only_to_length ( bool limit_only_to_length )

Set the class to sample all CDR sequences within a particular length, instead of by cluster, which is the default. Default False.

References limit_only_to_length_.

void protocols::antibody::task_operations::AddCDRProfileSetsOperation::set_picking_rounds ( core::Size rounds )

Set the number of times a sequence each chosen. Increase this number to increase variability of design. Default 1 round.

References picking_rounds_.

void protocols::antibody::task_operations::AddCDRProfileSetsOperation::set_use_outliers ( bool use_outliers )

Use cluster outliers as defined using DihedralDistance and RMSD. Default false.

References use_outliers_.

Member Data Documentation

AntibodyInfoCOP protocols::antibody::task_operations::AddCDRProfileSetsOperation::ab_info_

private

Referenced by AddCDRProfileSetsOperation(), apply(), and pre_load_data().

utility::vector1<bool> protocols::antibody::task_operations::AddCDRProfileSetsOperation::cdrs_

private

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

core::Size protocols::antibody::task_operations::AddCDRProfileSetsOperation::cutoff_

private

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

bool protocols::antibody::task_operations::AddCDRProfileSetsOperation::force_north_paper_db_

private

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

bool protocols::antibody::task_operations::AddCDRProfileSetsOperation::ignore_light_chain_ = false

private

Referenced by apply(), pre_load_data(), and set_ignore_light_chain().

bool protocols::antibody::task_operations::AddCDRProfileSetsOperation::include_native_restype_

private

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

bool protocols::antibody::task_operations::AddCDRProfileSetsOperation::limit_only_to_length_

private

Referenced by AddCDRProfileSetsOperation(), apply(), parse_tag(), pre_load_data(), set_defaults(), and set_limit_only_to_length().

AntibodyNumberingSchemeEnum protocols::antibody::task_operations::AddCDRProfileSetsOperation::numbering_scheme_

private

Needed for default and RS constructor.

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

core::Size protocols::antibody::task_operations::AddCDRProfileSetsOperation::picking_rounds_

private

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

bool protocols::antibody::task_operations::AddCDRProfileSetsOperation::pre_loaded_data_

private

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

CDRDBSequenceSet protocols::antibody::task_operations::AddCDRProfileSetsOperation::sequences_

private

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

bool protocols::antibody::task_operations::AddCDRProfileSetsOperation::use_outliers_

private

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

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

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

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation