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protocols::antibody::task_operations::AddCDRProfileSetsOperation Class Reference

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:
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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< boolpre_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< boolcdrs_
 
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 
)
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
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
void protocols::antibody::task_operations::AddCDRProfileSetsOperation::parse_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &   
)
overridevirtual
utility::vector1< bool > protocols::antibody::task_operations::AddCDRProfileSetsOperation::pre_load_data ( core::pose::Pose const &  pose)
void protocols::antibody::task_operations::AddCDRProfileSetsOperation::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
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 ( )
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
utility::vector1<bool> protocols::antibody::task_operations::AddCDRProfileSetsOperation::cdrs_
private
core::Size protocols::antibody::task_operations::AddCDRProfileSetsOperation::cutoff_
private
bool protocols::antibody::task_operations::AddCDRProfileSetsOperation::force_north_paper_db_
private
bool protocols::antibody::task_operations::AddCDRProfileSetsOperation::ignore_light_chain_ = false
private
bool protocols::antibody::task_operations::AddCDRProfileSetsOperation::include_native_restype_
private
bool protocols::antibody::task_operations::AddCDRProfileSetsOperation::limit_only_to_length_
private
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
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

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