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protocols::task_operations::ConservativeDesignOperation Class Reference

A TaskOperation that sets the allowed amino acids of designable residues to the native amino acid's conservative mutations. More...

#include <ConservativeDesignOperation.hh>

Inheritance diagram for protocols::task_operations::ConservativeDesignOperation:
Inheritance graph
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Public Member Functions

 ConservativeDesignOperation ()
 Default constructor. Will use native aa from apply (Changes each pack if tf is passed). More...
 
 ConservativeDesignOperation (std::string data_source)
 Constructor with setting of data source. More...
 
 ~ConservativeDesignOperation () override
 
 ConservativeDesignOperation (ConservativeDesignOperation const &src)
 
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 parse_tag (utility::tag::TagCOP, basic::datacache::DataMap &) override
 Used to parse an xml-like tag to load parameters and properties. More...
 
void limit_to_positions (utility::vector1< core::Size > const &positions)
 Limit to a subset of residue positions, already set to designable. More...
 
void include_residue (core::Size resnum)
 
void clear_positions ()
 Clear any set positions. More...
 
void include_native_aa (bool setting)
 Include native amino acid in the allowed_aas list. Default true. More...
 
void use_pose_sequence_as_native (core::pose::Pose const &pose)
 Will use native residues from the this pose to determine conserved aa. More...
 
void set_native_sequence (std::string const &seq)
 
void set_data_source (std::string const &data_source)
 Set the source of the data used to define what is conservative. Options are: chothia_76 and the Blosum matrices from 30 to 100; designated as blosum30, 62, etc. Default is blosum62. The higher the number, the more conservative the set of mutations (numbers are sequence identity cutoffs) More...
 
ConservativeDesignOperationoperator= (ConservativeDesignOperation const &rhs)
 
core::pack::task::operation::TaskOperationOP clone () const override
 Create another task operation of the type matching the most-derived version of the class. More...
 
- Public Member Functions inherited from core::pack::task::operation::TaskOperation
 ~TaskOperation () override
 
virtual bool task_operation_provides_citation_info () const
 Does this task operation provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool task_operation_is_unpublished () const
 Does this task_operation indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Static Public Member Functions

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

Protected Member Functions

bool skip_resid (core::Size resid, core::pack::task::PackerTask const &task, std::string const &seq) const
 

Private Member Functions

void load_data_from_db ()
 
void init_for_equal_operator_and_copy_constructor (ConservativeDesignOperation &lhs, ConservativeDesignOperation const &rhs)
 
void set_defaults ()
 

Private Attributes

utility::vector1
< utility::vector1< bool > > 
conserved_mutations_
 
utility::vector1< core::Sizepositions_
 
core::select::residue_selector::ResidueSelectorCOP residue_selector_
 
bool include_native_aa_
 
std::string pose_sequence_
 
std::string data_source_
 

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

A TaskOperation that sets the allowed amino acids of designable residues to the native amino acid's conservative mutations.

Default is to act on all designable residues. Use limit_to_positions to limit this. Default is to replace the allowed_aas with these conservative mutations. Data is loaded from database/sequence/resinfo.db.

Constructor & Destructor Documentation

protocols::task_operations::ConservativeDesignOperation::ConservativeDesignOperation ( )

Default constructor. Will use native aa from apply (Changes each pack if tf is passed).

References set_data_source(), and set_defaults().

protocols::task_operations::ConservativeDesignOperation::ConservativeDesignOperation ( std::string  data_source)

Constructor with setting of data source.

References set_data_source(), and set_defaults().

protocols::task_operations::ConservativeDesignOperation::~ConservativeDesignOperation ( )
overridedefault
protocols::task_operations::ConservativeDesignOperation::ConservativeDesignOperation ( ConservativeDesignOperation const &  src)

Member Function Documentation

void protocols::task_operations::ConservativeDesignOperation::apply ( core::pose::Pose const &  ,
core::pack::task::PackerTask  
) const
overridevirtual
void protocols::task_operations::ConservativeDesignOperation::clear_positions ( )

Clear any set positions.

References positions_.

core::pack::task::operation::TaskOperationOP protocols::task_operations::ConservativeDesignOperation::clone ( ) const
overridevirtual

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

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

void protocols::task_operations::ConservativeDesignOperation::include_native_aa ( bool  setting)
inline

Include native amino acid in the allowed_aas list. Default true.

References include_native_aa_.

Referenced by parse_tag().

void protocols::task_operations::ConservativeDesignOperation::include_residue ( core::Size  resnum)

References positions_.

void protocols::task_operations::ConservativeDesignOperation::init_for_equal_operator_and_copy_constructor ( ConservativeDesignOperation lhs,
ConservativeDesignOperation const &  rhs 
)
private
static std::string protocols::task_operations::ConservativeDesignOperation::keyname ( )
inlinestatic
void protocols::task_operations::ConservativeDesignOperation::limit_to_positions ( utility::vector1< core::Size > const &  positions)

Limit to a subset of residue positions, already set to designable.

References positions_.

void protocols::task_operations::ConservativeDesignOperation::load_data_from_db ( )
private
ConservativeDesignOperation & protocols::task_operations::ConservativeDesignOperation::operator= ( ConservativeDesignOperation const &  rhs)
void protocols::task_operations::ConservativeDesignOperation::parse_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  datamap 
)
overridevirtual
void protocols::task_operations::ConservativeDesignOperation::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::task_operations::ConservativeDesignOperation::set_data_source ( std::string const &  data_source)

Set the source of the data used to define what is conservative. Options are: chothia_76 and the Blosum matrices from 30 to 100; designated as blosum30, 62, etc. Default is blosum62. The higher the number, the more conservative the set of mutations (numbers are sequence identity cutoffs)

References data_source_, and load_data_from_db().

Referenced by ConservativeDesignOperation(), and parse_tag().

void protocols::task_operations::ConservativeDesignOperation::set_defaults ( )
private
void protocols::task_operations::ConservativeDesignOperation::set_native_sequence ( std::string const &  seq)
inline

References pose_sequence_.

Referenced by use_pose_sequence_as_native().

bool protocols::task_operations::ConservativeDesignOperation::skip_resid ( core::Size  resid,
core::pack::task::PackerTask const &  task,
std::string const &  seq 
) const
protected
void protocols::task_operations::ConservativeDesignOperation::use_pose_sequence_as_native ( core::pose::Pose const &  pose)

Will use native residues from the this pose to determine conserved aa.

References core::pose::Pose::sequence(), and set_native_sequence().

Member Data Documentation

utility::vector1< utility::vector1<bool> > protocols::task_operations::ConservativeDesignOperation::conserved_mutations_
private
std::string protocols::task_operations::ConservativeDesignOperation::data_source_
private
bool protocols::task_operations::ConservativeDesignOperation::include_native_aa_
private
std::string protocols::task_operations::ConservativeDesignOperation::pose_sequence_
private
utility::vector1< core::Size > protocols::task_operations::ConservativeDesignOperation::positions_
private
core::select::residue_selector::ResidueSelectorCOP protocols::task_operations::ConservativeDesignOperation::residue_selector_
private

Referenced by apply(), and parse_tag().


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