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protocols::task_operations::DsspDesignOperation Class Reference

TaskOperation that can be used to restrict AAs allowed at each position based on DSSP-assigned secondary structure. More...

#include <DsspDesignOperation.hh>

Inheritance diagram for protocols::task_operations::DsspDesignOperation:
Inheritance graph
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Public Types

typedef
core::pack::task::operation::TaskOperation 
parent
 
typedef
core::pack::task::operation::TaskOperationOP 
TaskOperationOP
 
typedef
protocols::parser::BluePrint 
BluePrint
 
typedef
protocols::parser::BluePrintOP 
BluePrintOP
 
typedef std::map< std::string,
std::string > 
SecStructResidues
 
typedef std::pair< std::string,
std::string > 
SecStruct
 
- Public Types inherited from core::pack::task::operation::TaskOperation
typedef utility::tag::TagCOP TagCOP
 
typedef basic::datacache::DataMap DataMap
 
typedef pose::Pose Pose
 

Public Member Functions

 DsspDesignOperation ()
 default constructor More...
 
 DsspDesignOperation (DsspDesignOperation const &rval)
 copy constructor More...
 
 ~DsspDesignOperation () override
 destructor More...
 
TaskOperationOP clone () const override
 make clone More...
 
void set_blueprint (BluePrintOP const bp)
 define secondary structure from a blueprint More...
 
void set_restrictions_aa (std::string const &sse, std::string const &aas)
 define allowed residues for some SSE More...
 
void set_restrictions_append (std::string const &sse, std::string const &aas)
 append allowed residues for some SSE More...
 
void set_restrictions_exclude (std::string const &sse, std::string const &aas)
 exclude allowed residues for some SSE More...
 
void parse_tag (TagCOP tag, DataMap &) override
 parse RosettaScripts XML More...
 
void apply (Pose const &pose, core::pack::task::PackerTask &task) const override
 apply 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 Does this task_operation indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)?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 ()
 

Private Member Functions

void set_default_sse_residues ()
 initialize allowed residue sets with defaults More...
 
utility::vector1< boolget_restrictions (std::string const &ss_type) const
 get the set of allowed residues for some secondary structure element More...
 

Private Attributes

SecStructResidues sse_residues_
 map sets of allowed residues to secondary structure elements More...
 
BluePrintOP blueprint_
 
std::string pose_secstruct_
 

Friends

class ::DsspDesignOperationTests
 

Detailed Description

TaskOperation that can be used to restrict AAs allowed at each position based on DSSP-assigned secondary structure.

Member Typedef Documentation

typedef std::pair< std::string, std::string > protocols::task_operations::DsspDesignOperation::SecStruct
typedef std::map< std::string, std::string > protocols::task_operations::DsspDesignOperation::SecStructResidues

Constructor & Destructor Documentation

protocols::task_operations::DsspDesignOperation::DsspDesignOperation ( )

default constructor

protocols::task_operations::DsspDesignOperation::DsspDesignOperation ( DsspDesignOperation const &  rval)
default

copy constructor

protocols::task_operations::DsspDesignOperation::~DsspDesignOperation ( )
overridedefault

destructor

Member Function Documentation

void protocols::task_operations::DsspDesignOperation::apply ( Pose const &  pose,
core::pack::task::PackerTask task 
) const
overridevirtual
TaskOperationOP protocols::task_operations::DsspDesignOperation::clone ( ) const
overridevirtual
utility::vector1< bool > protocols::task_operations::DsspDesignOperation::get_restrictions ( std::string const &  ss_type) const
private

get the set of allowed residues for some secondary structure element

References core::chemical::aa_from_oneletter_code(), and core::chemical::num_canonical_aas.

static std::string protocols::task_operations::DsspDesignOperation::keyname ( )
inlinestatic
void protocols::task_operations::DsspDesignOperation::parse_tag ( TagCOP  tag,
DataMap  
)
overridevirtual

parse RosettaScripts XML

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

References protocols::task_operations::TR().

void protocols::task_operations::DsspDesignOperation::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::task_operations::DsspDesignOperation::set_blueprint ( BluePrintOP const  bp)

define secondary structure from a blueprint

void protocols::task_operations::DsspDesignOperation::set_default_sse_residues ( )
private

initialize allowed residue sets with defaults

References protocols::task_operations::TR().

void protocols::task_operations::DsspDesignOperation::set_restrictions_aa ( std::string const &  sse,
std::string const &  aas 
)

define allowed residues for some SSE

void protocols::task_operations::DsspDesignOperation::set_restrictions_append ( std::string const &  sse,
std::string const &  aas 
)

append allowed residues for some SSE

void protocols::task_operations::DsspDesignOperation::set_restrictions_exclude ( std::string const &  sse,
std::string const &  aas 
)

exclude allowed residues for some SSE

References protocols::cluster::calibur::aa.

Friends And Related Function Documentation

friend class ::DsspDesignOperationTests
friend

Member Data Documentation

BluePrintOP protocols::task_operations::DsspDesignOperation::blueprint_
private
std::string protocols::task_operations::DsspDesignOperation::pose_secstruct_
private
SecStructResidues protocols::task_operations::DsspDesignOperation::sse_residues_
private

map sets of allowed residues to secondary structure elements


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