Rosetta Protocols  2014.35
Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::antibody::design::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>

Public Member Functions

 ConservativeDesignOperation ()
 Default constructor. Will use native aa from apply (Changes each pack if tf is passed). More...
 
virtual ~ConservativeDesignOperation ()
 
 ConservativeDesignOperation (ConservativeDesignOperation const &src)
 
virtual void apply (core::pose::Pose const &pose, core::pack::task::PackerTask &task) const
 
void limit_to_positions (vector1< Size > const positions)
 Limit to a subset of residue positions, already set to designable. More...
 
void clear_positions ()
 Clear any set positions. More...
 
void add_to_allowed_aas (bool const &setting)
 Add to the allowed amino acids list instead of replacing it. Default false. More...
 
void include_native_aa (bool const &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...
 
ConservativeDesignOperationoperator= (ConservativeDesignOperation const &rhs)
 
virtual
core::pack::task::operation::TaskOperationOP 
clone () const
 

Private Member Functions

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

Private Attributes

vector1< vector1< bool > > conserved_mutations_
 
vector1< Sizepositions_
 
bool add_to_allowed_aas_
 
bool include_native_aa_
 
std::string pose_sequence_
 

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.

Constructor & Destructor Documentation

protocols::antibody::design::ConservativeDesignOperation::ConservativeDesignOperation ( )

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

References conserved_mutations_, and load_data_from_db().

Referenced by clone().

protocols::antibody::design::ConservativeDesignOperation::~ConservativeDesignOperation ( )
virtual
protocols::antibody::design::ConservativeDesignOperation::ConservativeDesignOperation ( ConservativeDesignOperation const &  src)

Member Function Documentation

void protocols::antibody::design::ConservativeDesignOperation::add_to_allowed_aas ( bool const &  setting)

Add to the allowed amino acids list instead of replacing it. Default false.

References add_to_allowed_aas_.

void protocols::antibody::design::ConservativeDesignOperation::apply ( core::pose::Pose const &  pose,
core::pack::task::PackerTask task 
) const
virtual
void protocols::antibody::design::ConservativeDesignOperation::clear_positions ( )

Clear any set positions.

References positions_.

core::pack::task::operation::TaskOperationOP protocols::antibody::design::ConservativeDesignOperation::clone ( ) const
virtual
void protocols::antibody::design::ConservativeDesignOperation::include_native_aa ( bool const &  setting)

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

References include_native_aa_.

void protocols::antibody::design::ConservativeDesignOperation::init_for_equal_operator_and_copy_constructor ( ConservativeDesignOperation lhs,
ConservativeDesignOperation const &  rhs 
)
private
void protocols::antibody::design::ConservativeDesignOperation::limit_to_positions ( vector1< Size > const  positions)

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

References positions_.

void protocols::antibody::design::ConservativeDesignOperation::load_data_from_db ( )
private
void protocols::antibody::design::ConservativeDesignOperation::load_data_from_file ( )
private
ConservativeDesignOperation & protocols::antibody::design::ConservativeDesignOperation::operator= ( ConservativeDesignOperation const &  rhs)
void protocols::antibody::design::ConservativeDesignOperation::use_pose_sequence_as_native ( core::pose::Pose const &  pose)

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

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

Member Data Documentation

bool protocols::antibody::design::ConservativeDesignOperation::add_to_allowed_aas_
private
vector1< vector1<bool> > protocols::antibody::design::ConservativeDesignOperation::conserved_mutations_
private
bool protocols::antibody::design::ConservativeDesignOperation::include_native_aa_
private
std::string protocols::antibody::design::ConservativeDesignOperation::pose_sequence_
private
vector1< Size > protocols::antibody::design::ConservativeDesignOperation::positions_
private

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