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...
ConservativeDesignOperation &	operator= (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< Size >	positions_
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

)

References init_for_equal_operator_and_copy_constructor().

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

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

References core::chemical::aa_from_oneletter_code(), add_to_allowed_aas_, core::pack::task::ResidueLevelTask::allow_aa(), conserved_mutations_, core::pack::task::PackerTask::designing_residues(), include_native_aa_, core::pack::task::PackerTask::nonconst_residue_task(), core::chemical::oneletter_code_specifies_aa(), pose_sequence_, positions_, core::pack::task::ResidueLevelTask::restrict_absent_canonical_aas(), seq, core::pose::Pose::sequence(), and core::pose::Pose::total_residue().

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

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

References ConservativeDesignOperation().

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

References add_to_allowed_aas_, conserved_mutations_, include_native_aa_, and positions_.

Referenced by ConservativeDesignOperation(), and operator=().

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

References conserved_mutations_, basic::database::full_name(), basic::database::get_db_session(), basic::database::safely_prepare_statement(), basic::database::safely_read_from_database(), and protocols::antibody::TR.

Referenced by ConservativeDesignOperation().

void protocols::antibody::design::ConservativeDesignOperation::load_data_from_file ( )

private

ConservativeDesignOperation & protocols::antibody::design::ConservativeDesignOperation::operator=

(

ConservativeDesignOperation const &

rhs

)

References init_for_equal_operator_and_copy_constructor().

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

Referenced by add_to_allowed_aas(), apply(), and init_for_equal_operator_and_copy_constructor().

vector1< vector1<bool> > protocols::antibody::design::ConservativeDesignOperation::conserved_mutations_

private

Referenced by apply(), ConservativeDesignOperation(), init_for_equal_operator_and_copy_constructor(), and load_data_from_db().

bool protocols::antibody::design::ConservativeDesignOperation::include_native_aa_

private

Referenced by apply(), include_native_aa(), and init_for_equal_operator_and_copy_constructor().

std::string protocols::antibody::design::ConservativeDesignOperation::pose_sequence_

private

Referenced by apply(), and use_pose_sequence_as_native().

vector1< Size > protocols::antibody::design::ConservativeDesignOperation::positions_

private

Referenced by apply(), clear_positions(), init_for_equal_operator_and_copy_constructor(), and limit_to_positions().

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

• src/protocols/antibody/design/ConservativeDesignOperation.hh
• src/protocols/antibody/design/ConservativeDesignOperation.cc