A TaskOperation that allows amino acids at designable positions through a set of aa probabilities. More...

#include <ResidueProbDesignOperation.hh>

Public Member Functions
	ResidueProbDesignOperation ()

	ResidueProbDesignOperation (ResidueProbDesignOperation const &src)

virtual	~ResidueProbDesignOperation ()

virtual void	apply (core::pose::Pose const &pose, core::pack::task::PackerTask &task) const

void	set_aa_probability_set (PerResidueAAProbSet per_res_aa_probs)
	Sets the whole aa probability set. More...

void	set_aa_probabilities (Size const resnum, AAProbabilities aa_probs)
	Sets aa probabilities for a particular resnum. More...

void	set_overall_aa_probabilities (AAProbabilities aa_probs)
	Set the probability for a particular aa @ a particular resnum. More...

void	clear_prob_set ()
	Clears the probability matrix. More...

void	clear_overall_prob_set ()
	Clears the overall probabilities if any are set. More...

void	set_include_native_restype (bool include)
	Include current residuetype in packer in addition to selected mutation. Default is true. More...

bool	include_native_restype () const

void	set_sample_zero_probs_at (core::Real const probability)
	Sample any zero probabilities at this probability instead of not using them. More...

Real	sample_zero_probs_at () const

void	set_picking_rounds (core::Size picking_rounds)
	Max number of times to sample from the probability distribution. Default is once. More...

Size	picking_rounds () const

void	set_keep_task_allowed_aas (bool setting)
	Add the aa types chosen from the probabilities to the allowed aa at the position instead of overwriting it. More...

bool	keep_task_allowed_aas () const

bool	resnum_exists_in_set (core::Size const resnum) const

virtual core::pack::task::operation::TaskOperationOP	clone () const

Private Types
typedef std::map < core::chemical::AA, Real >	AAProbabilities

typedef std::map< Size, AAProbabilities >	PerResidueAAProbSet

Private Member Functions
void	init ()

void	init_for_equal_operator_and_copy_constructor (ResidueProbDesignOperation &lhs, ResidueProbDesignOperation const &rhs)

vector1< Real >	get_weights (AAProbabilities &aa_prob_set) const
	Create full weight set for all amino acids from a probability set. More...

bool	aa_exists (core::chemical::AA amino_acid, AAProbabilities const &aa_prob_set) const

Private Attributes
PerResidueAAProbSet	prob_set_

AAProbabilities	overall_prob_set_

bool	include_native_restype_

bool	keep_task_allowed_aa_

Real	zero_probs_overwrite_

Size	picking_rounds_

Detailed Description

A TaskOperation that allows amino acids at designable positions through a set of aa probabilities.

Default is for the TaskOp to control the allowed amino acids only if the class has probabilities to use for that resnum. If no probabilities were set, it will not do anything. Probabilities should add to one, but if not, they will act as weights.

Member Typedef Documentation

typedef std::map< core::chemical::AA, Real > protocols::antibody::design::ResidueProbDesignOperation::AAProbabilities

private

typedef std::map< Size, AAProbabilities > protocols::antibody::design::ResidueProbDesignOperation::PerResidueAAProbSet

private

Constructor & Destructor Documentation

protocols::antibody::design::ResidueProbDesignOperation::ResidueProbDesignOperation ( )

References init().

Referenced by clone().

protocols::antibody::design::ResidueProbDesignOperation::ResidueProbDesignOperation ( ResidueProbDesignOperation const & src )

References init_for_equal_operator_and_copy_constructor().

protocols::antibody::design::ResidueProbDesignOperation::~ResidueProbDesignOperation ( )

virtual

Member Function Documentation

bool protocols::antibody::design::ResidueProbDesignOperation::aa_exists	(	core::chemical::AA	amino_acid,
		AAProbabilities const &	aa_prob_set
	)		const

private

Referenced by get_weights().

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

virtual

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

References core::pack::task::ResidueLevelTask::allow_aa(), core::pack::task::PackerTask::designing_residues(), core::pack::task::ResidueLevelTask::get_original_residue(), get_weights(), include_native_restype_, keep_task_allowed_aa_, core::pack::task::PackerTask::nonconst_residue_task(), overall_prob_set_, picking_rounds_, prob_set_, resnum_exists_in_set(), core::pack::task::ResidueLevelTask::restrict_absent_canonical_aas(), protocols::RG, core::pose::Pose::total_residue(), and protocols::antibody::TR.

void protocols::antibody::design::ResidueProbDesignOperation::clear_overall_prob_set ( )

Clears the overall probabilities if any are set.

References overall_prob_set_.

void protocols::antibody::design::ResidueProbDesignOperation::clear_prob_set ( )

Clears the probability matrix.

References prob_set_.

core::pack::task::operation::TaskOperationOP protocols::antibody::design::ResidueProbDesignOperation::clone ( ) const

virtual

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

References ResidueProbDesignOperation().

vector1< Real > protocols::antibody::design::ResidueProbDesignOperation::get_weights ( AAProbabilities & aa_prob_set ) const

private

Create full weight set for all amino acids from a probability set.

References aa_exists(), and zero_probs_overwrite_.

Referenced by apply().

bool protocols::antibody::design::ResidueProbDesignOperation::include_native_restype ( ) const

References include_native_restype_.

void protocols::antibody::design::ResidueProbDesignOperation::init ( void )

private

References set_include_native_restype(), set_keep_task_allowed_aas(), set_picking_rounds(), and set_sample_zero_probs_at().

Referenced by ResidueProbDesignOperation().

void protocols::antibody::design::ResidueProbDesignOperation::init_for_equal_operator_and_copy_constructor	(	ResidueProbDesignOperation &	lhs,
		ResidueProbDesignOperation const &	rhs
	)

private

References include_native_restype_, keep_task_allowed_aa_, overall_prob_set_, picking_rounds_, prob_set_, and zero_probs_overwrite_.

Referenced by ResidueProbDesignOperation().

bool protocols::antibody::design::ResidueProbDesignOperation::keep_task_allowed_aas ( ) const

References keep_task_allowed_aa_.

Size protocols::antibody::design::ResidueProbDesignOperation::picking_rounds ( ) const

References picking_rounds_.

Referenced by set_picking_rounds().

bool protocols::antibody::design::ResidueProbDesignOperation::resnum_exists_in_set ( core::Size const resnum ) const

References prob_set_.

Referenced by apply().

Real protocols::antibody::design::ResidueProbDesignOperation::sample_zero_probs_at ( ) const

References zero_probs_overwrite_.

void protocols::antibody::design::ResidueProbDesignOperation::set_aa_probabilities	(	Size const	resnum,
		AAProbabilities	aa_probs
	)

Sets aa probabilities for a particular resnum.

References prob_set_.

void protocols::antibody::design::ResidueProbDesignOperation::set_aa_probability_set ( PerResidueAAProbSet per_res_aa_probs )

Sets the whole aa probability set.

References prob_set_.

void protocols::antibody::design::ResidueProbDesignOperation::set_include_native_restype ( bool include )

Include current residuetype in packer in addition to selected mutation. Default is true.

References include_native_restype_.

Referenced by init().

void protocols::antibody::design::ResidueProbDesignOperation::set_keep_task_allowed_aas ( bool setting )

Add the aa types chosen from the probabilities to the allowed aa at the position instead of overwriting it.

Will result in very different results. Used one wants to use this Op to sample other residues in addition within a specific probability.

References keep_task_allowed_aa_.

Referenced by init().

void protocols::antibody::design::ResidueProbDesignOperation::set_overall_aa_probabilities ( AAProbabilities aa_probs )

Set the probability for a particular aa @ a particular resnum.

Sets aa probabilities for all positions not given specifically. All designable residues will use this if not specified through other functions.

References overall_prob_set_.

void protocols::antibody::design::ResidueProbDesignOperation::set_picking_rounds ( core::Size picking_rounds )

Max number of times to sample from the probability distribution. Default is once.

This is to increase variability. Too many rounds will even out the distribution. Can also run the PackRotamers mover or equivalent multiple times for sampling.

References picking_rounds(), and picking_rounds_.

Referenced by init().

void protocols::antibody::design::ResidueProbDesignOperation::set_sample_zero_probs_at ( core::Real const probability )

Sample any zero probabilities at this probability instead of not using them.

References zero_probs_overwrite_.

Referenced by init().

Member Data Documentation

bool protocols::antibody::design::ResidueProbDesignOperation::include_native_restype_

private

Referenced by apply(), include_native_restype(), init_for_equal_operator_and_copy_constructor(), and set_include_native_restype().

bool protocols::antibody::design::ResidueProbDesignOperation::keep_task_allowed_aa_

private

Referenced by apply(), init_for_equal_operator_and_copy_constructor(), keep_task_allowed_aas(), and set_keep_task_allowed_aas().

AAProbabilities protocols::antibody::design::ResidueProbDesignOperation::overall_prob_set_

private

Referenced by apply(), clear_overall_prob_set(), init_for_equal_operator_and_copy_constructor(), and set_overall_aa_probabilities().

Size protocols::antibody::design::ResidueProbDesignOperation::picking_rounds_

private

Referenced by apply(), init_for_equal_operator_and_copy_constructor(), picking_rounds(), and set_picking_rounds().

PerResidueAAProbSet protocols::antibody::design::ResidueProbDesignOperation::prob_set_

private

Referenced by apply(), clear_prob_set(), init_for_equal_operator_and_copy_constructor(), resnum_exists_in_set(), set_aa_probabilities(), and set_aa_probability_set().

Real protocols::antibody::design::ResidueProbDesignOperation::zero_probs_overwrite_

private

Referenced by get_weights(), init_for_equal_operator_and_copy_constructor(), sample_zero_probs_at(), and set_sample_zero_probs_at().

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

src/protocols/antibody/design/ResidueProbDesignOperation.hh
src/protocols/antibody/design/ResidueProbDesignOperation.cc

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation