Rosetta Protocols  2014.35
Public Member Functions | Private Types | Private Member Functions | Private Attributes | List of all members
protocols::antibody::design::ResidueProbDesignOperation Class Reference

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< Realget_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

Constructor & Destructor Documentation

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

References init().

Referenced by clone().

protocols::antibody::design::ResidueProbDesignOperation::ResidueProbDesignOperation ( ResidueProbDesignOperation const &  src)
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
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
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
void protocols::antibody::design::ResidueProbDesignOperation::init ( void  )
private
void protocols::antibody::design::ResidueProbDesignOperation::init_for_equal_operator_and_copy_constructor ( ResidueProbDesignOperation lhs,
ResidueProbDesignOperation const &  rhs 
)
private
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
bool protocols::antibody::design::ResidueProbDesignOperation::keep_task_allowed_aa_
private
AAProbabilities protocols::antibody::design::ResidueProbDesignOperation::overall_prob_set_
private
Size protocols::antibody::design::ResidueProbDesignOperation::picking_rounds_
private
PerResidueAAProbSet protocols::antibody::design::ResidueProbDesignOperation::prob_set_
private
Real protocols::antibody::design::ResidueProbDesignOperation::zero_probs_overwrite_
private

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