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protocols::mean_field::AAProb Class Reference

#include <AAProb.hh>

Public Member Functions

 AAProb ()
 Default constructor. More...
 
 AAProb (core::Real prob, core::chemical::AA aa_ind, core::Size pos, core::Size nrot)
 standard constructor More...
 
 AAProb (protocols::mean_field::RotProb const &rp)
 constructor from RotProb More...
 
 AAProb (AAProb const &object_to_copy)
 Copy constructor. More...
 
AAProboperator= (AAProb const &object_to_copy)
 Assignment operator. More...
 
 ~AAProb ()
 Destructor. More...
 
bool operator== (AAProb const &obj) const
 overloaded equality operators to fix instantiation issues with PyRosetta More...
 
bool operator!= (AAProb const &obj) const
 overloaded equality operators to fix instantiation issues with PyRosetta More...
 
void operator+= (AAProb const &obj)
 overloaded arithmetic operators to allow for easier matrix arithmetic More...
 
void operator-= (AAProb const &obj)
 overloaded arithmetic operators to allow for easier matrix arithmetic More...
 
void operator*= (AAProb const &obj)
 overloaded arithmetic operators to allow for easier matrix arithmetic More...
 
void operator/= (AAProb const &obj)
 overloaded arithmetic operators to allow for easier matrix arithmetic More...
 
void operator+= (core::Real prob)
 overloaded arithmetic operator for arithmetic with Real probability More...
 
void operator-= (core::Real prob)
 overloaded arithmetic operator for arithmetic with Real probability More...
 
void operator*= (core::Real prob)
 overloaded arithmetic operator for arithmetic with Real probability More...
 
void operator/= (core::Real prob)
 overloaded arithmetic operator for arithmetic with Real probability More...
 
AAProb operator+ (core::Real prob)
 overloaded arithmetic operator for arithmetic with Real probability More...
 
AAProb operator- (core::Real prob)
 overloaded arithmetic operator for arithmetic with Real probability More...
 
AAProb operator* (core::Real prob)
 overloaded arithmetic operator for arithmetic with Real probability More...
 
AAProb operator/ (core::Real prob)
 overloaded arithmetic operator for arithmetic with Real probability More...
 
void show (std::ostream &output=std::cout) const
 Generate string representation of AAProb for debugging purposes. More...
 
core::Real probability () const
 returns probability More...
 
void probability (core::Real prob)
 sets probability More...
 
core::chemical::AA aa_ind () const
 returns AA identity More...
 
void aa_ind (core::chemical::AA aa)
 sets AA identity More...
 
core::Size pos () const
 returns position in pose numbering More...
 
void pos (core::Size p)
 sets position in pose numbering More...
 
core::Size nrot () const
 returns number of rotamers corresponding to AA identity at this position More...
 
void nrot (core::Size n)
 sets number of rotamers corresponding to AA identity at this position More...
 

Private Member Functions

void copy_data (AAProb &object_to_copy_to, AAProb const &object_to_copy_from)
 Copy all data members from <object_to_copy_from> to <object_to_copy_to>. More...
 

Private Attributes

core::Real probability_
 
core::chemical::AA aa_ind_
 
core::Size pos_
 
core::Size nrot_
 

Friends

std::ostream & operator<< (std::ostream &output, AAProb const &object_to_output)
 Insertion operator (overloaded so that AAProb can be "printed" in PyRosetta). More...
 

Detailed Description

encapsulates information about an amino acid at a position and its probability

Remarks
used as the base unit in the specificity profile (AAMatrix) class

Constructor & Destructor Documentation

protocols::mean_field::AAProb::AAProb ( )

Default constructor.

only necessary because will be used to initialize matrix of AAProb

initialized to nonsense values

protocols::mean_field::AAProb::AAProb ( core::Real  prob,
core::chemical::AA  aa_ind,
core::Size  pos,
core::Size  nrot 
)

standard constructor

Parameters
[in]prob- probability of Amino Acid occurring at the site
[in]aa_ind- AA enum of identity
[in]pos- position of the site in pose numbering
[in]nrot- number of rotamers corresponding to this amino acid at that site
protocols::mean_field::AAProb::AAProb ( protocols::mean_field::RotProb const &  rp)

constructor from RotProb

constructs AAProb from RotProb

protocols::mean_field::AAProb::AAProb ( AAProb const &  object_to_copy)

Copy constructor.

Copy constructor uses private member function

References copy_data().

protocols::mean_field::AAProb::~AAProb ( )
default

Destructor.

Member Function Documentation

core::chemical::AA protocols::mean_field::AAProb::aa_ind ( ) const
inline

returns AA identity

References aa_ind_.

Referenced by copy_data(), operator==(), and show().

void protocols::mean_field::AAProb::aa_ind ( core::chemical::AA  aa)
inline

sets AA identity

References protocols::cluster::calibur::aa, and aa_ind_.

void protocols::mean_field::AAProb::copy_data ( AAProb object_to_copy_to,
AAProb const &  object_to_copy_from 
)
private

Copy all data members from <object_to_copy_from> to <object_to_copy_to>.

References aa_ind(), nrot(), pos(), and probability().

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

core::Size protocols::mean_field::AAProb::nrot ( ) const
inline

returns number of rotamers corresponding to AA identity at this position

References nrot_.

Referenced by copy_data(), operator+=(), operator-=(), and operator==().

void protocols::mean_field::AAProb::nrot ( core::Size  n)
inline

sets number of rotamers corresponding to AA identity at this position

References nrot_.

bool protocols::mean_field::AAProb::operator!= ( AAProb const &  obj) const
inline

overloaded equality operators to fix instantiation issues with PyRosetta

AAProb protocols::mean_field::AAProb::operator* ( core::Real  prob)
inline

overloaded arithmetic operator for arithmetic with Real probability

multiplies probability by prob

void protocols::mean_field::AAProb::operator*= ( AAProb const &  obj)
inline

overloaded arithmetic operators to allow for easier matrix arithmetic

multiplies probability of obj by its own probability

Remarks
only overloading operators that modify object so as to avoid confusion about identity of non-probability data members

References probability().

void protocols::mean_field::AAProb::operator*= ( core::Real  prob)
inline

overloaded arithmetic operator for arithmetic with Real probability

multiplies its own probability by prob

References probability().

AAProb protocols::mean_field::AAProb::operator+ ( core::Real  prob)
inline

overloaded arithmetic operator for arithmetic with Real probability

adds prob to probability

void protocols::mean_field::AAProb::operator+= ( AAProb const &  obj)
inline

overloaded arithmetic operators to allow for easier matrix arithmetic

adds probability of obj to its own probability

Remarks
only overloading operators that modify object so as to avoid confusion about identity of non-probability data members

References nrot(), and probability().

void protocols::mean_field::AAProb::operator+= ( core::Real  prob)
inline

overloaded arithmetic operator for arithmetic with Real probability

adds prob to its own probability

References probability().

AAProb protocols::mean_field::AAProb::operator- ( core::Real  prob)
inline

overloaded arithmetic operator for arithmetic with Real probability

subtracts prob from probability

void protocols::mean_field::AAProb::operator-= ( AAProb const &  obj)
inline

overloaded arithmetic operators to allow for easier matrix arithmetic

subtracts probability of obj from its own probability

Remarks
only overloading operators that modify object so as to avoid confusion about identity of non-probability data members

References nrot(), and probability().

void protocols::mean_field::AAProb::operator-= ( core::Real  prob)
inline

overloaded arithmetic operator for arithmetic with Real probability

subtracts prob from its own probability

References probability().

AAProb protocols::mean_field::AAProb::operator/ ( core::Real  prob)
inline

overloaded arithmetic operator for arithmetic with Real probability

divides probability by prob

void protocols::mean_field::AAProb::operator/= ( AAProb const &  obj)
inline

overloaded arithmetic operators to allow for easier matrix arithmetic

divides its own probability by probability of obj

Remarks
only overloading operators that modify object so as to avoid confusion about identity of non-probability data members

References probability().

void protocols::mean_field::AAProb::operator/= ( core::Real  prob)
inline

overloaded arithmetic operator for arithmetic with Real probability

divides its own probability by prob

References probability().

AAProb & protocols::mean_field::AAProb::operator= ( AAProb const &  object_to_copy)

Assignment operator.

Assignment constructor uses private member function

References copy_data().

bool protocols::mean_field::AAProb::operator== ( AAProb const &  obj) const
inline

overloaded equality operators to fix instantiation issues with PyRosetta

References aa_ind(), nrot(), pos(), and probability().

core::Size protocols::mean_field::AAProb::pos ( ) const
inline

returns position in pose numbering

References pos_.

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

void protocols::mean_field::AAProb::pos ( core::Size  p)
inline

sets position in pose numbering

References pos_.

core::Real protocols::mean_field::AAProb::probability ( ) const
inline

returns probability

References probability_.

Referenced by copy_data(), operator*=(), operator+=(), operator-=(), operator/=(), and operator==().

void protocols::mean_field::AAProb::probability ( core::Real  prob)
inline

sets probability

References probability_.

void protocols::mean_field::AAProb::show ( std::ostream &  output = std::cout) const

Generate string representation of AAProb for debugging purposes.

prints AAProb name, pos, and probability. ex: LEU132 0.5

References aa_ind(), core::chemical::name_from_aa(), pos_, and probability_.

Referenced by protocols::mean_field::operator<<().

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  output,
AAProb const &  object_to_output 
)
friend

Insertion operator (overloaded so that AAProb can be "printed" in PyRosetta).

Member Data Documentation

core::chemical::AA protocols::mean_field::AAProb::aa_ind_
private

Referenced by aa_ind().

core::Size protocols::mean_field::AAProb::nrot_
private

Referenced by nrot().

core::Size protocols::mean_field::AAProb::pos_
private

Referenced by pos(), and show().

core::Real protocols::mean_field::AAProb::probability_
private

Referenced by probability(), and show().


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