#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...

AAProb &	operator= (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:

src/protocols/mean_field/AAProb.hh
src/protocols/mean_field/AAProb.cc

Public Member Functions

Private Member Functions

Private Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation