#include <RotProb.hh>

Public Member Functions
	RotProb ()
	Default constructor. More...

	RotProb (core::Real prob, core::Size rot_ind, core::Size pos, core::conformation::ResidueCOP res)
	main constructor to initialize RotProb according to parameters More...

	RotProb (RotProb const &object_to_copy)
	Copy constructor. More...

RotProb &	operator= (RotProb const &object_to_copy)
	Assignment operator. More...

	~RotProb ()
	Destructor. More...

bool	operator== (RotProb const &obj) const
	overloaded equality operators to fix instantiation issues with PyRosetta More...

bool	operator!= (RotProb const &obj) const
	overloaded equality operators to fix instantiation issues with PyRosetta More...

void	operator+= (RotProb const &obj)
	overloaded arithmetic operators to allow for easier matrix arithmetic More...

void	operator-= (RotProb const &obj)
	overloaded arithmetic operators to allow for easier matrix arithmetic More...

void	operator*= (RotProb const &obj)
	overloaded arithmetic operator not necessary but implemented due to its being expected More...

void	operator/= (RotProb const &obj)
	overloaded arithmetic operator not necessary but implemented due to its being expected 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...

RotProb	operator+ (core::Real prob)
	overloaded arithmetic operator for arithmetic with Real probability More...

RotProb	operator- (core::Real prob)
	overloaded arithmetic operator for arithmetic with Real probability More...

RotProb	operator* (core::Real prob)
	overloaded arithmetic operator for arithmetic with Real probability More...

RotProb	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 RotProb for debugging and reporting purposes. More...

core::Real	probability () const
	returns probability More...

void	probability (core::Real prob)
	set probability More...

core::Size	rot_ind () const
	returns rotamer index More...

void	rot_ind (core::Size aa)
	set rotamer index More...

core::Size	pos () const
	returns position More...

void	pos (core::Size p)
	set position More...

core::conformation::ResidueCOP	res () const
	returns COP to residue More...

void	res (core::conformation::ResidueCOP r)
	set ResidueCOP More...

core::chemical::AA	aa_ind () const
	returns AA type based on residue More...

Private Member Functions
void	copy_data (RotProb &object_to_copy_to, RotProb 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::Size	rot_ind_

core::Size	pos_

core::conformation::ResidueCOP	res_

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

Detailed Description

encapsulates information about a rotamer at a position and its probability

Remarks: used as the base unit in the conformational matrix (RotMatrix) class

Constructor & Destructor Documentation

protocols::mean_field::RotProb::RotProb ( )

Default constructor.

Remarks: only necessary because will be used to initialize matrix of RotProb

initialized to nonsense values

protocols::mean_field::RotProb::RotProb	(	core::Real	prob,
		core::Size	rot_ind,
		core::Size	pos,
		core::conformation::ResidueCOP	res
	)

main constructor to initialize RotProb according to parameters

main constructor

Parameters

[in]	prob	- probability of Rotamer occurring at the site
[in]	rot_ind	- used to uniquely identify rotamer across backbones
[in]	pos	- position of the site in pose numbering
[in]	res	- COP to current residue at site (useful for AA identity)

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

Copy constructor.

Copy constructor uses private member function

References copy_data().

protocols::mean_field::RotProb::~RotProb ( )

default

Destructor.

Member Function Documentation

core::chemical::AA protocols::mean_field::RotProb::aa_ind ( ) const

returns AA type based on residue

uses ResidueCOP to access AA identity of RotProb

References res().

Referenced by show().

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

private

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

References pos(), probability(), res(), and rot_ind().

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

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

inline

overloaded equality operators to fix instantiation issues with PyRosetta

RotProb protocols::mean_field::RotProb::operator* ( core::Real prob )

inline

overloaded arithmetic operator for arithmetic with Real probability

multiplies probability by prob

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

inline

overloaded arithmetic operator not necessary but implemented due to its being expected

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::RotProb::operator*= ( core::Real prob )

inline

overloaded arithmetic operator for arithmetic with Real probability

multiplies probability by prob

References probability().

RotProb protocols::mean_field::RotProb::operator+ ( core::Real prob )

inline

overloaded arithmetic operator for arithmetic with Real probability

adds prob to probability

void protocols::mean_field::RotProb::operator+= ( RotProb 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 probability().

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

inline

overloaded arithmetic operator for arithmetic with Real probability

adds prob to probability

References probability().

RotProb protocols::mean_field::RotProb::operator- ( core::Real prob )

inline

overloaded arithmetic operator for arithmetic with Real probability

subtracts prob from probability

void protocols::mean_field::RotProb::operator-= ( RotProb 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 probability().

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

inline

overloaded arithmetic operator for arithmetic with Real probability

subtracts prob from probability

References probability().

RotProb protocols::mean_field::RotProb::operator/ ( core::Real prob )

inline

overloaded arithmetic operator for arithmetic with Real probability

divides probability by prob

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

inline

overloaded arithmetic operator not necessary but implemented due to its being expected

divides its 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::RotProb::operator/= ( core::Real prob )

inline

overloaded arithmetic operator for arithmetic with Real probability

divides probability by prob

References probability().

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

Assignment operator.

Assignment operator uses private member function

References copy_data().

bool protocols::mean_field::RotProb::operator== ( RotProb const & obj ) const

inline

overloaded equality operators to fix instantiation issues with PyRosetta

References pos(), probability(), res(), and rot_ind().

core::Size protocols::mean_field::RotProb::pos ( ) const

inline

returns position

References pos_.

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

void protocols::mean_field::RotProb::pos ( core::Size p )

inline

set position

References pos_.

core::Real protocols::mean_field::RotProb::probability ( ) const

inline

returns probability

References probability_.

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

void protocols::mean_field::RotProb::probability ( core::Real prob )

inline

set probability

References probability_.

core::conformation::ResidueCOP protocols::mean_field::RotProb::res ( ) const

returns COP to residue

References res_.

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

void protocols::mean_field::RotProb::res ( core::conformation::ResidueCOP r )

set ResidueCOP

References res_.

core::Size protocols::mean_field::RotProb::rot_ind ( ) const

inline

returns rotamer index

References rot_ind_.

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

void protocols::mean_field::RotProb::rot_ind ( core::Size aa )

inline

set rotamer index

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

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

Generate string representation of RotProb for debugging and reporting purposes.

prints RotProb 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,
		RotProb const &	object_to_output
	)

friend

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

Member Data Documentation

core::Size protocols::mean_field::RotProb::pos_

private

Referenced by pos(), and show().

core::Real protocols::mean_field::RotProb::probability_

private

Referenced by probability(), and show().

core::conformation::ResidueCOP protocols::mean_field::RotProb::res_

private

Referenced by res().

core::Size protocols::mean_field::RotProb::rot_ind_

private

Referenced by rot_ind().

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

src/protocols/mean_field/RotProb.hh
src/protocols/mean_field/RotProb.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