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protocols::mean_field::RotProb Class Reference

#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...
 
RotProboperator= (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: