#include <RotMatrix.hh>

Inheritance diagram for protocols::mean_field::RotMatrix:

Public Member Functions
	RotMatrix ()
	default constructor, can be useful More...

	RotMatrix (core::Size const option, core::pack::rotamer_set::RotamerSetsOP rs)
	Standard constructor. More...

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

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

	~RotMatrix () override
	Destructor. More...

void	show (std::ostream &output=std::cout) const
	Generate string representation of RotMatrix for debugging purposes. More...

utility::vector1< core::Size > const &	curr_rot () const
	returns a vector of the current rotamers at each position More...

void	curr_rot (utility::vector1< core::Size > cr)
	sets the curr_rot vector More...

utility::vector1< bool > const &	is_designed () const
	returns a vector of bools designating whether each position allows design or not More...

void	is_designed (utility::vector1< bool > id)
	sets a vector of bools designating whether each position allows design or not More...

bool	is_designed (core::Size pos) const
	returns a bool designating whether a specified position allows design More...

core::Size	n_designed () const
	returns the number of positions that allow design More...

utility::vector1< RotProb >	curr_rot_prob () const
	returns a vector of RotProbs corresponding to the current rotamer at each position More...

void	build_rot_matrix (core::Size const option, core::pack::rotamer_set::RotamerSetsOP rs)
	calls init so as to reinitialize the RotMatrix with the given params More...

Public Member Functions inherited from protocols::mean_field::jagged_array< RotProb >
	jagged_array (allocator_type const &alloc=allocator_type())
	Default constructor. More...

	jagged_array (jagged_array< RotProb > const &v)
	Copy constructor. More...

	jagged_array (utility::vector1< utility::vector1< RotProb, A > > const &v)
	Assignable copy constructor. More...

	jagged_array (size_type const num)
	Size constructor constructs an empty jagged_array of size num. More...

	jagged_array (size_type const num, utility::vector1< RotProb > const &vals)
	Size and vals constructor constructs a jagged_array of size num filled with copies of vals. More...

	jagged_array (utility::vector1< size_type > const &dims)
	Uniform value constructor. More...

	jagged_array (utility::vector1< size_type > const &dims, utility::vector1< RotProb > const &vals)
	Constructor that reserves size based on vector of size types, fills vectors with vals. More...

	jagged_array (InputIterator const beg, InputIterator const ending, allocator_type const &alloc=allocator_type())
	Iterator range constructor. More...

	~jagged_array () override
	Destructor. More...

jagged_array &	operator= (jagged_array< RotProb > const &v)
	Copy assignment. More...

jagged_array &	operator= (utility::vector1< utility::vector1< RotProb, A > > const &v)
	Assignable copy assignment. More...

void	assign (utility::vector1< size_type > const &dims)
	clears jagged_array and reserves size based on vector of size types More...

void	assign (utility::vector1< size_type > const &dims, utility::vector1< RotProb > const &vals)
	clears jagged_array and reserves size based on vector of size types, fills vectors with vals More...

int	index (RotProbconst &t) const
	Find the index of an element. If not found then return 0;. More...

bool	has_value (RotProbconst &t) const
	Checks if element is present and returns bool depending whether present. More...

void	show (std::ostream &output=std::cout) const
	shows a string representation of the jagged_array More...

void	apply_func_to_all (typename func_T2< T_2 >::two_param_func func, T_2 operand)
	applies param *func to all values in the jagged_array (1-param func) More...

void	apply_func_to_each_col (typename func_T2< T_2 >::two_param_func func, utility::vector1< T_2 > operands)
	applies param *func to all values in the jagged_array (2-param func) using column_dependent operand More...

void	apply_func_to_each_elem (typename func_T2< T_2 >::two_param_func func, jagged_array< T_2 > operands)
	applies param *func to all values in the jagged_array (2-param func) using 2D-index dependent operand (i.e. matrix arithmetic) More...

void	apply_func_to_each_elem (typename func_T2< T_2 >::three_param_func func, jagged_array< RotProb > operands, T_2 third_oper)
	applies param *func to all values in the jagged_array (3-param func) using 2D-index dependent operand and a third, general operand More...

utility::vector1< RotProb >	get_totals_columns () const
	returns vector1 of totals of columns of jagged_array More...

RotProb	get_total () const
	returns total of all elements in jagged array More...

Size	size_col (Size col) const
	returns size of specified column More...

Size	max_size_col () const
	returns the maximum size of any columns More...

bool	equal_size (jagged_array< RotProb > const &other) const
	checks if a second jagged_array is of equal size for all columns More...

bool	equal_size (jagged_array< T_2 > const &other) const
	checks if a second jagged_array (of different type) is of equal size for all columns More...

Private Member Functions
void	copy_data (RotMatrix &object_to_copy_to, RotMatrix const &object_to_copy_from)
	Copy all data members from <object_to_copy_from> to <object_to_copy_to>. More...

void	init (core::Size const option, core::pack::rotamer_set::RotamerSetsOP rs)
	private method called by constructors to initialize the RotMatrix More...

Private Attributes
utility::vector1< core::Size >	curr_rot_

utility::vector1< bool >	is_designed_

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

Additional Inherited Members
Public Types inherited from protocols::mean_field::jagged_array< RotProb >
typedef super::value_type	value_type

typedef super::reference	reference

typedef super::const_reference	const_reference

typedef super::pointer	pointer

typedef super::const_pointer	const_pointer

typedef super::iterator	iterator

typedef super::const_iterator	const_iterator

typedef super::reverse_iterator	reverse_iterator

typedef super::const_reverse_iterator	const_reverse_iterator

typedef super::size_type	size_type

typedef super::difference_type	difference_type

typedef super::allocator_type	allocator_type

typedef super::index_type	index_type

typedef super::ssize_type	ssize_type

typedef super::Value	Value

typedef super::Reference	Reference

typedef super::ConstReference	ConstReference

typedef super::Pointer	Pointer

typedef super::ConstPointer	ConstPointer

typedef super::Iterator	Iterator

typedef super::ConstIterator	ConstIterator

typedef super::ReverseIterator	ReverseIterator

typedef super::ConstReverseIterator	ConstReverseIterator

typedef super::Size	Size

typedef super::Difference	Difference

typedef super::Allocator	Allocator

typedef super::Index	Index

typedef super::SSize	SSize

Detailed Description

derived from a jagged_array of RotProbs

Remarks: used in MeanField family of classes

Constructor & Destructor Documentation

protocols::mean_field::RotMatrix::RotMatrix ( )

default constructor, can be useful

References curr_rot().

protocols::mean_field::RotMatrix::RotMatrix	(	core::Size const	option,
		core::pack::rotamer_set::RotamerSetsOP	rs
	)

Standard constructor.

standard constructor calls private member function

Parameters

[in]	option	- determines which numbers to initialize RotMatrix with
[in]	rs	- RotamerSetsOP used to gather the rest of the information used to build the RotMatrix

References init().

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

Copy constructor.

Copy constructor calls private member function

References copy_data().

protocols::mean_field::RotMatrix::~RotMatrix ( )

overridedefault

Destructor.

Member Function Documentation

void protocols::mean_field::RotMatrix::build_rot_matrix	(	core::Size const	option,
		core::pack::rotamer_set::RotamerSetsOP	rs
	)

calls init so as to reinitialize the RotMatrix with the given params

References init().

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

private

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

References curr_rot_, and is_designed_.

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

utility::vector1< core::Size > const& protocols::mean_field::RotMatrix::curr_rot ( ) const

inline

returns a vector of the current rotamers at each position

References curr_rot_.

Referenced by protocols::mean_field::AAMatrix::init(), and RotMatrix().

void protocols::mean_field::RotMatrix::curr_rot ( utility::vector1< core::Size > cr )

inline

sets the curr_rot vector

References curr_rot_.

utility::vector1< RotProb > protocols::mean_field::RotMatrix::curr_rot_prob ( ) const

returns a vector of RotProbs corresponding to the current rotamer at each position

returns vector with probabilities of the current rotamers based on curr_rot_ vector

References curr_rot_.

Referenced by show().

void protocols::mean_field::RotMatrix::init	(	core::Size const	option,
		core::pack::rotamer_set::RotamerSetsOP	rs
	)

private

private method called by constructors to initialize the RotMatrix

private method used to initialize RotMatrix as jagged_array of RotProbs

called by constructors and build_rot_matrix

also builds curr_rot_ and is_designed_ vectors

Parameters

[in]	option	- determines which numbers to initialize RotMatrix with
[in]	rs	- RotamerSetsOP used to gather the rest of the information used to build the RotMatrix

References protocols::cluster::calibur::aa, curr_rot_, is_designed_, and rot().

Referenced by build_rot_matrix(), and RotMatrix().

utility::vector1< bool > const& protocols::mean_field::RotMatrix::is_designed ( ) const

inline

returns a vector of bools designating whether each position allows design or not

References is_designed_.

Referenced by protocols::mean_field::AAMatrix::init().

void protocols::mean_field::RotMatrix::is_designed ( utility::vector1< bool > id )

inline

sets a vector of bools designating whether each position allows design or not

References is_designed_.

bool protocols::mean_field::RotMatrix::is_designed ( core::Size pos ) const

inline

returns a bool designating whether a specified position allows design

Parameters

[in] pos - position to be examined within the RotMatrix

Remarks: RotMatrix numbering may or may not match pose numbering

References is_designed_.

Size protocols::mean_field::RotMatrix::n_designed ( ) const

returns the number of positions that allow design

counts the number of positions for which design is on

References is_designed_.

Referenced by protocols::mean_field::AAMatrix::init().

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

Assignment operator.

Assignment operator calls private member function

References copy_data().

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

Generate string representation of RotMatrix for debugging purposes.

prints representation of RotMatrix using show() function of RotProbs

in the outputted table, each column represents the probabilities of rotamers at that position

if current rotamers are set, outputs a vector of current rotamers and their probability

References curr_rot_prob(), and protocols::mean_field::jagged_array< T, A >::show().

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

Friends And Related Function Documentation

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

friend

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

Member Data Documentation

utility::vector1< core::Size > protocols::mean_field::RotMatrix::curr_rot_

private

Referenced by copy_data(), curr_rot(), curr_rot_prob(), and init().

utility::vector1< bool > protocols::mean_field::RotMatrix::is_designed_

private

Referenced by copy_data(), init(), is_designed(), and n_designed().

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

src/protocols/mean_field/RotMatrix.hh
src/protocols/mean_field/RotMatrix.cc

Public Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation