#include <AAMatrix.hh>

Inheritance diagram for protocols::mean_field::AAMatrix:

Public Member Functions
	AAMatrix ()
	Standard constructor. More...

	AAMatrix (std::istream &aa_matrix_file)
	Constructor to build AAMatrix from a file. More...

	AAMatrix (RotMatrix const &rm, protocols::mean_field::jagged_array< core::Real > em, core::Real temp)
	Constructs a AAMatrix from a RotMatrix (standard way of constructing AAMatrix) More...

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

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

	~AAMatrix () override
	Destructor. More...

utility::vector1< core::Real >	cosine_distance (AAMatrix const &aa_matrix) const
	calculates vector of cosine distances between vectors of this AAMatrix and a second AAMatrix More...

utility::vector1< core::Real >	frob_distance (AAMatrix const &aa_matrix) const
	calculates vector of frob distances between vectors of this AAMatrix and a second AAMatrix More...

utility::vector1< core::Real >	ave_abs_diff (AAMatrix const &aa_matrix) const
	calculates vector of average absolute differences between vectors of this AAMatrix and a second AAMatrix More...

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

void	dump_transfac (std::string const &filename) const
	outputs AA Matrix in transfac format for dumping purposes More...

bool	empty () const
	returns true if all probabilities are 0 More...

utility::vector1< core::Size > const &	curr_aa () const
	returns vector of current amino acids at each position (if current rotamer is set for that position) More...

utility::vector1< AAProb >	curr_aa_prob () const
	returns vector of probabilities of current amino acids at each position (if current rotamer is set for that position) More...

void	build_aa_matrix (RotMatrix const &rm, protocols::mean_field::jagged_array< core::Real > em, core::Real temp)
	builds AAMatrix from RotMatrix rm using private method init More...

void	build_aa_matrix (std::istream &aa_matrix_file)
	builds AAMatrix from transfac file using private method init More...

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

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

	jagged_array (utility::vector1< utility::vector1< AAProb, 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< AAProb > 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< AAProb > 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< AAProb > const &v)
	Copy assignment. More...

jagged_array &	operator= (utility::vector1< utility::vector1< AAProb, 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< AAProb > const &vals)
	clears jagged_array and reserves size based on vector of size types, fills vectors with vals More...

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

bool	has_value (AAProbconst &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< AAProb > 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< AAProb >	get_totals_columns () const
	returns vector1 of totals of columns of jagged_array More...

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

void	init (protocols::mean_field::RotMatrix const &rm, protocols::mean_field::jagged_array< core::Real > em, core::Real temp)
	private method called by constructors to initialize the AAMatrix from a RotMatrix More...

void	init (std::istream &aa_matrix_file)
	private method called by constructors to initialize the AAMatrix from a transfac file More...

utility::vector1< AAProb >	parse_aa_matrix_line (utility::vector1< std::string > const &tokens, utility::vector1< core::chemical::AA > const &aa_names)
	parse line of transfac file to add a vector of probabilities for one position to the AAMatrix More...

void	parse_aa_line (utility::vector1< std::string > const &tokens, utility::vector1< core::chemical::AA > &aa_names)
	parse header (AA codes) line of the AAMatrix More...

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

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

Additional Inherited Members
Public Types inherited from protocols::mean_field::jagged_array< AAProb >
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

Remarks

Constructor & Destructor Documentation

protocols::mean_field::AAMatrix::AAMatrix ( )

Standard constructor.

protocols::mean_field::AAMatrix::AAMatrix ( std::istream & aa_matrix_file )

Constructor to build AAMatrix from a file.

Builds AAMatrix from a standard transfac file

References init().

protocols::mean_field::AAMatrix::AAMatrix	(	RotMatrix const &	rm,
		protocols::mean_field::jagged_array< core::Real >	em,
		core::Real	temp
	)

Constructs a AAMatrix from a RotMatrix (standard way of constructing AAMatrix)

Builds AAMatrix from a RotMatrix using private method init

References init().

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

Copy constructor.

References copy_data().

protocols::mean_field::AAMatrix::~AAMatrix ( )

overridedefault

Destructor.

Member Function Documentation

utility::vector1< Real > protocols::mean_field::AAMatrix::ave_abs_diff ( AAMatrix const & obj ) const

calculates vector of average absolute differences between vectors of this AAMatrix and a second AAMatrix

number of elements is the number of positions + 1. last element is the average abs diff between entire matrices

param [out] results - vector1 of Frobenius distances, calculated per-column and for the entire matrix.

Remarks: distance is calculated between corresponding columns, determined by pos() of the AAProbs in the columns; if there are no corresponding columns, returns empty vector1

References protocols::cluster::calibur::aa, protocols::mean_field::jagged_array< T, A >::assign(), empty(), protocols::mean_field::num_elements(), protocols::simple_moves::bb_sampler::probability, and protocols::hybridization::val.

Referenced by protocols::mean_field::GenMeanFieldMover::report_dist().

void protocols::mean_field::AAMatrix::build_aa_matrix	(	RotMatrix const &	rm,
		protocols::mean_field::jagged_array< core::Real >	em,
		core::Real	temp
	)

inline

builds AAMatrix from RotMatrix rm using private method init

References init().

Referenced by protocols::mean_field::GenMeanFieldMover::read_aa_matrix().

void protocols::mean_field::AAMatrix::build_aa_matrix ( std::istream & aa_matrix_file )

inline

builds AAMatrix from transfac file using private method init

References init().

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

private

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

References curr_aa_.

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

utility::vector1< Real > protocols::mean_field::AAMatrix::cosine_distance ( AAMatrix const & obj ) const

calculates vector of cosine distances between vectors of this AAMatrix and a second AAMatrix

number of elements is the number of positions + 1. last element is the cosine distance between entire matrices

param [out] results - vector1 of cosine distances, calculated per-column and for the entire matrix.

Remarks: distance is calculated between corresponding columns, determined by pos() of the AAProbs in the columns; if there are no corresponding columns, returns empty vector1

References protocols::mean_field::jagged_array< T, A >::get_total(), protocols::mean_field::jagged_array< T, A >::get_totals_columns(), and protocols::simple_moves::bb_sampler::probability.

Referenced by protocols::mean_field::GenMeanFieldMover::report_dist().

utility::vector1< core::Size > const& protocols::mean_field::AAMatrix::curr_aa ( ) const

inline

returns vector of current amino acids at each position (if current rotamer is set for that position)

References curr_aa_.

utility::vector1< AAProb > protocols::mean_field::AAMatrix::curr_aa_prob ( ) const

returns vector of probabilities of current amino acids at each position (if current rotamer is set for that position)

returns vector with probabilities of the current amino acids based on curr_aa_ vector

References curr_aa_.

Referenced by show().

void protocols::mean_field::AAMatrix::dump_transfac ( std::string const & filename ) const

outputs AA Matrix in transfac format for dumping purposes

Parameters

[in] filename - specifies file for transfac output

output AAMatrix in transfac file format to file specified by filename

Error if filename cannot be opened

References protocols::cluster::calibur::aa, and core::chemical::oneletter_code_from_aa().

Referenced by protocols::mean_field::GenMeanFieldMover::report_aa_matrix().

bool protocols::mean_field::AAMatrix::empty ( ) const

returns true if all probabilities are 0

returns true if AAMatrix is empty of AAProbs or if AAMatrix is full of nonsense AAProbs

References protocols::mean_field::jagged_array< AAProb >::get_total(), and protocols::simple_moves::bb_sampler::probability.

Referenced by ave_abs_diff(), frob_distance(), protocols::mean_field::GenMeanFieldMover::report_aa_matrix(), and protocols::mean_field::GenMeanFieldMover::report_dist().

utility::vector1< Real > protocols::mean_field::AAMatrix::frob_distance ( AAMatrix const & obj ) const

calculates vector of frob distances between vectors of this AAMatrix and a second AAMatrix

number of elements is the number of positions + 1. last element is the frob dist between entire matrices

param [out] results - vector1 of Frobenius distances, calculated per-column and for the entire matrix.

Remarks: distance is calculated between corresponding columns, determined by pos() of the AAProbs in the columns; if there are no corresponding columns, returns empty vector1

References protocols::cluster::calibur::aa, protocols::mean_field::jagged_array< T, A >::assign(), empty(), protocols::simple_moves::bb_sampler::probability, and protocols::hybridization::val.

Referenced by protocols::mean_field::GenMeanFieldMover::report_dist().

void protocols::mean_field::AAMatrix::init	(	protocols::mean_field::RotMatrix const &	rm,
		protocols::mean_field::jagged_array< core::Real >	em,
		core::Real	temp
	)

private

private method called by constructors to initialize the AAMatrix from a RotMatrix

private method used to initialize AAMatrix as jagged_array of AAProbs from RotMatrix

called by constructors

also builds curr_aa_ vector

Parameters

[in] RotMatrix - used to initialize AAMatrix by summing over probabilities of all rotamers for each amino acid for each position

References protocols::cluster::calibur::aa, curr_aa_, protocols::mean_field::RotMatrix::curr_rot(), protocols::mean_field::RotMatrix::is_designed(), protocols::mean_field::RotMatrix::n_designed(), core::chemical::num_canonical_aas, protocols::simple_moves::bb_sampler::probability, and rot().

Referenced by AAMatrix(), and build_aa_matrix().

void protocols::mean_field::AAMatrix::init ( std::istream & aa_matrix_file )

private

private method called by constructors to initialize the AAMatrix from a transfac file

private method used to initialize AAMatrix as jagged_array of AAProbs from input transfac file

called by constructors

curr_aa_ vector left empty

Parameters

[in] aa_matrix_file - transfac file

References curr_aa_, core::chemical::num_canonical_aas, parse_aa_line(), parse_aa_matrix_line(), and core::pack::task::tokenize_line().

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

Assignment operator.

References copy_data().

void protocols::mean_field::AAMatrix::parse_aa_line	(	utility::vector1< std::string > const &	tokens,
		utility::vector1< core::chemical::AA > &	aa_names
	)

private

parse header (AA codes) line of the AAMatrix

parses header (2nd line) of transfac file into list of aa_names

necessary to determine which probability is which AA for subsequent lines

References core::chemical::aa_from_oneletter_code().

Referenced by init().

utility::vector1< AAProb > protocols::mean_field::AAMatrix::parse_aa_matrix_line	(	utility::vector1< std::string > const &	tokens,
		utility::vector1< core::chemical::AA > const &	aa_names
	)

private

parse line of transfac file to add a vector of probabilities for one position to the AAMatrix

parses line of transfac i.e. 200 0.5 0.2 0.3...

pushes back appropriate vector into AAMatrix

References protocols::cluster::calibur::aa, protocols::pack_daemon::error_message, and core::chemical::num_canonical_aas.

Referenced by init().

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

Generate string representation of AAMatrix for debugging purposes.

prints representation of AAMatrix using show() function of AAProbs

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

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

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

Referenced by protocols::mean_field::operator<<(), protocols::mean_field::GenMeanFieldMover::read_aa_matrix(), and protocols::mean_field::GenMeanFieldMover::report_aa_matrix().

Friends And Related Function Documentation

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

friend

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

Member Data Documentation

utility::vector1< core::Size > protocols::mean_field::AAMatrix::curr_aa_

private

Referenced by copy_data(), curr_aa(), curr_aa_prob(), and init().

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

src/protocols/mean_field/AAMatrix.hh
src/protocols/mean_field/AAMatrix.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