#include <BinTransitionCalculator.hh>

Inheritance diagram for core::scoring::bin_transitions::BinTransitionCalculator:

Public Member Functions
	BinTransitionCalculator ()
	Default constructor for BinTransitionCalculator. More...

	BinTransitionCalculator (BinTransitionCalculator const &src)
	Copy constructor for BinTransitionCalculator. More...

	~BinTransitionCalculator ()
	Default destructor for BinTransitionCalculator. More...

BinTransitionCalculatorOP	clone () const
	Clone operation for BinTransitionCalculator. More...

std::string	summarize_stored_data (bool const verbose) const
	Prints a report summarizing the data stored in this object, including all of the BinTransitionData objects. More...

void	load_bin_params (std::string const &filename)
	Set the bin params file, and load all the bin params and transition probabilities. More...

void	load_bin_params_from_file_contents (std::string const &filecontents)
	Loads all bin params from a string representing file contents. More...

void	find_data_and_bin (std::string const &bin_name, core::conformation::Residue const &res, core::Size &data_index, core::Size &bin_index, bool const use_iplus1) const
	Given a bin name and a residue, find a BinTransitionsData object describing that residue, and the index of the bin within that object. More...

bool	find_data (core::conformation::Residue const &res_i, core::conformation::Residue const &res_iplus1, core::Size &data_index) const
	Given residues at positions i and iplus1, find a bin transition probability data object that describes the pair. More...

bool	p_iplus1_given_i (core::conformation::Residue const &rsd_i, core::conformation::Residue const &rsd_iplus1, core::Real &probability) const
	Given two residues (rsd_i and rsd_iplus1 at positions i and i+1, respectively), give me the probability of seeing rsd_iplus1 in its bin given that rsd_i is in its bin. More...

bool	p_i_given_iplus1 (core::conformation::Residue const &rsd_i, core::conformation::Residue const &rsd_iplus1, core::Real &probability) const
	Given two residues (rsd_i and rsd_iplus1 at positions i and i+1, respectively), give me the probability of seeing rsd_i in its bin given that rsd_iplus1 is in its bin. More...

bool	is_in_bin (core::conformation::Residue const &res, std::string const &bin_name) const
	Is the given residue in the given bin? More...

bool	is_in_bin (core::conformation::Residue const &res, core::Size const data_index, core::Size const bin_index, bool const use_iplus1) const
	Is the given residue in the bin given by a data object index and a bin index? More...

void	random_mainchain_torsions_from_bins (core::conformation::Conformation const &conformation, utility::vector1< core::Size > const &res_indices, utility::vector1< utility::vector1< core::Real > > &mainchain_torsions) const
	Initialize a string of residues to a bunch of random bins, based on bin transition probabilities; then draw random mainchain torsion angles from those bins. More...

void	random_mainchain_torsions_from_bin (std::string const &bin_name, core::conformation::Conformation const &conformation, utility::vector1< core::Size > const &res_indices, utility::vector1< utility::vector1< core::Real > > &mainchain_torsions) const
	Draw random mainchain torsion values for a set of residues, given a bin from which the values should be drawn. More...

void	random_mainchain_torsions_using_adjacent_bins (core::conformation::Conformation const &conformation, core::Size const res_index, bool const must_switch_bins, utility::vector1< core::Real > &mainchain_torsions) const
	Randomly pick mainchain torsions for a residue based on the torsion bins of its i+1 and i-1 neighbours. More...

core::Size	random_bin (core::conformation::Residue const &res, bool &iplus1, core::Size &data_index) const
	Randomly pick a bin, given an input residue. More...

void	random_mainchain_torsions_from_bin (core::Size const bin_index, bool const iplus1, core::Size const data_index, utility::vector1< core::Real > &mainchain_torsions) const
	Randomly pick mainchain torsion values from within a bin. More...

core::Size	random_bin_based_on_previous (core::conformation::Residue const &thisres, core::conformation::Residue const &prevres, utility::vector1< core::Real > const &prev_torsions, core::Size &data_index) const
	Given the current residue and the previous residue, as well as the mainchain torsion values for the previous residue, pick a bin for the current residue based on bin transition probabilities. More...

core::Size	random_bin_based_on_prev_and_next (core::conformation::Conformation const &conformation, core::Size const res_index, bool const must_switch_bins, core::Size &data_index_i, core::Size &data_index_iplus1) const
	Given the current residue and its conformation, pick a bin for the current residue based on the bins of the previous and next residues, and the bin transition probabilities. More...

bool	bin_params_loaded () const
	Return whether the bin params file has been loaded. More...

core::Size	n_bin_transition_data () const
	Number of BinTransitionData objects stored (i.e. number of transition probability matrices stored). More...

bool	bin_definition_exists (std::string const &name) const
	Is a particular bin defined for at least one residue type? More...

Private Member Functions
void	parse_lines (utility::vector1< std::string > const &lines)
	Given a file split into lines, parse the lines and set up this object. More...

void	biased_mainchain_torsions (core::Size const bin_index, bool const iplus1, core::Size const data_index, utility::vector1< core::Real > &mainchain_torsions) const
	Given a bin, generate phi and psi values from within the bin, biased by the sub-bin cumulative probability distribution function. More...

void	uniform_mainchain_torsions (core::Size const bin_index, bool const iplus1, core::Size const data_index, utility::vector1< core::Real > &mainchain_torsions) const
	Given a bin, generate phi and psi values randomly from within the bin, with uniform distribution. More...

bool	has_another_matrix (utility::vector1< std::string > const &lines, core::Size &firstline, core::Size &lastline) const
	Get the first and last lines of the next set of lines flanked by "BEGIN" and "END" lines. More...

BinTransitionDataOP	add_bin_transition_data ()
	Add a BinTransitionData object to the list of BinTransitionData objects, and return an owning pointer to the newly-added object. More...

void	parse_mainchain_torsions (utility::vector1< std::string > const &lines, core::Size const firstline, core::Size const lastline, BinTransitionDataOP curdata)
	Parse the number of mainchain torsions for the ith and i+1st residues defined in the current block of lines from the bin_params file. More...

void	initialize_matrix (utility::vector1< std::string > const &lines, core::Size const firstline, core::Size const lastline, BinTransitionDataOP curdata)
	Parse the number of torsion bins for the ith and i+1st residues as defined in the current block of lines, and initialize the probability matrix to a grid of zeroes of appropiate dimensions. More...

void	set_up_bins (utility::vector1< std::string > const &lines, core::Size const firstline, core::Size const lastline, BinTransitionDataOP curdata)
	Parse the names and angle ranges for each bin for the ith and i+1st residue. More...

void	populate_matrix (utility::vector1< std::string > const &lines, core::Size const firstline, core::Size const lastline, BinTransitionDataOP curdata)
	Parse the transition probabilities in the probability matrix, and store the values. More...

void	store_properties (utility::vector1< std::string > const &lines, core::Size const firstline, core::Size const lastline, BinTransitionDataOP curdata)
	Parse the required and prohibited properties for the ith and i+1st residues. More...

void	store_residue_identities (utility::vector1< std::string > const &lines, core::Size const firstline, core::Size const lastline, BinTransitionDataOP curdata)
	Parse the required and prohibited residue types (three-letter codes) for the ith and i+1st residues. More...

BinTransitionDataCOP	bin_transition_data (core::Size const index) const
	Access one of the bin_transition_data objects (const-access). More...

bool	are_normally_bonded (core::conformation::Residue const &thisres, core::conformation::Residue const &prevres) const
	Is thisres connected to prevres at the lower connection of thisres and the upper connection of prevres? More...

Private Attributes
bool	bin_params_loaded_
	Has a bin params file been loaded? More...

std::string	bin_params_file_
	The filename for the bin params file that defines the bins and their transition probabilities. More...

BinTransitionDataOPs	bin_transition_data_
	Vector1 of BinTransitionData objects. More...

Constructor & Destructor Documentation

core::scoring::bin_transitions::BinTransitionCalculator::BinTransitionCalculator ( )

Default constructor for BinTransitionCalculator.

Referenced by clone().

core::scoring::bin_transitions::BinTransitionCalculator::BinTransitionCalculator ( BinTransitionCalculator const & src )

Copy constructor for BinTransitionCalculator.

References bin_transition_data_.

core::scoring::bin_transitions::BinTransitionCalculator::~BinTransitionCalculator ( )

Default destructor for BinTransitionCalculator.

Member Function Documentation

BinTransitionDataOP core::scoring::bin_transitions::BinTransitionCalculator::add_bin_transition_data ( )

inlineprivate

Add a BinTransitionData object to the list of BinTransitionData objects, and return an owning pointer to the newly-added object.

Each BinTransitionData object stores the BinTransition matrix for a particular i / i+1 pair. For example, there might be one matrix for i=L-amino acid, i+1=L-amino acid, and another for i=D-amino acid, i+1=D-amino acid.

References bin_transition_data_.

Referenced by parse_lines().

bool core::scoring::bin_transitions::BinTransitionCalculator::are_normally_bonded	(	core::conformation::Residue const &	thisres,
		core::conformation::Residue const &	prevres
	)		const

private

Is thisres connected to prevres at the lower connection of thisres and the upper connection of prevres?

Returns true or false based on whether this is the case.

References core::conformation::Residue::has_lower_connect(), core::conformation::Residue::has_upper_connect(), core::chemical::ResidueType::lower_connect_id(), core::conformation::Residue::residue_connection_partner(), core::conformation::Residue::seqpos(), core::conformation::Residue::type(), and core::chemical::ResidueType::upper_connect_id().

Referenced by random_bin_based_on_prev_and_next(), and random_bin_based_on_previous().

void core::scoring::bin_transitions::BinTransitionCalculator::biased_mainchain_torsions	(	core::Size const	bin_index,
		bool const	iplus1,
		core::Size const	data_index,
		utility::vector1< core::Real > &	mainchain_torsions
	)		const

private

Given a bin, generate phi and psi values from within the bin, biased by the sub-bin cumulative probability distribution function.

bin_index, iplus1, and data_index are inputs, mainchain_torsions vector is cleared and set by this function (i.e. it's output).

References bin_params_loaded(), bin_transition_data(), bin_transition_data_, core::sequence::end, n_bin_transition_data(), core::scoring::rg, and protocols::loops::start.

Referenced by random_mainchain_torsions_from_bin().

bool core::scoring::bin_transitions::BinTransitionCalculator::bin_definition_exists ( std::string const & name ) const

Is a particular bin defined for at least one residue type?

References bin_transition_data_.

bool core::scoring::bin_transitions::BinTransitionCalculator::bin_params_loaded ( ) const

inline

Return whether the bin params file has been loaded.

References bin_params_loaded_.

Referenced by biased_mainchain_torsions(), load_bin_params(), load_bin_params_from_file_contents(), p_i_given_iplus1(), p_iplus1_given_i(), random_bin(), random_bin_based_on_previous(), and uniform_mainchain_torsions().

BinTransitionDataCOP core::scoring::bin_transitions::BinTransitionCalculator::bin_transition_data ( core::Size const index ) const

inlineprivate

Access one of the bin_transition_data objects (const-access).

References bin_transition_data_.

Referenced by biased_mainchain_torsions(), find_data(), find_data_and_bin(), is_in_bin(), p_i_given_iplus1(), p_iplus1_given_i(), random_bin(), random_bin_based_on_prev_and_next(), random_bin_based_on_previous(), random_mainchain_torsions_from_bin(), and uniform_mainchain_torsions().

BinTransitionCalculatorOP core::scoring::bin_transitions::BinTransitionCalculator::clone ( ) const

Clone operation for BinTransitionCalculator.

Returns an owning pointer to a copy of this object.

References BinTransitionCalculator().

bool core::scoring::bin_transitions::BinTransitionCalculator::find_data	(	core::conformation::Residue const &	res_i,
		core::conformation::Residue const &	res_iplus1,
		core::Size &	data_index
	)		const

Given residues at positions i and iplus1, find a bin transition probability data object that describes the pair.

Inputs are res_i and res_iplus1. Outputs are data_i and data_iplus1 (BinTransitionData indices). Function returns true if data are found successfully, false if no BinTransitionData object could be found describing the residues in question.

References bin_transition_data(), and n_bin_transition_data().

Referenced by p_i_given_iplus1(), and p_iplus1_given_i().

void core::scoring::bin_transitions::BinTransitionCalculator::find_data_and_bin	(	std::string const &	bin_name,
		core::conformation::Residue const &	res,
		core::Size &	data_index,
		core::Size &	bin_index,
		bool const	use_iplus1
	)		const

Given a bin name and a residue, find a BinTransitionsData object describing that residue, and the index of the bin within that object.

data_index and bin_index are outputs. Both are set to 0 if the search fails. Everything else is const input. If bin_name is set to "", then the bin index that is returned is the index corresponding to the residue's mainchain torsion vector.

References bin_transition_data(), core::conformation::Residue::mainchain_torsions(), and n_bin_transition_data().

Referenced by is_in_bin(), and random_mainchain_torsions_from_bin().

bool core::scoring::bin_transitions::BinTransitionCalculator::has_another_matrix	(	utility::vector1< std::string > const &	lines,
		core::Size &	firstline,
		core::Size &	lastline
	)		const

private

Get the first and last lines of the next set of lines flanked by "BEGIN" and "END" lines.

This function returns "true" if another BEGIN/END pair is found, false otherwise. It starts searching at lastline+1, and continues to the end of lines. If it finds a BEGIN/END pair, it sets firstline to the position of the BEGIN line and lastline to the position of the END line. It throws an error if a BEGIN line does not have a corresponding END line.

Referenced by parse_lines().

void core::scoring::bin_transitions::BinTransitionCalculator::initialize_matrix	(	utility::vector1< std::string > const &	lines,
		core::Size const	firstline,
		core::Size const	lastline,
		BinTransitionDataOP	curdata
	)

private

Parse the number of torsion bins for the ith and i+1st residues as defined in the current block of lines, and initialize the probability matrix to a grid of zeroes of appropiate dimensions.

Referenced by parse_lines().

bool core::scoring::bin_transitions::BinTransitionCalculator::is_in_bin	(	core::conformation::Residue const &	res,
		std::string const &	bin_name
	)		const

Is the given residue in the given bin?

For the bin definitions, this uses the first BinTransitionsData object that it finds where residue i matches the properties of the given residue. Checks the i+1 definitions if nothing is found for the i transitions. Fails if no bin definitions for the given residue type are found.

References find_data_and_bin().

bool core::scoring::bin_transitions::BinTransitionCalculator::is_in_bin	(	core::conformation::Residue const &	res,
		core::Size const	data_index,
		core::Size const	bin_index,
		bool const	use_iplus1
	)		const

Is the given residue in the bin given by a data object index and a bin index?

References bin_transition_data().

void core::scoring::bin_transitions::BinTransitionCalculator::load_bin_params ( std::string const & filename )

Set the bin params file, and load all the bin params and transition probabilities.

References bin_params_file_, bin_params_loaded(), bin_params_loaded_, protocols::abinitio::filename(), and parse_lines().

void core::scoring::bin_transitions::BinTransitionCalculator::load_bin_params_from_file_contents ( std::string const & filecontents )

Loads all bin params from a string representing file contents.

Provided as an alternative to direct load from disk.

References bin_params_loaded(), bin_params_loaded_, and parse_lines().

core::Size core::scoring::bin_transitions::BinTransitionCalculator::n_bin_transition_data ( ) const

inline

Number of BinTransitionData objects stored (i.e. number of transition probability matrices stored).

References bin_transition_data_.

Referenced by biased_mainchain_torsions(), find_data(), find_data_and_bin(), random_bin(), random_bin_based_on_prev_and_next(), random_bin_based_on_previous(), random_mainchain_torsions_from_bin(), and uniform_mainchain_torsions().

bool core::scoring::bin_transitions::BinTransitionCalculator::p_i_given_iplus1	(	core::conformation::Residue const &	res_i,
		core::conformation::Residue const &	res_iplus1,
		core::Real &	probability
	)		const

Given two residues (rsd_i and rsd_iplus1 at positions i and i+1, respectively), give me the probability of seeing rsd_i in its bin given that rsd_iplus1 is in its bin.

The probability value is set to a number from 0 to 1. Inputs are rsd_i and rsd_iplus1. Function returns true if data are found successfully, false if no BinTransitionData object could be found describing the residues in question.

References bin_params_loaded(), bin_transition_data(), find_data(), core::conformation::Residue::mainchain_torsions(), and core::conformation::Residue::seqpos().

bool core::scoring::bin_transitions::BinTransitionCalculator::p_iplus1_given_i	(	core::conformation::Residue const &	res_i,
		core::conformation::Residue const &	res_iplus1,
		core::Real &	probability
	)		const

Given two residues (rsd_i and rsd_iplus1 at positions i and i+1, respectively), give me the probability of seeing rsd_iplus1 in its bin given that rsd_i is in its bin.

The probability value is set to a number from 0 to 1. Inputs are rsd_i and rsd_iplus1. Function returns true if data are found successfully, false if no BinTransitionData object could be found describing the residues in question.

References bin_params_loaded(), bin_transition_data(), find_data(), core::conformation::Residue::mainchain_torsions(), and core::conformation::Residue::seqpos().

void core::scoring::bin_transitions::BinTransitionCalculator::parse_lines ( utility::vector1< std::string > const & lines )

private

Given a file split into lines, parse the lines and set up this object.

References add_bin_transition_data(), has_another_matrix(), initialize_matrix(), parse_mainchain_torsions(), populate_matrix(), set_up_bins(), store_properties(), store_residue_identities(), and summarize_stored_data().

Referenced by load_bin_params(), and load_bin_params_from_file_contents().

void core::scoring::bin_transitions::BinTransitionCalculator::parse_mainchain_torsions	(	utility::vector1< std::string > const &	lines,
		core::Size const	firstline,
		core::Size const	lastline,
		BinTransitionDataOP	curdata
	)

private

Parse the number of mainchain torsions for the ith and i+1st residues defined in the current block of lines from the bin_params file.

Referenced by parse_lines().

void core::scoring::bin_transitions::BinTransitionCalculator::populate_matrix	(	utility::vector1< std::string > const &	lines,
		core::Size const	firstline,
		core::Size const	lastline,
		BinTransitionDataOP	curdata
	)

private

Parse the transition probabilities in the probability matrix, and store the values.

Referenced by parse_lines().

core::Size core::scoring::bin_transitions::BinTransitionCalculator::random_bin	(	core::conformation::Residue const &	res,
		bool &	iplus1,
		core::Size &	data_index
	)		const

Randomly pick a bin, given an input residue.

The residue's properties and name are used to find the first BinTransitionData object matching the properties and name. A random bin is then picked based on the frequency with which that bin is observed for that class of residues. If the bin ends up being from the i+1st residue, iplus1 is set to "true"; otherwise, it remains "false". The data_index variable is set by this function to the index of the BinTransitionData object that provides the transition probability data.

References bin_params_loaded(), bin_transition_data(), n_bin_transition_data(), and core::conformation::Residue::name3().

Referenced by random_bin_based_on_prev_and_next(), and random_mainchain_torsions_from_bins().

core::Size core::scoring::bin_transitions::BinTransitionCalculator::random_bin_based_on_prev_and_next	(	core::conformation::Conformation const &	conformation,
		core::Size const	res_index,
		bool const	must_switch_bins,
		core::Size &	data_index_i,
		core::Size &	data_index_iplus1
	)		const

Given the current residue and its conformation, pick a bin for the current residue based on the bins of the previous and next residues, and the bin transition probabilities.

Bin transition probabilities are assumed to be independent. That is, P(ABC) = P(B | A & C) = P (B | A ) * P(B | C). This function also finds and returns the indices of the BinTransitionData objects that describe the AB transition (data_index_iplus1) and the BC transition (data_index_i). So conformation and res_index are const inputs, and data_index_i and data_index_iplus1 are outputs. If must_switch_bins is true, then the current bin for the current residue is never chosen; otherwise, it is in the pool to be picked.

References are_normally_bonded(), bin_transition_data(), n_bin_transition_data(), random_bin(), core::conformation::Conformation::residue(), core::scoring::rg, and core::conformation::Conformation::size().

Referenced by random_mainchain_torsions_using_adjacent_bins().

core::Size core::scoring::bin_transitions::BinTransitionCalculator::random_bin_based_on_previous	(	core::conformation::Residue const &	thisres,
		core::conformation::Residue const &	prevres,
		utility::vector1< core::Real > const &	prev_torsions,
		core::Size &	data_index
	)		const

Given the current residue and the previous residue, as well as the mainchain torsion values for the previous residue, pick a bin for the current residue based on bin transition probabilities.

This function takes thisres (the current residue) and prevres (the previous residue) as inputs, using them for their properties and identities to find a BinTransitionData object that matches the criteria at the i and i+1st residues. It then sets data_index to the index of that BinTransitionData object before returning the index of a bin chosen for the current (i+1st) residue at random, based on the relative probabilities of bins given the previous (ith) residue.

References are_normally_bonded(), bin_params_loaded(), bin_transition_data(), n_bin_transition_data(), and core::conformation::Residue::name3().

Referenced by random_mainchain_torsions_from_bins().

void core::scoring::bin_transitions::BinTransitionCalculator::random_mainchain_torsions_from_bin	(	std::string const &	bin_name,
		core::conformation::Conformation const &	conformation,
		utility::vector1< core::Size > const &	res_indices,
		utility::vector1< utility::vector1< core::Real > > &	mainchain_torsions
	)		const

Draw random mainchain torsion values for a set of residues, given a bin from which the values should be drawn.

Takes a bin name, a const conformation, and a const list of residue indices as input; the conformation is just for checking residues types, numbers of mainchain torsions, etc. Output is the mainchain_torsions vector of vectors (reset and replaced by this operation). The distribution WITHIN the bin depends on the BinTransitionData object and what was specified in the bin_params file. Default is uniform within each bin, though Ramachandran-biased distributions are also permitted for alpha-amino acids. Note that this function uses bins for residue i, and only checks i+1 if no suitable data are found for i.

References find_data_and_bin(), core::conformation::Residue::mainchain_torsions(), and core::conformation::Conformation::residue().

Referenced by random_mainchain_torsions_from_bins(), and random_mainchain_torsions_using_adjacent_bins().

void core::scoring::bin_transitions::BinTransitionCalculator::random_mainchain_torsions_from_bin	(	core::Size const	bin_index,
		bool const	iplus1,
		core::Size const	data_index,
		utility::vector1< core::Real > &	mainchain_torsions
	)		const

Randomly pick mainchain torsion values from within a bin.

The residue's properties and name are used to find the first BinTransitionData object matching the properties and name. Mainchain torsion values are then picked randomly from within the bin. The distribution WITHIN the bin depends on the BinTransitionData object and what was specified in the bin_params file. Default is uniform within each bin, though Ramachandran-biased distributions are also permitted for alpha-amino acids. If iplus1 is true, we draw from the bins for the i+1st residue; otherwise, we draw from the bins for the ith residue. The data_index value tells this function which BinTransitionData object to use.

References biased_mainchain_torsions(), bin_transition_data(), core::scoring::bin_transitions::BTSB_D_AA, core::scoring::bin_transitions::BTSB_GLY, core::scoring::bin_transitions::BTSB_L_AA, n_bin_transition_data(), and uniform_mainchain_torsions().

void core::scoring::bin_transitions::BinTransitionCalculator::random_mainchain_torsions_from_bins	(	core::conformation::Conformation const &	conformation,
		utility::vector1< core::Size > const &	res_indices,
		utility::vector1< utility::vector1< core::Real > > &	mainchain_torsions
	)		const

Initialize a string of residues to a bunch of random bins, based on bin transition probabilities; then draw random mainchain torsion angles from those bins.

Takes a const conformation and a const list of residue indices as input; the conformation is just for checking residues types, numbers of mainchain torsions, etc. The residue indices must be in order, defining a contiguous chain (running backwards or forwards). Output is the mainchain_torsions vector of vectors (reset and replaced by this operation). The distribution WITHIN the bin depends on the BinTransitionData object and what was specified in the bin_params file. Default is uniform within each bin, though Ramachandran-biased distributions are also permitted for alpha-amino acids.

References core::conformation::Residue::mainchain_torsions(), random_bin(), random_bin_based_on_previous(), random_mainchain_torsions_from_bin(), and core::conformation::Conformation::residue().

void core::scoring::bin_transitions::BinTransitionCalculator::random_mainchain_torsions_using_adjacent_bins	(	core::conformation::Conformation const &	conformation,
		core::Size const	res_index,
		bool const	must_switch_bins,
		utility::vector1< core::Real > &	mainchain_torsions
	)		const

Randomly pick mainchain torsions for a residue based on the torsion bins of its i+1 and i-1 neighbours.

Takes a const conformatoin, a const residue index, and a boolean valueas input. The conformation is for checking residue types, numbers of mainchain torsions, etc. The boolean determines whether this residue should be allowed to stay in its own bin or be required to switch to another bin. Output is the mainchain_torsions vector of Reals, with one entry for each mainchain torsion of the residue.

Takes a const conformatoin, a const residue index, and a boolean valueas input. The conformation is for checking residue types, numbers of mainchain torsions, etc. The boolean determines whether this residue should be allowed to stay in its own bin or be required to switch to another bin. Output is the mainchain_torsions vector of Reals, with one entry for each mainchain torsion of the residue. Note that random mainchain torsions are drawn using the sub-bins for the case where the current residue is the ith residue.

References random_bin_based_on_prev_and_next(), and random_mainchain_torsions_from_bin().

void core::scoring::bin_transitions::BinTransitionCalculator::set_up_bins	(	utility::vector1< std::string > const &	lines,
		core::Size const	firstline,
		core::Size const	lastline,
		BinTransitionDataOP	curdata
	)

private

Parse the names and angle ranges for each bin for the ith and i+1st residue.

Referenced by parse_lines().

void core::scoring::bin_transitions::BinTransitionCalculator::store_properties	(	utility::vector1< std::string > const &	lines,
		core::Size const	firstline,
		core::Size const	lastline,
		BinTransitionDataOP	curdata
	)

private

Parse the required and prohibited properties for the ith and i+1st residues.

Referenced by parse_lines().

void core::scoring::bin_transitions::BinTransitionCalculator::store_residue_identities	(	utility::vector1< std::string > const &	lines,
		core::Size const	firstline,
		core::Size const	lastline,
		BinTransitionDataOP	curdata
	)

private

Parse the required and prohibited residue types (three-letter codes) for the ith and i+1st residues.

Referenced by parse_lines().

std::string core::scoring::bin_transitions::BinTransitionCalculator::summarize_stored_data ( bool const verbose ) const

Prints a report summarizing the data stored in this object, including all of the BinTransitionData objects.

If verbose is true, the full sub-bin information is printed, too.

References bin_params_file_, and bin_transition_data_.

Referenced by parse_lines().

void core::scoring::bin_transitions::BinTransitionCalculator::uniform_mainchain_torsions	(	core::Size const	bin_index,
		bool const	iplus1,
		core::Size const	data_index,
		utility::vector1< core::Real > &	mainchain_torsions
	)		const

private

Given a bin, generate phi and psi values randomly from within the bin, with uniform distribution.

bin_index, iplus1, and data_index are inputs, mainchain_torsions vector is cleared and set by this function (i.e. it's output).

References bin_params_loaded(), bin_transition_data(), bin_transition_data_, n_bin_transition_data(), and core::scoring::rg.

Referenced by random_mainchain_torsions_from_bin().

Member Data Documentation

std::string core::scoring::bin_transitions::BinTransitionCalculator::bin_params_file_

private

The filename for the bin params file that defines the bins and their transition probabilities.

Referenced by load_bin_params(), and summarize_stored_data().

bool core::scoring::bin_transitions::BinTransitionCalculator::bin_params_loaded_

private

Has a bin params file been loaded?

Default false; set to true by the load_bin_params() function.

Referenced by bin_params_loaded(), load_bin_params(), and load_bin_params_from_file_contents().

BinTransitionDataOPs core::scoring::bin_transitions::BinTransitionCalculator::bin_transition_data_

private

Vector1 of BinTransitionData objects.

Each BinTransitionData object stores the BinTransition matrix for a particular i / i+1 pair. For example, there might be one matrix for i=L-amino acid, i+1=L-amino acid, and another for i=D-amino acid, i+1=D-amino acid.

Referenced by add_bin_transition_data(), biased_mainchain_torsions(), bin_definition_exists(), bin_transition_data(), BinTransitionCalculator(), n_bin_transition_data(), summarize_stored_data(), and uniform_mainchain_torsions().

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

src/core/scoring/bin_transitions/BinTransitionCalculator.hh
src/core/scoring/bin_transitions/BinTransitionCalculator.cc

Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation