A helper class to assist in parsing rotamer libraries. More...

#include <RotamericSingleResidueDunbrackLibraryParser.hh>

Inheritance diagram for core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser:

Public Member Functions
	RotamericSingleResidueDunbrackLibraryParser (core::Size const num_mainchain_torsions, core::Size const max_possible_chis, core::Size const max_possible_rotamers, bool const correct_rotamer_well_order_on_read, bool const symmetrize_rotamer_library)
	Default constructor. More...

	RotamericSingleResidueDunbrackLibraryParser (RotamericSingleResidueDunbrackLibraryParser const &src)

	~RotamericSingleResidueDunbrackLibraryParser () override

RotamericSingleResidueDunbrackLibraryParserOP	clone () const

void	clear_imporated_data ()
	Clear all of the data read from a file. More...

std::string	read_file (utility::io::izstream &infile, bool first_line_three_letter_code_already_read, core::chemical::AA const aa)
	Read an input stream to set up this object. More...

template<core::Size T, core::Size N>
void	configure_rotameric_single_residue_dunbrack_library (RotamericSingleResidueDunbrackLibrary< T, N > &library, utility::fixedsizearray1< Size, N > const &n_bb_bins) const
	Based on the material read from the file and stored in this object, configure a dunbrack library. More...

template<Size N>
Size	calc_product (utility::fixedsizearray1< Size, N > factors) const
	Calculate the product of elements in a fixedsizearray. More...

Private Member Functions
bool	check_for_extra_column (utility::io::izstream &infile, bool const first_line_three_letter_code_already_read) const
	When the first non-comment line is read from a rotamer file, check whether there's an extra column (signifying that this is a Shapovalov file, which has an extra column in the middle.) More...

bool	correct_for_duplicated_mainchain_data ()
	The legacy reader had a check for mainchain torsions equal to -180, in which case the last rotamer read was discarded. Maintaining that here. More...

void	remove_last_entry_in_vectors ()
	Delete the last entry in all of the data vectors. More...

void	check_correct_vector_lengths () const
	Confirm that all data vectors have the same length. Throw an error if they don't. More...

bool	determine_rotamer_well_order (utility::vector1< std::map< core::Size, core::Size > > &rotamer_well_reordering, std::string const &filename) const
	Determine the remapping for the indices of the rotamer wells read from disk to ensure that they have the order consistent with the Rosetta convention. More...

bool	check_rotamer_well_order () const
	This does a simple check of all of the rotamer well order, to determine whether it's consistent with the Rosetta convention. More...

void	update_rotamer_well_order (utility::vector1< std::map< core::Size, core::Size > > const &rotamer_well_reordering)
	Given a map defining a reordering of rotamer wells, reorder rotamer wells. More...

void	symmetrize_library (std::string const &filename)
	Given a rotamer library, symmetrize it. More...

void	do_all_checks_and_corrections (std::string const &filename)
	Performs a number of checks and corrections. More...

bool	is_canonical_talaris_library (std::string const &filename) const
	Given a filename, return true if this is a talaris library for a canonical amino acid, false otherwise. More...

bool	is_canonical_beta_nov16_library (std::string const &filename) const
	Given a filename, return true if this is a beta_nov16 library for a canonical amino acid, false otherwise. More...

bool	is_old_canonical_dun02_library (std::string const &filename) const
	Given a filename, return true if this is an old Dunbrack 2002 library for a canonical amino acid, false otherwise. More...

bool	value_is_in_map (std::map< core::Size, core::Size > const &the_map, core::Size the_value) const
	Given a Size->Size map, determine whether there exists a key that maps to a given value. More...

void	hacky_parser_init_workaround ()
	This function forces the instantiation of virtual templated methods in the derived classes. Functions like this one are necessary when combining polymorphism and templates. Though these functions must be compiled, they need never be called. Do not call this function. More...

Private Attributes
bool	read_file_was_called_
	Was the read_file() method called? More...

core::Size	num_mainchain_torsions_
	Number of mainchain torsions upon which this rotamer library depends. More...

core::Size	max_possible_chis_
	Max number of chis allowed. More...

core::Size	max_possible_rotamers_
	The maximum number of possible rotamers. More...

utility::vector1 < utility::vector1< core::Real > >	backbone_torsions_
	Backbone torsions for each rotamer. More...

utility::vector1< core::Size >	counts_
	Counts for each rotamer. Not actually used. More...

utility::vector1 < utility::vector1< core::Size > >	rotwells_
	Rotamer indices for each rotamer. Only used for warnings. More...

utility::vector1< core::Real >	probabilities_
	Probabilities for each rotamer. Used in scoring. More...

utility::vector1 < utility::vector1< core::Real > >	chimeans_
	The chimean values, which define the centres of each rotamer. More...

utility::vector1 < utility::vector1< core::Real > >	chi_std_devs_
	The chi standard deviation values, which define the ramping of each chi well. More...

bool	is_canonical_dun02_library_
	Is this library a canonical amino acid's Dunbrack2002 library? More...

bool	correct_rotamer_well_order_on_read_
	Should the rotamer wells be auto-corrected? More...

bool	symmetrize_rotamer_library_
	Should this rotamer library be symmetrized? More...

Detailed Description

A helper class to assist in parsing rotamer libraries.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Constructor & Destructor Documentation

core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::RotamericSingleResidueDunbrackLibraryParser	(	core::Size const	num_mainchain_torsions,
		core::Size const	max_possible_chis,
		core::Size const	max_possible_rotamers,
		bool const	correct_rotamer_well_order_on_read,
		bool const	symmetrize_rotamer_library
	)

Default constructor.

Parameters

[in]	num_mainchain_torsions	The number of mainchain torsions on which this rotamer library depends.
[in]	max_possible_chis	The maximum number of chis allowed in this rotamer library. This is the number of chi columns in the file (usually 4).
[in]	max_possible_rotamers	The maximum number of rotamers that this rotamer library can define.
[in]	correct_rotamer_well_order_on_read	Should rotamer wells be auto-sorted so that they're in order form least to greatest in the interval [0,360)? Note that this should not be necessary, so this defaults to false.
[in]	symmetrize_rotamer_library	If true, the rotamer library is symmetrized by averaging. Useful for peptoids with achiral sidechains.

References max_possible_chis_, max_possible_rotamers_, and num_mainchain_torsions_.

core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::RotamericSingleResidueDunbrackLibraryParser ( RotamericSingleResidueDunbrackLibraryParser const & src )

References max_possible_chis_, max_possible_rotamers_, and num_mainchain_torsions_.

core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::~RotamericSingleResidueDunbrackLibraryParser ( )

override

Member Function Documentation

template<Size N>

Size core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::calc_product ( utility::fixedsizearray1< Size, N > factors ) const

inline

Calculate the product of elements in a fixedsizearray.

References core::chemical::element::N.

Referenced by configure_rotameric_single_residue_dunbrack_library().

void core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::check_correct_vector_lengths ( ) const

private

Confirm that all data vectors have the same length. Throw an error if they don't.

References backbone_torsions_, chi_std_devs_, chimeans_, counts_, probabilities_, and rotwells_.

Referenced by do_all_checks_and_corrections().

bool core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::check_for_extra_column	(	utility::io::izstream &	infile,
		bool const	first_line_three_letter_code_already_read
	)		const

private

When the first non-comment line is read from a rotamer file, check whether there's an extra column (signifying that this is a Shapovalov file, which has an extra column in the middle.)

Author: Vikram K. Mulligan, Baker laboratory (vmull.nosp@m.ig@u.nosp@m.w.edu)

References max_possible_chis_, and num_mainchain_torsions_.

Referenced by read_file().

bool core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::check_rotamer_well_order ( ) const

private

This does a simple check of all of the rotamer well order, to determine whether it's consistent with the Rosetta convention.

Rotamers should be in order from lowest to highest in the range [0, 360). Returns true if this is NOT the case, false otherwise.

Note: This checks ALL backbone bins.

References backbone_torsions_, chimeans_, and rotwells_.

Referenced by do_all_checks_and_corrections().

void core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::clear_imporated_data ( )

Clear all of the data read from a file.

Also resets read_file_was_called_ to false.

References backbone_torsions_, chi_std_devs_, chimeans_, counts_, is_canonical_dun02_library_, max_possible_rotamers_, probabilities_, read_file_was_called_, and rotwells_.

Referenced by read_file().

RotamericSingleResidueDunbrackLibraryParserOP core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::clone ( ) const

template<core::Size T, core::Size N>

void core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library	(	RotamericSingleResidueDunbrackLibrary< T, N > &	library,
		utility::fixedsizearray1< Size, N > const &	n_bb_bins
	)		const

Based on the material read from the file and stored in this object, configure a dunbrack library.

read_file() must be called first.

Parameters

[in]	library	Pass in *this from a RotamericSingleResidueDunbrackLibrary member function.
[in]	n_bb_bins	Pass in N_BB_BINS.

Note: Implemented in RotamericSingleResidueDunbrackLibraryParser.tmpl.hh.

Referenced by hacky_parser_init_workaround(), and core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::read_from_file().

bool core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::correct_for_duplicated_mainchain_data ( )

private

The legacy reader had a check for mainchain torsions equal to -180, in which case the last rotamer read was discarded. Maintaining that here.

Returns: Returns true for correction applied (i.e. last rotamer deleted), false otherwise.

References backbone_torsions_, num_mainchain_torsions_, and remove_last_entry_in_vectors().

Referenced by read_file().

bool core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::determine_rotamer_well_order	(	utility::vector1< std::map< core::Size, core::Size > > &	rotamer_well_reordering,
		std::string const &	filename
	)		const

private

Determine the remapping for the indices of the rotamer wells read from disk to ensure that they have the order consistent with the Rosetta convention.

Rotamers should be in order from lowest to highest in the range [0, 360). Returns true if this is NOT the case, false otherwise. If true, the rotamer_well_reordering map (which is cleared by this operation) is populated with a remapping that sorts the rotamers properly.

Note: This uses the first backbone bin to determine the reordering. After applying this to all rotamer wells, it is necessary to check that no further reordering is needed. The filename parameter is only used for error messages.

References backbone_torsions_, chimeans_, rotwells_, core::pack::dunbrack::TR(), and value_is_in_map().

Referenced by do_all_checks_and_corrections().

void core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::do_all_checks_and_corrections ( std::string const & filename )

private

Performs a number of checks and corrections.

Calls check_correct_vector_lengths(), determine_rotamer_well_order(), check_rotamer_well_order(), update_rotamer_well_order(), and symmetrize_library() (for peptoids). Additional checks and corrections may be added in the future.

Parameters

[in] filename The name of the rotamer file currently being read. This is only used for error messages.

References check_correct_vector_lengths(), check_rotamer_well_order(), correct_rotamer_well_order_on_read_, determine_rotamer_well_order(), is_canonical_beta_nov16_library(), is_canonical_dun02_library_, is_canonical_talaris_library(), is_old_canonical_dun02_library(), symmetrize_library(), symmetrize_rotamer_library_, core::pack::dunbrack::TR(), and update_rotamer_well_order().

Referenced by read_file().

void core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::hacky_parser_init_workaround ( )

private

This function forces the instantiation of virtual templated methods in the derived classes. Functions like this one are necessary when combining polymorphism and templates. Though these functions must be compiled, they need never be called. Do not call this function.

THIS FUNCTION SHOULD NEVER BE CALLED!

References configure_rotameric_single_residue_dunbrack_library(), and core::chemical::ResidueType::make().

bool core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::is_canonical_beta_nov16_library ( std::string const & filename ) const

private

Given a filename, return true if this is a beta_nov16 library for a canonical amino acid, false otherwise.

References protocols::abinitio::filename(), and protocols::hybridization::path.

Referenced by do_all_checks_and_corrections().

bool core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::is_canonical_talaris_library ( std::string const & filename ) const

private

Given a filename, return true if this is a talaris library for a canonical amino acid, false otherwise.

References protocols::abinitio::filename(), and protocols::hybridization::path.

Referenced by do_all_checks_and_corrections().

bool core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::is_old_canonical_dun02_library ( std::string const & filename ) const

private

Given a filename, return true if this is an old Dunbrack 2002 library for a canonical amino acid, false otherwise.

References protocols::abinitio::filename().

Referenced by do_all_checks_and_corrections().

std::string core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::read_file	(	utility::io::izstream &	infile,
		bool	first_line_three_letter_code_already_read,
		core::chemical::AA const	aa
	)

Read an input stream to set up this object.

The RotamericSingleResidueDunbrackLibraryParser stores the information from the rotamer library in a very one-to-one format, and can subsequently be used to configure a RotamericSingleResidueDunbrackLibrary object (requiring some interpretation of the data).

Note: We might be starting the read in the middle of the file, and the three-letter code from the first line might already have been read.

Returns: The name of the next amino acid specified in the input stream, or alternatively an empty string if EOF is reached.

References backbone_torsions_, BOGUS_CHI_STD_DEV, check_for_extra_column(), chi_std_devs_, chimeans_, clear_imporated_data(), correct_for_duplicated_mainchain_data(), counts_, do_all_checks_and_corrections(), is_canonical_dun02_library_, core::chemical::is_canonical_L_aa_or_gly(), max_possible_chis_, MIN_CHI_STD_DEV, MIN_PROBABILITY, core::chemical::name_from_aa(), num_mainchain_torsions_, probabilities_, protocols::simple_moves::bb_sampler::probability, read_file_was_called_, and rotwells_.

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::read_from_file().

void core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::remove_last_entry_in_vectors ( )

private

Delete the last entry in all of the data vectors.

References backbone_torsions_, chi_std_devs_, chimeans_, counts_, probabilities_, and rotwells_.

Referenced by correct_for_duplicated_mainchain_data().

void core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::symmetrize_library ( std::string const & filename )

private

Given a rotamer library, symmetrize it.

Called for peptoids with achiral side-chains.

Parameters

[in] filename The filename of this library, used for logging and error messages.

References backbone_torsions_, chi_std_devs_, chimeans_, counts_, MIN_DELTA, probabilities_, protocols::noesy_assign::round(), symmetrize_rotamer_library_, and core::pack::dunbrack::TR().

Referenced by do_all_checks_and_corrections().

void core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::update_rotamer_well_order ( utility::vector1< std::map< core::Size, core::Size > > const & rotamer_well_reordering )

private

Given a map defining a reordering of rotamer wells, reorder rotamer wells.

References rotwells_.

Referenced by do_all_checks_and_corrections().

bool core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::value_is_in_map	(	std::map< core::Size, core::Size > const &	the_map,
		core::Size	the_value
	)		const

private

Given a Size->Size map, determine whether there exists a key that maps to a given value.

Referenced by determine_rotamer_well_order().

Member Data Documentation

utility::vector1< utility::vector1< core::Real > > core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::backbone_torsions_

private

Backbone torsions for each rotamer.

Referenced by check_correct_vector_lengths(), check_rotamer_well_order(), clear_imporated_data(), configure_rotameric_single_residue_dunbrack_library(), correct_for_duplicated_mainchain_data(), determine_rotamer_well_order(), read_file(), remove_last_entry_in_vectors(), and symmetrize_library().

utility::vector1< utility::vector1 < core::Real > > core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::chi_std_devs_

private

The chi standard deviation values, which define the ramping of each chi well.

Referenced by check_correct_vector_lengths(), clear_imporated_data(), configure_rotameric_single_residue_dunbrack_library(), read_file(), remove_last_entry_in_vectors(), and symmetrize_library().

utility::vector1< utility::vector1 < core::Real > > core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::chimeans_

private

The chimean values, which define the centres of each rotamer.

Referenced by check_correct_vector_lengths(), check_rotamer_well_order(), clear_imporated_data(), configure_rotameric_single_residue_dunbrack_library(), determine_rotamer_well_order(), read_file(), remove_last_entry_in_vectors(), and symmetrize_library().

bool core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::correct_rotamer_well_order_on_read_

private

Should the rotamer wells be auto-corrected?

Probably no longer necessary if Voronoi-based interpolation is used.

Referenced by do_all_checks_and_corrections().

utility::vector1< core::Size > core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::counts_

private

Counts for each rotamer. Not actually used.

Referenced by check_correct_vector_lengths(), clear_imporated_data(), read_file(), remove_last_entry_in_vectors(), and symmetrize_library().

bool core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::is_canonical_dun02_library_

private

Is this library a canonical amino acid's Dunbrack2002 library?

If it is, we need to skip the correction step, since the canonical Dun02 library has wonky rotamer well orders that are corrected some other way.

Referenced by clear_imporated_data(), do_all_checks_and_corrections(), and read_file().

core::Size core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::max_possible_chis_

private

Max number of chis allowed.

Referenced by check_for_extra_column(), read_file(), and RotamericSingleResidueDunbrackLibraryParser().

core::Size core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::max_possible_rotamers_

private

The maximum number of possible rotamers.

Referenced by clear_imporated_data(), and RotamericSingleResidueDunbrackLibraryParser().

core::Size core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::num_mainchain_torsions_

private

Number of mainchain torsions upon which this rotamer library depends.

Referenced by check_for_extra_column(), correct_for_duplicated_mainchain_data(), read_file(), and RotamericSingleResidueDunbrackLibraryParser().

utility::vector1< core::Real > core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::probabilities_

private

Probabilities for each rotamer. Used in scoring.

Referenced by check_correct_vector_lengths(), clear_imporated_data(), configure_rotameric_single_residue_dunbrack_library(), read_file(), remove_last_entry_in_vectors(), and symmetrize_library().

bool core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::read_file_was_called_

private

Was the read_file() method called?

Referenced by clear_imporated_data(), configure_rotameric_single_residue_dunbrack_library(), and read_file().

utility::vector1< utility::vector1 < core::Size > > core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::rotwells_

private

Rotamer indices for each rotamer. Only used for warnings.

Referenced by check_correct_vector_lengths(), check_rotamer_well_order(), clear_imporated_data(), configure_rotameric_single_residue_dunbrack_library(), determine_rotamer_well_order(), read_file(), remove_last_entry_in_vectors(), and update_rotamer_well_order().

bool core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::symmetrize_rotamer_library_

private

Should this rotamer library be symmetrized?

Referenced by do_all_checks_and_corrections(), and symmetrize_library().

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

src/core/pack/dunbrack/RotamericSingleResidueDunbrackLibraryParser.hh
src/core/pack/dunbrack/RotamericSingleResidueDunbrackLibraryParser.cc
src/core/pack/dunbrack/RotamericSingleResidueDunbrackLibraryParser.tmpl.hh

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation