A class to manage the Dunbrack Rotamer Libraries. More...

#include <RotamerLibrary.hh>

Inheritance diagram for core::pack::dunbrack::RotamerLibrary:

Public Types
typedef chemical::AA	AA

typedef conformation::Residue	Residue

typedef chemical::ResidueType	ResidueType

Public Member Functions
	RotamerLibrary (utility::options::OptionCollection const &options)
	a new RotamerLibrary based on the option collection More...

virtual	~RotamerLibrary ()

Real	rotamer_energy (Residue const &rsd, pose::Pose const &pose, RotamerLibraryScratchSpace &scratch) const

Real	best_rotamer_energy (Residue const &rsd, pose::Pose const &pose, bool curr_rotamer_only, RotamerLibraryScratchSpace &scratch) const

Real	rotamer_energy_deriv (Residue const &rsd, pose::Pose const &pose, RotamerLibraryScratchSpace &scratch) const
	to do: More...

rotamers::SingleResidueRotamerLibraryCOP	get_library_by_aa (chemical::AA const &aa) const

bool	validate_dunbrack_binary ()
	Reload the Dunbrack Rotamer libraries from ASCII, and make sure that they match the ones loaded from binary. Return true if the binary file is valid, false if the binary is invalid. NOTE WELL: This is not a const function, as reloading from ASCII modifies internals. It's also VERY thread unsafe. Never call this function from a multithreaded context. More...

bool	decide_read_from_binary () const

std::string	get_binary_name () const

Static Public Member Functions
static void	initialize_dun02_aa_parameters (utility::vector1< Size > &nchi_for_aa, utility::vector1< Size > &nbb_for_aa, Size &n_rotameric_aas)

Private Types
typedef utility::vector1 < rotamers::SingleResidueRotamerLibraryCOP >	library_iterator

Private Member Functions
bool	decide_read_from_binary_02 () const

bool	decide_read_from_binary_10 () const

bool	binary_is_up_to_date (utility::io::izstream &binlib) const

bool	binary_is_up_to_date_02 (utility::io::izstream &binlib) const

bool	binary_is_up_to_date_10 (utility::io::izstream &binlib) const

bool	decide_write_binary () const

bool	decide_write_binary_02 () const

bool	decide_write_binary_10 () const

std::string	get_library_name_02 () const

std::string	get_library_name_10 () const

std::string	get_binary_name_02 (bool for_writing=false) const

std::string	get_binary_name_10 (bool for_writing=false) const

Size	current_binary_format_version_id_02 () const

Size	current_binary_format_version_id_10 () const

void	create_fa_dunbrack_libraries ()
	Main interface for reading in dunbrack libraries. Version option checks are handled inside. More...

void	create_fa_dunbrack_libraries_from_ASCII ()

void	create_fa_dunbrack_libraries_from_binary ()

void	create_fa_dunbrack_libraries_02_from_ASCII ()

void	create_fa_dunbrack_libraries_02_from_binary ()

void	create_fa_dunbrack_libraries_10_from_ASCII ()

void	create_fa_dunbrack_libraries_10_from_binary ()

void	add_residue_library (AA const &aa, rotamers::SingleResidueRotamerLibraryCOP rot_lib)
	Add a fullatom canonical AA Dunbrack library. More...

void	write_binary_fa_dunbrack_libraries () const

void	write_binary_fa_dunbrack_libraries_02 () const

void	write_binary_fa_dunbrack_libraries_10 () const

std::string	random_tempname (std::string const &same_dir_as, std::string const &prefix) const

SingleResidueDunbrackLibraryOP	create_rotameric_dunlib (chemical::ResidueType const &rt, Size const n_chi, Size const n_bb, utility::io::izstream &library, bool dun02, std::string &next_aa_in_library, bool first_three_letter_code_already_read) const
	Instantiate the appropriate RSRDL< T > library given the n_chi input and initialize the library from the input stream. Return the string that the library returns after reading the from the stream (which may be the empty string, or the three letter code for the next AA in the input stream). If the first three letter code for this amino acid has already been retrieved from the input stream, indicate so with the "first_three_letter_code_alread_read" boolean. More...

SingleResidueDunbrackLibraryOP	create_rotameric_dunlib (chemical::ResidueType const &rt, Size const n_chi, Size const n_bb, bool const dun02, bool const reduced_resolution_library=false) const

SingleResidueDunbrackLibraryOP	create_rotameric_dunlib (chemical::ResidueType const &rt, Size const n_chi, bool dun02) const

SingleResidueDunbrackLibraryOP	create_semi_rotameric_dunlib (chemical::ResidueType const &rt, Size const nchi, Size const nbb, bool const use_bbind_rnchi_scoring, bool const use_bbind_rnchi_sampling, bool const nrchi_is_symmetric, Real const nrchi_start_angle, utility::io::izstream &rotamer_definitions, utility::io::izstream &regular_library, utility::io::izstream &continuous_minimization_bbdep) const
	Instantiate the appropriate SRSRDL< T > library given the nchi input. nchi indicates the number of rotameric chi – there are nchi+1 chi described by the library, the last of which is non-rotameric. (E.g. Tyrosine has an nchi of 1, its chi2 is non-rotameric and its chi3 is not described by the library.) The input streams are either read or not read depending on the boolean variables. More...

SingleResidueDunbrackLibraryOP	create_semi_rotameric_dunlib (chemical::ResidueType const &rt, Size const nchi, bool const use_bbind_rnchi_scoring, bool const use_bbind_rnchi_sampling, bool const nrchi_is_symmetric, Real const nrchi_start_angle) const

SingleResidueDunbrackLibraryOP	create_semi_rotameric_dunlib (chemical::ResidueType const &rt, Size const nchi, Size const nbb, bool const use_bbind_rnchi_scoring, bool const use_bbind_rnchi_sampling, bool const nrchi_is_symmetric, Real const nrchi_start_angle) const

SingleResidueDunbrackLibraryOP	create_srdl (chemical::ResidueType const &rt, DunbrackAAParameterSet const &ps, bool const reduced_resolution_library=false) const

void	write_to_binary (utility::io::ozstream &out) const
	Generic "write out a library to binary" which has a straightforward nlibraries (aa, aa_data)* format. Works for both 02 and 08 libraries. The kind of aa_data written is left to the discression of the SinResDunLib derived classes. More...

void	read_from_binary (utility::io::izstream &in)
	Initialize the RotamerLibrary from the stored binary. More...

	RotamerLibrary ()

void	initialize_from_options (utility::options::OptionCollection const &options)

	RotamerLibrary (RotamerLibrary const &)

RotamerLibrary const &	operator= (RotamerLibrary const &)

Private Attributes
bool	no_binary_dunlib_

bool	dont_rewrite_dunbrack_database_

bool	use_bicubic_

bool	entropy_correction_

core::Real	prob_buried_

core::Real	prob_nonburied_

core::Real	prob_buried_semi_

core::Real	prob_nonburied_semi_

std::string	dun02_file_

bool	dun10_

std::string	dun10_dir_

bool	shapovalov_lib_fixes_enable_

bool	shap_dun10_enable_

std::string	shap_dun10_dir_

std::string	shap_dun10_smooth_level_

utility::vector1 < rotamers::SingleResidueRotamerLibraryCOP >	aa_libraries_

Friends
class	utility::SingletonBase< RotamerLibrary >

Detailed Description

A class to manage the Dunbrack Rotamer Libraries.

This class no longer manages arbitrary rotamer libraries. Use core::pack::rotamers::SingleResidueRotamerLibraryFactory::get_instance()->get( restype ); to get rotamer libraries for an arbitrary ResidueType.

Member Typedef Documentation

typedef chemical::AA core::pack::dunbrack::RotamerLibrary::AA

typedef utility::vector1< rotamers::SingleResidueRotamerLibraryCOP > core::pack::dunbrack::RotamerLibrary::library_iterator

private

typedef conformation::Residue core::pack::dunbrack::RotamerLibrary::Residue

typedef chemical::ResidueType core::pack::dunbrack::RotamerLibrary::ResidueType

Constructor & Destructor Documentation

core::pack::dunbrack::RotamerLibrary::RotamerLibrary ( utility::options::OptionCollection const & options )

a new RotamerLibrary based on the option collection

The addtion of this constructor means that RotamerLibrary is no longer a true singleton. That said, the anticipated usage of RotamerLibrary is to use the single version initialized from the default global option collection, which is provided by RotamerLibrary::get_instance() The options-dependent constructor is provided for advanced usage only.

References create_fa_dunbrack_libraries(), and initialize_from_options().

core::pack::dunbrack::RotamerLibrary::~RotamerLibrary ( )

virtualdefault

core::pack::dunbrack::RotamerLibrary::RotamerLibrary ( )

private

References create_fa_dunbrack_libraries(), and initialize_from_options().

core::pack::dunbrack::RotamerLibrary::RotamerLibrary ( RotamerLibrary const & )

private

Member Function Documentation

void core::pack::dunbrack::RotamerLibrary::add_residue_library	(	AA const &	aa,
		rotamers::SingleResidueRotamerLibraryCOP	rot_lib
	)

private

Add a fullatom canonical AA Dunbrack library.

This, along with the create_* functions, are private and should only be called during singleton construction. If you need to make it public, you need to add a mutex

References protocols::cluster::calibur::aa, aa_libraries_, core::chemical::num_canonical_aas, and core::pack::dunbrack::TR().

Referenced by create_fa_dunbrack_libraries_02_from_ASCII(), create_fa_dunbrack_libraries_10_from_ASCII(), and read_from_binary().

Real core::pack::dunbrack::RotamerLibrary::best_rotamer_energy	(	Residue const &	rsd,
		pose::Pose const &	pose,
		bool	curr_rotamer_only,
		RotamerLibraryScratchSpace &	scratch
	)		const

References core::conformation::Residue::type().

bool core::pack::dunbrack::RotamerLibrary::binary_is_up_to_date ( utility::io::izstream & binlib ) const

private

Dispatches binary file is up-to-date to appropriate library given flag status (dun10 or dun08 yes/no).

References binary_is_up_to_date_02(), binary_is_up_to_date_10(), and dun10_.

Referenced by decide_read_from_binary(), and decide_write_binary().

bool core::pack::dunbrack::RotamerLibrary::binary_is_up_to_date_02 ( utility::io::izstream & binlib ) const

private

References current_binary_format_version_id_02().

Referenced by binary_is_up_to_date().

bool core::pack::dunbrack::RotamerLibrary::binary_is_up_to_date_10 ( utility::io::izstream & binlib ) const

private

Binary file is up-to-date if all the following are true:

Version # for binary file is equal to the current version #
All the hard coded constants for the rotameric and semirotameric libraries are the same from the previous hard coded values.

DANGER DANGER DANGER - True for dun10 as well? -JAB When we reopen the binary file in create_fa_dunbrack_libraries_08_from_binary we will want to skip past all this data; the code in that section assumes that it will read 8 arrays: 2 representing the rotameric amino acids, and 6 representing the semirotameric amino acids. The arithmetic it performs depends on this basic structure not changing, therefore, if you change this structure, you must also change the seekg arithmetic in the create...08_from_binary function.

References core::pack::dunbrack::DunbrackAAParameterSet::astr, current_binary_format_version_id_10(), core::pack::dunbrack::DunbrackAAParameterSet::get_dun10_aa_parameters(), core::pack::dunbrack::DunbrackAAParameterSet::rotameric_amino_acids, core::pack::dunbrack::DunbrackAAParameterSet::rotameric_n_chi, core::pack::dunbrack::DunbrackAAParameterSet::sampind, core::pack::dunbrack::DunbrackAAParameterSet::scind, core::pack::dunbrack::DunbrackAAParameterSet::sraa, core::pack::dunbrack::DunbrackAAParameterSet::srnchi, and core::pack::dunbrack::DunbrackAAParameterSet::sym.

Referenced by binary_is_up_to_date().

void core::pack::dunbrack::RotamerLibrary::create_fa_dunbrack_libraries ( )

private

Main interface for reading in dunbrack libraries. Version option checks are handled inside.

Generic decision tree for both 02 and 2010 libraries. Requires that low-level subroutines dispatch to 02 and 2010 versions based on the dun10 flag.

References create_fa_dunbrack_libraries_from_ASCII(), create_fa_dunbrack_libraries_from_binary(), decide_read_from_binary(), decide_write_binary(), shapovalov_lib_fixes_enable_, core::pack::dunbrack::TR(), and write_binary_fa_dunbrack_libraries().

Referenced by RotamerLibrary().

void core::pack::dunbrack::RotamerLibrary::create_fa_dunbrack_libraries_02_from_ASCII ( )

private

References core::chemical::ResidueTypeBase::aa(), add_residue_library(), create_rotameric_dunlib(), core::chemical::FA_STANDARD, get_library_name_02(), initialize_dun02_aa_parameters(), core::chemical::num_canonical_aas, and core::pack::dunbrack::TR().

Referenced by create_fa_dunbrack_libraries_from_ASCII().

void core::pack::dunbrack::RotamerLibrary::create_fa_dunbrack_libraries_02_from_binary ( )

private

References current_binary_format_version_id_02(), get_binary_name_02(), core::conformation::membrane::in, read_from_binary(), and core::pack::dunbrack::TR().

Referenced by create_fa_dunbrack_libraries_from_binary().

void core::pack::dunbrack::RotamerLibrary::create_fa_dunbrack_libraries_10_from_ASCII ( )

private

Referenced by create_fa_dunbrack_libraries_from_ASCII().

void core::pack::dunbrack::RotamerLibrary::create_fa_dunbrack_libraries_10_from_binary ( )

private

References get_binary_name_10(), core::conformation::membrane::in, read_from_binary(), and core::pack::dunbrack::TR().

Referenced by create_fa_dunbrack_libraries_from_binary().

void core::pack::dunbrack::RotamerLibrary::create_fa_dunbrack_libraries_from_ASCII ( )

private

References create_fa_dunbrack_libraries_02_from_ASCII(), create_fa_dunbrack_libraries_10_from_ASCII(), and dun10_.

Referenced by create_fa_dunbrack_libraries(), and validate_dunbrack_binary().

void core::pack::dunbrack::RotamerLibrary::create_fa_dunbrack_libraries_from_binary ( )

private

References create_fa_dunbrack_libraries_02_from_binary(), create_fa_dunbrack_libraries_10_from_binary(), and dun10_.

Referenced by create_fa_dunbrack_libraries().

SingleResidueDunbrackLibraryOP core::pack::dunbrack::RotamerLibrary::create_rotameric_dunlib	(	chemical::ResidueType const &	rt,
		Size const	n_chi,
		Size const	n_bb,
		utility::io::izstream &	library,
		bool	dun02,
		std::string &	next_aa_in_library,
		bool	first_three_letter_code_already_read
	)		const

private

Instantiate the appropriate RSRDL< T > library given the n_chi input and initialize the library from the input stream. Return the string that the library returns after reading the from the stream (which may be the empty string, or the three letter code for the next AA in the input stream). If the first three letter code for this amino acid has already been retrieved from the input stream, indicate so with the "first_three_letter_code_alread_read" boolean.

References entropy_correction_, prob_buried_, prob_nonburied_, protocols::hybridization::r1, protocols::hybridization::r2, core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::read_from_file(), core::id::to_string(), and use_bicubic_.

Referenced by create_fa_dunbrack_libraries_02_from_ASCII(), create_fa_dunbrack_libraries_10_from_ASCII(), create_rotameric_dunlib(), and create_srdl().

SingleResidueDunbrackLibraryOP core::pack::dunbrack::RotamerLibrary::create_rotameric_dunlib	(	chemical::ResidueType const &	rt,
		Size const	n_chi,
		Size const	n_bb,
		bool const	dun02,
		bool const	reduced_resolution_library = `false`
	)		const

private

References entropy_correction_, prob_buried_, prob_nonburied_, core::id::to_string(), and use_bicubic_.

SingleResidueDunbrackLibraryOP core::pack::dunbrack::RotamerLibrary::create_rotameric_dunlib	(	chemical::ResidueType const &	rt,
		Size const	n_chi,
		bool	dun02
	)		const

private

References create_rotameric_dunlib().

SingleResidueDunbrackLibraryOP core::pack::dunbrack::RotamerLibrary::create_semi_rotameric_dunlib	(	chemical::ResidueType const &	rt,
		Size const	nchi,
		Size const	nbb,
		bool const	use_bbind_rnchi_scoring,
		bool const	use_bbind_rnchi_sampling,
		bool const	nrchi_is_symmetric,
		Real const	nrchi_start_angle,
		utility::io::izstream &	rotamer_definitions,
		utility::io::izstream &	regular_library,
		utility::io::izstream &	continuous_minimization_bbdep
	)		const

private

Instantiate the appropriate SRSRDL< T > library given the nchi input. nchi indicates the number of rotameric chi – there are nchi+1 chi described by the library, the last of which is non-rotameric. (E.g. Tyrosine has an nchi of 1, its chi2 is non-rotameric and its chi3 is not described by the library.) The input streams are either read or not read depending on the boolean variables.

References entropy_correction_, core::pack::dunbrack::initialize_and_read_srsrdl(), prob_buried_semi_, prob_nonburied_semi_, protocols::hybridization::r1, shap_dun10_enable_, shapovalov_lib_fixes_enable_, core::id::to_string(), and use_bicubic_.

Referenced by create_fa_dunbrack_libraries_10_from_ASCII(), create_semi_rotameric_dunlib(), and create_srdl().

SingleResidueDunbrackLibraryOP core::pack::dunbrack::RotamerLibrary::create_semi_rotameric_dunlib	(	chemical::ResidueType const &	rt,
		Size const	nchi,
		bool const	use_bbind_rnchi_scoring,
		bool const	use_bbind_rnchi_sampling,
		bool const	nrchi_is_symmetric,
		Real const	nrchi_start_angle
	)		const

private

References create_semi_rotameric_dunlib().

SingleResidueDunbrackLibraryOP core::pack::dunbrack::RotamerLibrary::create_semi_rotameric_dunlib	(	chemical::ResidueType const &	rt,
		Size const	nchi,
		Size const	nbb,
		bool const	use_bbind_rnchi_scoring,
		bool const	use_bbind_rnchi_sampling,
		bool const	nrchi_is_symmetric,
		Real const	nrchi_start_angle
	)		const

private

References entropy_correction_, core::pack::dunbrack::initialize_srsrdl(), prob_buried_semi_, prob_nonburied_semi_, protocols::hybridization::r1, shap_dun10_enable_, shapovalov_lib_fixes_enable_, core::id::to_string(), and use_bicubic_.

SingleResidueDunbrackLibraryOP core::pack::dunbrack::RotamerLibrary::create_srdl	(	chemical::ResidueType const &	rt,
		DunbrackAAParameterSet const &	dps,
		bool const	reduced_resolution_library = `false`
	)		const

private

Build and initialize some of the data in an SRDL in preparation for binary file input – that is, the SRDL does not have "read_from_file(s)" called before it is returned to the calling function.

Referenced by read_from_binary().

Size core::pack::dunbrack::RotamerLibrary::current_binary_format_version_id_02 ( ) const

private

The older binary formats did not have a version number, instead, a somewhat stupid time-stamp was hard coded and compared against the time stamp of the binary file that existed... e.g. if a new binary format was committed to trunk on 1/1/08 12:00 pm, and the time stamp on a particular binary was from 12/1/07, then the old binary file would be overwritten. However, if the time stamp on some other binary file was from 2/1/08, the code assumed that the binary file was up to date. This is a poor assumption, since the code from 12/1/07 might have been run on 2/1/08 to generate a binary file. The time stamp would have falsely indicated that the 2/1/08 generated file was of the same binary format imposed on 1/1/08.

Version numbering avoids this issue. If the 12/1/07 code wrote version # 3, the 1/1/08 code could look for version # 4 in a file generated on 2/1/08 and use the mismatch as an indication of an out-of-date binary format.

The challenge is to come up with a versioning scheme that handles the fact that until now, there haven't been version #'s in the binary files. How can a binary file generated by a pre-versioning piece of code be detected? The trick is to look at the data in the older binary file at the position which will in the future be used to hold a version number. The first piece of data in the old binary files was a count of the number of libraries in the binary file:

Therefore, any starting version number beyond 18 would distinguish the pre-versioned files from the versioned files.

When changing the binary format, document the date of the change in the comment section below and increment the version number in the function. Do not delete old comments from the comment block below.

Version 19: start vesion number. 8/9/08. Andrew Leaver-Fay Version 20: Limit zero-probability rotamers to the resolution of the library (1e-4). 6/16/2009. Andrew Leaver-Fay Version 21: Write out bicubic spline parameters for -log(p(rot|phi,psi)). 3/28/2012. Andrew Leaver-Fay Version 22: Bicubic spline bugfix 3/29/2012. Andrew Leaver-Fay Version 23: Derivatives now are output in different order for better generality with respect to number of backbone dihedrals. Also, resolution limit repaired ( prob <= 1e-6 not prob == 0 ) 1/12/15 Andy Watkins Version 24: Changed to templating on number of bbs, can't prove that this isn't needed 1/15/15 Andy Watkins Version 25: Fixed input bug that was definitely having real effects 1/22/15 Andy Watkins Version 26: Store derivatives as double precision 4/22/20 Rocco Moretti

Referenced by binary_is_up_to_date_02(), create_fa_dunbrack_libraries_02_from_binary(), and write_binary_fa_dunbrack_libraries_02().

Size core::pack::dunbrack::RotamerLibrary::current_binary_format_version_id_10 ( ) const

private

Version number for binary format. See comments for 02 version.

When changing the binary format, document the date of the change in the comment section below and increment the version number in the function. Do not delete old comments from the comment block below.

Version 1: start vesion number. 6/3/11. Andrew Leaver-Fay Version 2: Rotameric residues write out bicubic spline parameters for -log(p(rot|phi,psi)). 3/28/2012. Andrew Leaver-Fay Version 3: Tricubic interpolation data for semi-rotameric residues. 3/29/2012. Andrew Leaver-Fay Version 4: Generate and write out bicubic spline data for the rotameric portion of the semi-rotameric residues . 3/29/2012. Andrew Leaver-Fay Version 5: Derivatives now are output in different order for better generality with respect to number of backbone dihedrals. Also, resolution limit repaired ( prob <= 1e-6 not prob == 0 ) 1/12/15 Andy Watkins Version 6: Changed to templating on number of bbs, can't prove that this isn't needed 1/15/15 Andy Watkins Version 7: Fixed input bug that was definitely having real effects 1/22/15 Andy Watkins Version 8: Update to beta_nov16 corrected library 3/2017 fpd Verison 9: Store derivatives as double precision 4/22/20 Rocco Moretti

Referenced by binary_is_up_to_date_10(), and write_binary_fa_dunbrack_libraries_10().

bool core::pack::dunbrack::RotamerLibrary::decide_read_from_binary ( ) const

References binary_is_up_to_date(), decide_read_from_binary_02(), decide_read_from_binary_10(), dun10_, get_binary_name(), core::conformation::membrane::in, no_binary_dunlib_, shap_dun10_enable_, shap_dun10_smooth_level_, shapovalov_lib_fixes_enable_, and core::pack::dunbrack::TR().

Referenced by create_fa_dunbrack_libraries(), and validate_dunbrack_binary().

bool core::pack::dunbrack::RotamerLibrary::decide_read_from_binary_02 ( ) const

private

Put specific objections to reading the 02 library from binary here. This function alone will not answer whether the binary file should be read; rather, it is called by the more generic "decide_read_from_binary" function.

Referenced by decide_read_from_binary().

bool core::pack::dunbrack::RotamerLibrary::decide_read_from_binary_10 ( ) const

private

Put specific objections to reading the 10 library from binary here. This function alone will not answer whether the binary file should be read; rather, it is called by the more generic "decide_read_from_binary" function.

Referenced by decide_read_from_binary().

bool core::pack::dunbrack::RotamerLibrary::decide_write_binary ( ) const

private

First checks general conditions under which a binary library file should not be writen. It relies on get_binary_name() and binary_is_up_to_date() to dispatch to the 02 and 08 data. If the binary file doesn't exist or isn't up-to-date it then checks if there are any specific 02 or 08 objections to writing the binary file. If no one objects, then this function gives a green light.

References binary_is_up_to_date(), decide_write_binary_02(), decide_write_binary_10(), dont_rewrite_dunbrack_database_, dun10_, get_binary_name(), core::conformation::membrane::in, and no_binary_dunlib_.

Referenced by create_fa_dunbrack_libraries().

bool core::pack::dunbrack::RotamerLibrary::decide_write_binary_02 ( ) const

private

Add specific objections to the writing of the 02 library here.

Referenced by decide_write_binary().

bool core::pack::dunbrack::RotamerLibrary::decide_write_binary_10 ( ) const

private

Add specific objections to the writing of the 10 library here.

Referenced by decide_write_binary().

std::string core::pack::dunbrack::RotamerLibrary::get_binary_name ( ) const

References dun10_, get_binary_name_02(), and get_binary_name_10().

Referenced by decide_read_from_binary(), decide_write_binary(), and validate_dunbrack_binary().

std::string core::pack::dunbrack::RotamerLibrary::get_binary_name_02 ( bool for_writing = false ) const

private

References dun02_file_, and get_library_name_02().

Referenced by create_fa_dunbrack_libraries_02_from_binary(), get_binary_name(), and write_binary_fa_dunbrack_libraries_02().

std::string core::pack::dunbrack::RotamerLibrary::get_binary_name_10 ( bool for_writing = false ) const

private

References dun10_dir_, get_library_name_10(), shap_dun10_dir_, shap_dun10_enable_, and shapovalov_lib_fixes_enable_.

Referenced by create_fa_dunbrack_libraries_10_from_binary(), get_binary_name(), and write_binary_fa_dunbrack_libraries_10().

SingleResidueRotamerLibraryCOP core::pack::dunbrack::RotamerLibrary::get_library_by_aa ( chemical::AA const & aa ) const

References protocols::cluster::calibur::aa, aa_libraries_, and core::pack::dunbrack::TR().

std::string core::pack::dunbrack::RotamerLibrary::get_library_name_02 ( ) const

private

References dun02_file_.

Referenced by create_fa_dunbrack_libraries_02_from_ASCII(), and get_binary_name_02().

std::string core::pack::dunbrack::RotamerLibrary::get_library_name_10 ( ) const

private

References dun10_dir_, shap_dun10_dir_, shap_dun10_enable_, shapovalov_lib_fixes_enable_, and core::pack::dunbrack::TR().

Referenced by create_fa_dunbrack_libraries_10_from_ASCII(), and get_binary_name_10().

void core::pack::dunbrack::RotamerLibrary::initialize_dun02_aa_parameters	(	utility::vector1< Size > &	nchi_for_aa,
		utility::vector1< Size > &	nbb_for_aa,
		Size &	n_rotameric_aas
	)

static

void core::pack::dunbrack::RotamerLibrary::initialize_from_options ( utility::options::OptionCollection const & options )

private

References dont_rewrite_dunbrack_database_, dun02_file_, dun10_, dun10_dir_, entropy_correction_, no_binary_dunlib_, prob_buried_, prob_buried_semi_, prob_nonburied_, prob_nonburied_semi_, shap_dun10_dir_, shap_dun10_enable_, shap_dun10_smooth_level_, shapovalov_lib_fixes_enable_, and use_bicubic_.

Referenced by RotamerLibrary().

RotamerLibrary const& core::pack::dunbrack::RotamerLibrary::operator= ( RotamerLibrary const & )

private

std::string core::pack::dunbrack::RotamerLibrary::random_tempname	(	std::string const &	same_dir_as,
		std::string const &	prefix
	)		const

private

References core::pack::dunbrack::TR().

Referenced by write_binary_fa_dunbrack_libraries_02(), and write_binary_fa_dunbrack_libraries_10().

void core::pack::dunbrack::RotamerLibrary::read_from_binary ( utility::io::izstream & in )

private

Initialize the RotamerLibrary from the stored binary.

Invoked through constructor. Not threadsafe in itself. Do not call directly.

Generic binary file reader. Intended to work for both 02 and 08 Libraries. If a "preamble" starts the binary format, the input stream to this function must have already been walked past it. Somewhat circularly, the preamble is anything in the binary file that leads the "nlibraries (aa, aa_data)*" format perscribed in this function.

References core::chemical::aa_unk, add_residue_library(), create_srdl(), dun10_, core::chemical::FA_STANDARD, core::pack::dunbrack::DunbrackAAParameterSet::get_dun02_aa_parameters(), core::pack::dunbrack::DunbrackAAParameterSet::get_dun10_aa_parameters(), core::chemical::ResidueType::is_beta_aa(), and core::chemical::name_from_aa().

Referenced by create_fa_dunbrack_libraries_02_from_binary(), and create_fa_dunbrack_libraries_10_from_binary().

Real core::pack::dunbrack::RotamerLibrary::rotamer_energy	(	Residue const &	rsd,
		pose::Pose const &	pose,
		RotamerLibraryScratchSpace &	scratch
	)		const

References core::conformation::Residue::type().

Referenced by protocols::simple_moves::sidechain_moves::SidechainMover::dunbrack_accept().

Real core::pack::dunbrack::RotamerLibrary::rotamer_energy_deriv	(	Residue const &	rsd,
		pose::Pose const &	pose,
		RotamerLibraryScratchSpace &	scratch
	)		const

to do:

References core::pack::dunbrack::RotamerLibraryScratchSpace::dE_dbb(), core::pack::dunbrack::RotamerLibraryScratchSpace::dE_dchi(), and core::conformation::Residue::type().

bool core::pack::dunbrack::RotamerLibrary::validate_dunbrack_binary ( )

Reload the Dunbrack Rotamer libraries from ASCII, and make sure that they match the ones loaded from binary. Return true if the binary file is valid, false if the binary is invalid. NOTE WELL: This is not a const function, as reloading from ASCII modifies internals. It's also VERY thread unsafe. Never call this function from a multithreaded context.

Reload the Dunbrack Rotamer libraries from ASCII, and make sure that they match the ones loaded from binary. NOTE WELL: This is not a const function, as reloading from ASCII modifies internals.

References protocols::cluster::calibur::aa, aa_libraries_, create_fa_dunbrack_libraries_from_ASCII(), decide_read_from_binary(), get_binary_name(), core::chemical::name_from_aa(), core::chemical::num_canonical_aas, and core::pack::dunbrack::TR().

void core::pack::dunbrack::RotamerLibrary::write_binary_fa_dunbrack_libraries ( ) const

private

References dun10_, write_binary_fa_dunbrack_libraries_02(), and write_binary_fa_dunbrack_libraries_10().

Referenced by create_fa_dunbrack_libraries().

void core::pack::dunbrack::RotamerLibrary::write_binary_fa_dunbrack_libraries_02 ( ) const

private

References current_binary_format_version_id_02(), get_binary_name_02(), core::conformation::membrane::out, random_tempname(), core::pack::dunbrack::TR(), and write_to_binary().

Referenced by write_binary_fa_dunbrack_libraries().

void core::pack::dunbrack::RotamerLibrary::write_binary_fa_dunbrack_libraries_10 ( ) const

private

Referenced by write_binary_fa_dunbrack_libraries().

void core::pack::dunbrack::RotamerLibrary::write_to_binary ( utility::io::ozstream & out ) const

private

Generic "write out a library to binary" which has a straightforward nlibraries (aa, aa_data)* format. Works for both 02 and 08 libraries. The kind of aa_data written is left to the discression of the SinResDunLib derived classes.

References aa_libraries_, and core::pack::dunbrack::SingleResidueDunbrackLibrary::write_to_binary().

Referenced by write_binary_fa_dunbrack_libraries_02(), and write_binary_fa_dunbrack_libraries_10().