#include <RotamerLibrary.hh>

Collaboration diagram for core::pack::dunbrack::RotamerLibrary:

Public Types
typedef chemical::AA	AA

typedef conformation::Residue	Residue

typedef chemical::ResidueType	ResidueType

Public Member Functions
virtual	~RotamerLibrary ()

Real	rotamer_energy (Residue const &rsd, RotamerLibraryScratchSpace &scratch) const

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

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

void	add_residue_library (AA const &aa, SingleResidueRotamerLibraryCOP rot_lib) const

void	add_residue_library (ResidueType const &rsd_type, SingleResidueRotamerLibraryCOP rot_lib) const
	Overrides the library for AA. More...

bool	rsd_library_already_loaded (chemical::ResidueType const &rsd_type) const
	Returns true if the singleton has already loaded a library for a given residue type. More...

SingleResidueRotamerLibraryCAP	get_rsd_library (chemical::ResidueType const &rsd_type) const

SingleResidueRotamerLibraryCAP	get_library_by_aa (chemical::AA const &aa) const

void	write_to_file (std::string filename) const

void	create_fa_dunbrack_libraries ()
	Public interface to read in dunbrack libraries. dun10 option checks are handled inside. More...

pack::dunbrack::SingleResidueRotamerLibraryCAP	get_NCAARotamerLibrary (chemical::ResidueType const &rsd_type) const

Static Public Member Functions
static RotamerLibrary &	get_instance ()

static void	initialize_dun10_aa_parameters (utility::vector1< chemical::AA > &rotameric_amino_acids, utility::vector1< Size > &rotameric_n_chi, utility::vector1< chemical::AA > &sraa, utility::vector1< Size > &srnchi, utility::vector1< bool > &scind, utility::vector1< bool > &sampind, utility::vector1< bool > &sym, utility::vector1< Real > &astr)

static void	initialize_dun02_aa_parameters (utility::vector1< chemical::AA > &rotameric_amino_acids, utility::vector1< Size > &rotameric_n_chi)

static void	initialize_dun02_aa_parameters (utility::vector1< Size > &nchi_for_aa, Size &n_rotameric_aas)

Private Types
typedef std::map< AA, SingleResidueRotamerLibraryCAP >	LibraryMap

typedef LibraryMap::const_iterator	library_iterator

typedef std::map< std::string, SingleResidueRotamerLibraryCAP >	ResLibraryMap

typedef ResLibraryMap::const_iterator	reslibrary_iterator

Private Member Functions
bool	decide_read_from_binary () const

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_binary_name () const

std::string	get_binary_name_02 () const

std::string	get_binary_name_10 () const

Size	current_binary_format_version_id_02 () const

Size	current_binary_format_version_id_10 () const

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	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 &prefix) const

template<Size T>
void	initialize_and_read_srsrdl (SemiRotamericSingleResidueDunbrackLibrary< T > &srsrdl, 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

template<Size T>
void	initialize_srsrdl (SemiRotamericSingleResidueDunbrackLibrary< T > &srsrdl, bool const nrchi_is_symmetric, Real const nrchi_start_angle) const

SingleResidueDunbrackLibraryOP	create_rotameric_dunlib (chemical::AA aa, Size const n_chi, 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::AA aa, Size const n_chi, bool dun02) const

SingleResidueDunbrackLibraryOP	create_semi_rotameric_dunlib (chemical::AA aa, 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, 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::AA aa, 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_srdl (chemical::AA aa_in) 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)

	RotamerLibrary ()

	RotamerLibrary (RotamerLibrary const &)

RotamerLibrary const &	operator= (RotamerLibrary const &)

Private Attributes
ResLibraryMap	reslibraries_

LibraryMap	libraries_

utility::vector1 < SingleResidueRotamerLibraryCAP >	aa_libraries_

utility::vector1 < SingleResidueRotamerLibraryCOP >	libraries_ops_

std::map< std::string, pack::dunbrack::SingleResidueRotamerLibraryCOP >	ncaa_rotlibs_

Static Private Attributes
static RotamerLibrary *	rotamer_library_

Detailed Description

Definition at line 190 of file RotamerLibrary.hh.

Member Typedef Documentation

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

Definition at line 194 of file RotamerLibrary.hh.

typedef LibraryMap::const_iterator core::pack::dunbrack::RotamerLibrary::library_iterator

private

Definition at line 437 of file RotamerLibrary.hh.

typedef std::map< AA, SingleResidueRotamerLibraryCAP > core::pack::dunbrack::RotamerLibrary::LibraryMap

private

Definition at line 436 of file RotamerLibrary.hh.

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

Definition at line 195 of file RotamerLibrary.hh.

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

Definition at line 196 of file RotamerLibrary.hh.

typedef ResLibraryMap::const_iterator core::pack::dunbrack::RotamerLibrary::reslibrary_iterator

private

Definition at line 442 of file RotamerLibrary.hh.

typedef std::map< std::string, SingleResidueRotamerLibraryCAP > core::pack::dunbrack::RotamerLibrary::ResLibraryMap

private

Definition at line 441 of file RotamerLibrary.hh.

Constructor & Destructor Documentation

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

virtual

Definition at line 354 of file RotamerLibrary.cc.

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

private

Definition at line 347 of file RotamerLibrary.cc.

Referenced by get_instance().

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

private

Member Function Documentation

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

Definition at line 434 of file RotamerLibrary.cc.

References aa_libraries_, libraries_, libraries_ops_, and core::chemical::num_canonical_aas.

Referenced by get_rsd_library(), and read_from_binary().

void core::pack::dunbrack::RotamerLibrary::add_residue_library	(	ResidueType const &	rsd_type,
		SingleResidueRotamerLibraryCOP	rot_lib
	)		const

Overrides the library for AA.

Definition at line 450 of file RotamerLibrary.cc.

References libraries_ops_, core::chemical::ResidueTypeSet::name(), core::chemical::ResidueType::name(), core::chemical::ResidueType::residue_type_set(), and reslibraries_.

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

Definition at line 372 of file RotamerLibrary.cc.

References get_rsd_library(), and 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).

Definition at line 610 of file RotamerLibrary.cc.

References binary_is_up_to_date_02(), and binary_is_up_to_date_10().

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

Definition at line 623 of file RotamerLibrary.cc.

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.

Definition at line 644 of file RotamerLibrary.cc.

References current_binary_format_version_id_10(), and initialize_dun10_aa_parameters().

Referenced by binary_is_up_to_date().

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

Public interface to read in dunbrack libraries. dun10 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.

Definition at line 548 of file RotamerLibrary.cc.

References create_fa_dunbrack_libraries_from_ASCII(), create_fa_dunbrack_libraries_from_binary(), decide_read_from_binary(), decide_write_binary(), and write_binary_fa_dunbrack_libraries().

Referenced by core::pack::dunbrack::read_dunbrack_library().

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

private

Definition at line 906 of file RotamerLibrary.cc.

References core::chemical::aa_from_name(), aa_libraries_, core::chemical::aa_unk, create_rotameric_dunlib(), get_library_name_02(), initialize_dun02_aa_parameters(), libraries_, libraries_ops_, 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

Definition at line 972 of file RotamerLibrary.cc.

References current_binary_format_version_id_02(), get_binary_name_02(), 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

Definition at line 1002 of file RotamerLibrary.cc.

References aa_libraries_, create_rotameric_dunlib(), create_semi_rotameric_dunlib(), initialize_dun10_aa_parameters(), libraries_, libraries_ops_, core::chemical::name_from_aa(), and core::pack::dunbrack::TR().

Referenced by create_fa_dunbrack_libraries_from_ASCII().

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

private

Definition at line 1178 of file RotamerLibrary.cc.

References get_binary_name_10(), 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

Definition at line 880 of file RotamerLibrary.cc.

References create_fa_dunbrack_libraries_02_from_ASCII(), and create_fa_dunbrack_libraries_10_from_ASCII().

Referenced by create_fa_dunbrack_libraries().

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

private

Definition at line 893 of file RotamerLibrary.cc.

References create_fa_dunbrack_libraries_02_from_binary(), and create_fa_dunbrack_libraries_10_from_binary().

Referenced by create_fa_dunbrack_libraries().

SingleResidueDunbrackLibraryOP core::pack::dunbrack::RotamerLibrary::create_rotameric_dunlib	(	chemical::AA	aa,
		Size const	n_chi,
		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.

Definition at line 1412 of file RotamerLibrary.cc.

References core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::read_from_file().

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

SingleResidueDunbrackLibraryOP core::pack::dunbrack::RotamerLibrary::create_rotameric_dunlib	(	chemical::AA	aa,
		Size const	n_chi,
		bool	dun02
	)		const

private

Definition at line 1461 of file RotamerLibrary.cc.

SingleResidueDunbrackLibraryOP core::pack::dunbrack::RotamerLibrary::create_semi_rotameric_dunlib	(	chemical::AA	aa,
		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,
		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.

Definition at line 1491 of file RotamerLibrary.cc.

References initialize_and_read_srsrdl().

Referenced by create_fa_dunbrack_libraries_10_from_ASCII(), and create_srdl().

SingleResidueDunbrackLibraryOP core::pack::dunbrack::RotamerLibrary::create_semi_rotameric_dunlib	(	chemical::AA	aa,
		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

Definition at line 1534 of file RotamerLibrary.cc.

References initialize_srsrdl().

SingleResidueDunbrackLibraryOP core::pack::dunbrack::RotamerLibrary::create_srdl ( chemical::AA aa_in) 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. ATM not threadsafe.

Definition at line 1572 of file RotamerLibrary.cc.

References create_rotameric_dunlib(), create_semi_rotameric_dunlib(), initialize_dun02_aa_parameters(), and initialize_dun10_aa_parameters().

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

Definition at line 857 of file RotamerLibrary.cc.

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

Definition at line 874 of file RotamerLibrary.cc.

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

private

Definition at line 560 of file RotamerLibrary.cc.

References binary_is_up_to_date(), decide_read_from_binary_02(), decide_read_from_binary_10(), and get_binary_name().

Referenced by create_fa_dunbrack_libraries().

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.

Definition at line 590 of file RotamerLibrary.cc.

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.

Definition at line 601 of file RotamerLibrary.cc.

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.

Definition at line 727 of file RotamerLibrary.cc.

References binary_is_up_to_date(), decide_write_binary_02(), decide_write_binary_10(), and get_binary_name().

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.

Definition at line 770 of file RotamerLibrary.cc.

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.

Definition at line 778 of file RotamerLibrary.cc.

Referenced by decide_write_binary().

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

private

Definition at line 793 of file RotamerLibrary.cc.

References get_binary_name_02(), and get_binary_name_10().

Referenced by decide_read_from_binary(), and decide_write_binary().

std::string core::pack::dunbrack::RotamerLibrary::get_binary_name_02 ( ) const

private

Definition at line 806 of file RotamerLibrary.cc.

References 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 ( ) const

private

Definition at line 814 of file RotamerLibrary.cc.

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

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

static

Definition at line 1862 of file RotamerLibrary.cc.

References core::pack::dunbrack::read_dunbrack_library(), rotamer_library_, and RotamerLibrary().

Referenced by protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO::alter_rotamer_set(), protocols::ligand_docking::RandomConformerMover::apply(), protocols::enzdes::DetectProteinLigandInterface::apply(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::best_rotamer_energy(), protocols::match::upstream::ProteinUpstreamBuilder::build(), core::pack::rotamer_set::ContinuousRotamerSet::build_rotamers(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), core::pack::dunbrack::DunbrackEnergy::eval_dof_derivative(), core::pack::dunbrack::DunbrackEnergy::eval_residue_dof_derivative(), protocols::optimize_weights::IterativeOptEDriver::get_nat_rot_opte_data(), protocols::ligand_docking::LigandBaseProtocol::get_non_bb_clashing_rotamers(), protocols::match::downstream::LigandConformerBuilder::initialize_conformers(), protocols::match::Matcher::initialize_from_file(), protocols::features::RotamerInitializer< T >::initialize_rotamer(), core::pack::dunbrack::load_unboundrot(), core::pack::dunbrack::DunbrackEnergy::residue_energy(), core::pack::dunbrack::rotamer_from_chi(), and protocols::ligand_docking::rotamers_for_trials().

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

Definition at line 535 of file RotamerLibrary.cc.

References aa_libraries_.

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

private

Definition at line 785 of file RotamerLibrary.cc.

Referenced by create_fa_dunbrack_libraries_02_from_ASCII(), and get_binary_name_02().

SingleResidueRotamerLibraryCAP core::pack::dunbrack::RotamerLibrary::get_NCAARotamerLibrary ( chemical::ResidueType const & rsd_type) const

Definition at line 1873 of file RotamerLibrary.cc.

References core::chemical::ResidueType::aa(), protocols::viewer::empty_string(), core::chemical::ResidueType::get_ncaa_rotlib_n_bin_per_rot(), core::chemical::ResidueType::get_ncaa_rotlib_path(), core::chemical::ResidueType::n_proton_chi(), core::chemical::ResidueType::name3(), ncaa_rotlibs_, core::chemical::ResidueType::nchi(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::read_from_file(), and core::pack::dunbrack::SingleResidueDunbrackLibrary::set_n_chi_bins().

Referenced by get_rsd_library().

SingleResidueRotamerLibraryCAP core::pack::dunbrack::RotamerLibrary::get_rsd_library ( chemical::ResidueType const & rsd_type) const

returns NULL if no library is available for the given residue type and no pdb rotamers have been defined for the given residue; if PDB rotamers HAVE been defined, then

Definition at line 497 of file RotamerLibrary.cc.

References aa_libraries_, add_residue_library(), core::chemical::CENTROID, core::chemical::FA_STANDARD, get_NCAARotamerLibrary(), core::chemical::ResidueType::get_RotamerLibraryName(), core::chemical::ResidueType::get_use_ncaa_rotlib(), core::chemical::ResidueType::is_ligand(), libraries_, core::chemical::ResidueTypeSet::name(), core::chemical::ResidueType::name(), core::chemical::num_canonical_aas, core::chemical::ResidueType::residue_type_set(), reslibraries_, core::chemical::ResidueType::rotamer_aa(), and core::pack::dunbrack::TR().

Referenced by protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO::alter_rotamer_set(), protocols::ligand_docking::RandomConformerMover::apply(), protocols::enzdes::DetectProteinLigandInterface::apply(), best_rotamer_energy(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::best_rotamer_energy(), core::pack::rotamer_set::ContinuousRotamerSet::build_rotamers(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), core::pack::dunbrack::DunbrackEnergy::eval_dof_derivative(), core::pack::dunbrack::DunbrackEnergy::eval_residue_dof_derivative(), protocols::ligand_docking::LigandBaseProtocol::get_non_bb_clashing_rotamers(), protocols::match::downstream::LigandConformerBuilder::initialize_conformers(), protocols::match::Matcher::initialize_from_file(), protocols::features::RotamerInitializer< T >::initialize_rotamer(), protocols::simple_moves::sidechain_moves::SidechainMover::make_move(), protocols::simple_moves::sidechain_moves::SidechainMover::proposal_density(), core::pack::dunbrack::DunbrackEnergy::residue_energy(), rotamer_energy(), rotamer_energy_deriv(), core::pack::dunbrack::rotamer_from_chi(), protocols::ligand_docking::rotamers_for_trials(), and protocols::match::upstream::DunbrackSCSampler::samples().

template<Size T>

void core::pack::dunbrack::RotamerLibrary::initialize_and_read_srsrdl	(	SemiRotamericSingleResidueDunbrackLibrary< T > &	srsrdl,
		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

Definition at line 1735 of file RotamerLibrary.cc.

References initialize_srsrdl(), and core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::read_from_files().

Referenced by create_semi_rotameric_dunlib().

void core::pack::dunbrack::RotamerLibrary::initialize_dun02_aa_parameters	(	utility::vector1< chemical::AA > &	rotameric_amino_acids,
		utility::vector1< Size > &	rotameric_n_chi
	)

static

Definition at line 1678 of file RotamerLibrary.cc.

References core::chemical::num_canonical_aas.

Referenced by create_fa_dunbrack_libraries_02_from_ASCII(), create_srdl(), and protocols::features::RotamerFeatures::report_features().

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

static

void core::pack::dunbrack::RotamerLibrary::initialize_dun10_aa_parameters	(	utility::vector1< chemical::AA > &	rotameric_amino_acids,
		utility::vector1< Size > &	rotameric_n_chi,
		utility::vector1< chemical::AA > &	sraa,
		utility::vector1< Size > &	srnchi,
		utility::vector1< bool > &	scind,
		utility::vector1< bool > &	sampind,
		utility::vector1< bool > &	sym,
		utility::vector1< Real > &	astr
	)

static

Hard code this data in a single place; adjust the booleans for the backbone independent

Definition at line 1628 of file RotamerLibrary.cc.

References core::chemical::aa_arg, core::chemical::aa_asn, core::chemical::aa_asp, core::chemical::aa_cys, core::chemical::aa_gln, core::chemical::aa_glu, core::chemical::aa_his, core::chemical::aa_ile, core::chemical::aa_leu, core::chemical::aa_lys, core::chemical::aa_met, core::chemical::aa_phe, core::chemical::aa_pro, core::chemical::aa_ser, core::chemical::aa_thr, core::chemical::aa_trp, core::chemical::aa_tyr, and core::chemical::aa_val.

Referenced by binary_is_up_to_date_10(), create_fa_dunbrack_libraries_10_from_ASCII(), create_srdl(), protocols::features::RotamerFeatures::report_features(), and write_binary_fa_dunbrack_libraries_10().

template<Size T>

void core::pack::dunbrack::RotamerLibrary::initialize_srsrdl	(	SemiRotamericSingleResidueDunbrackLibrary< T > &	srsrdl,
		bool const	nrchi_is_symmetric,
		Real const	nrchi_start_angle
	)		const

private

Definition at line 1752 of file RotamerLibrary.cc.

References core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::set_nonrotameric_chi_bbdep_scoring_step_size(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::set_nonrotameric_chi_bbind_scoring_step_size(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::set_nonrotameric_chi_start_angle(), and core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::set_nrchi_periodicity().

Referenced by create_semi_rotameric_dunlib(), and initialize_and_read_srsrdl().

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

private

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

private

Definition at line 1370 of file RotamerLibrary.cc.

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

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.

Definition at line 1836 of file RotamerLibrary.cc.

References core::chemical::aa_unk, add_residue_library(), create_srdl(), 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,
		RotamerLibraryScratchSpace &	scratch
	)		const

Definition at line 358 of file RotamerLibrary.cc.

References get_rsd_library(), and 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,
		RotamerLibraryScratchSpace &	scratch
	)		const

to do:

Definition at line 391 of file RotamerLibrary.cc.

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

bool core::pack::dunbrack::RotamerLibrary::rsd_library_already_loaded ( chemical::ResidueType const & rsd_type) const

Returns true if the singleton has already loaded a library for a given residue type.

Definition at line 468 of file RotamerLibrary.cc.

References aa_libraries_, core::chemical::CENTROID, core::chemical::FA_STANDARD, libraries_, core::chemical::ResidueTypeSet::name(), core::chemical::ResidueType::name(), core::chemical::ResidueType::name3(), ncaa_rotlibs_, core::chemical::num_canonical_aas, core::chemical::ResidueType::residue_type_set(), reslibraries_, and core::chemical::ResidueType::rotamer_aa().

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

private

Definition at line 1231 of file RotamerLibrary.cc.

References 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

Definition at line 1244 of file RotamerLibrary.cc.

References current_binary_format_version_id_02(), get_binary_name_02(), 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

Definition at line 1275 of file RotamerLibrary.cc.

References current_binary_format_version_id_10(), get_binary_name_10(), initialize_dun10_aa_parameters(), random_tempname(), core::pack::dunbrack::TR(), and write_to_binary().

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.

Definition at line 1797 of file RotamerLibrary.cc.

References libraries_.

Referenced by write_binary_fa_dunbrack_libraries_02(), and write_binary_fa_dunbrack_libraries_10().

void core::pack::dunbrack::RotamerLibrary::write_to_file ( std::string filename) const

Definition at line 1784 of file RotamerLibrary.cc.

References libraries_.