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Rosetta Core
2014.35
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Rosetta Core
2014.35
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#include <RotamerLibrary.hh>
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... | |
| SingleResidueRotamerLibraryCAP | get_NCAA_rotamer_library (chemical::ResidueType const &rsd_type) const |
| Get the rotamer library specified by the NCAA_ROTLIB flag in the residue type paramater file in the residue type paramater file if it exists. More... | |
| SingleResidueRotamerLibraryCAP | get_peptoid_rotamer_library (chemical::ResidueType const &rsd_type) const |
| Get the rotamer library specified by the PEPTOID_ROTLIB flag in the residue type paramater file in the residue type paramater file if it exists. More... | |
Static Public Member Functions | |
| static RotamerLibrary & | get_instance () |
| static function to get the instance of ( pointer to) this singleton class More... | |
| 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_centroid_rotamer_libraries_from_ASCII () |
| 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 ®ular_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 ®ular_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 &) |
Static Private Member Functions | |
| static RotamerLibrary * | create_singleton_instance () |
| private singleton creation function to be used with utility::thread::threadsafe_singleton More... | |
Private Attributes | |
| ResLibraryMap | reslibraries_ |
| LibraryMap | libraries_ |
| utility::vector1 < SingleResidueRotamerLibraryCAP > | aa_libraries_ |
| utility::vector1 < SingleResidueRotamerLibraryCOP > | libraries_ops_ |
| std::map< std::string, SingleResidueRotamerLibraryCOP > | ncaa_rotlibs_ |
| Map that associates three letter codes with SRRLCOPs for the noncanonical alpha-amino acid sidechain rotamer libraries. More... | |
| std::map< std::string, SingleResidueRotamerLibraryCOP > | peptoid_rotlibs_ |
| Map that associates three letter codes with SRRLCOPs for the peptoid sidechain rotamer libraries. More... | |
Static Private Attributes | |
| static RotamerLibrary * | rotamer_library_ |
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References chemical.
Referenced by create_singleton_instance().
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| void core::pack::dunbrack::RotamerLibrary::add_residue_library | ( | AA const & | aa, |
| SingleResidueRotamerLibraryCOP | rot_lib | ||
| ) | const |
| void core::pack::dunbrack::RotamerLibrary::add_residue_library | ( | ResidueType const & | rsd_type, |
| SingleResidueRotamerLibraryCOP | rot_lib | ||
| ) | const |
Overrides the library for AA.
References key, 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 |
References get_rsd_library(), and core::conformation::Residue::type().
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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(), corrections::score::dun10, and option.
Referenced by decide_read_from_binary(), and decide_write_binary().
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References current_binary_format_version_id_02(), utility::io::izstream::read(), and version.
Referenced by binary_is_up_to_date().
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Binary file is up-to-date if all the following are true:
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 current_binary_format_version_id_10(), initialize_dun10_aa_parameters(), utility::io::izstream::read(), and version.
Referenced by binary_is_up_to_date().
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References core::chemical::aa_from_name(), core::chemical::aa_unk, add_residue_library(), chemical, utility::io::izstream::close(), basic::database::full_name(), core::chemical::ChemicalManager::get_instance(), core::chemical::ChemicalManager::residue_type_set(), and core::pack::dunbrack::TR.
Referenced by create_singleton_instance().
| 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.
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().
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References core::chemical::aa_from_name(), aa_libraries_, core::chemical::aa_unk, chemical, utility::io::izstream::close(), create_rotameric_dunlib(), get_library_name_02(), initialize_dun02_aa_parameters(), libraries_, libraries_ops_, core::chemical::num_canonical_aas, core::pack::dunbrack::TR, and utility_exit.
Referenced by create_fa_dunbrack_libraries_from_ASCII().
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References aa_libraries_, chemical, utility::io::izstream::close(), create_rotameric_dunlib(), create_semi_rotameric_dunlib(), basic::options::OptionKeys::corrections::score::dun10_dir, basic::database::full_name(), initialize_dun10_aa_parameters(), libraries_, libraries_ops_, core::chemical::name_from_aa(), basic::options::option, to_string(), core::pack::dunbrack::TR, utility_exit, and utility_exit_with_message.
Referenced by create_fa_dunbrack_libraries_from_ASCII().
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References get_binary_name_10(), read_from_binary(), core::pack::dunbrack::TR, utility_exit_with_message, and version.
Referenced by create_fa_dunbrack_libraries_from_binary().
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References create_fa_dunbrack_libraries_02_from_ASCII(), create_fa_dunbrack_libraries_10_from_ASCII(), corrections::score::dun10, and option.
Referenced by create_fa_dunbrack_libraries().
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References create_fa_dunbrack_libraries_02_from_binary(), create_fa_dunbrack_libraries_10_from_binary(), corrections::score::dun10, and option.
Referenced by create_fa_dunbrack_libraries().
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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 r1, r2, core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::read_from_file(), and utility_exit_with_message.
Referenced by create_fa_dunbrack_libraries_02_from_ASCII(), create_fa_dunbrack_libraries_10_from_ASCII(), and create_srdl().
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References utility_exit_with_message.
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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 initialize_and_read_srsrdl(), r1, r2, and utility_exit_with_message.
Referenced by create_fa_dunbrack_libraries_10_from_ASCII(), and create_srdl().
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References initialize_srsrdl(), r1, r2, and utility_exit_with_message.
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private singleton creation function to be used with utility::thread::threadsafe_singleton
References basic::options::OptionKeys::corrections::score::cenrot, create_centroid_rotamer_libraries_from_ASCII(), basic::options::option, core::pack::dunbrack::read_dunbrack_library(), and RotamerLibrary().
Referenced by get_instance().
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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.
References create_rotameric_dunlib(), create_semi_rotameric_dunlib(), corrections::score::dun10, initialize_dun02_aa_parameters(), initialize_dun10_aa_parameters(), and option.
Referenced by read_from_binary().
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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:
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
Referenced by binary_is_up_to_date_02(), create_fa_dunbrack_libraries_02_from_binary(), and write_binary_fa_dunbrack_libraries_02().
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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
Referenced by binary_is_up_to_date_10(), and write_binary_fa_dunbrack_libraries_10().
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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().
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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().
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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(), out::file::dont_rewrite_dunbrack_database, corrections::score::dun10, get_binary_name(), in::file::no_binary_dunlib, and option.
Referenced by create_fa_dunbrack_libraries().
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Add specific objections to the writing of the 02 library here.
Referenced by decide_write_binary().
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Add specific objections to the writing of the 10 library here.
Referenced by decide_write_binary().
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References corrections::score::dun10, get_binary_name_02(), get_binary_name_10(), and option.
Referenced by decide_read_from_binary(), and decide_write_binary().
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References get_library_name_02().
Referenced by create_fa_dunbrack_libraries_02_from_binary(), get_binary_name(), and write_binary_fa_dunbrack_libraries_02().
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References corrections::score::dun10_dir, basic::database::full_name(), and option.
Referenced by create_fa_dunbrack_libraries_10_from_binary(), get_binary_name(), and write_binary_fa_dunbrack_libraries_10().
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static function to get the instance of ( pointer to) this singleton class
References create_singleton_instance(), rotamer_library_, and utility::thread::safely_create_singleton().
Referenced by core::util::add_covalent_linkage_helper(), 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::cenrot::CenRotDunEnergy::eval_dof_derivative(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_derivatives(), core::pack::dunbrack::DunbrackEnergy::eval_residue_dof_derivative(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_dof_derivative(), core::pack::dunbrack::load_unboundrot(), core::pack::dunbrack::DunbrackEnergy::residue_energy(), core::pack::dunbrack::cenrot::CenRotDunEnergy::residue_energy(), and core::pack::dunbrack::rotamer_from_chi().
| SingleResidueRotamerLibraryCAP core::pack::dunbrack::RotamerLibrary::get_library_by_aa | ( | chemical::AA const & | aa | ) | const |
References aa_libraries_.
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References corrections::score::dun02_file, basic::database::full_name(), and option.
Referenced by create_fa_dunbrack_libraries_02_from_ASCII(), and get_binary_name_02().
| SingleResidueRotamerLibraryCAP core::pack::dunbrack::RotamerLibrary::get_NCAA_rotamer_library | ( | chemical::ResidueType const & | rsd_type | ) | const |
Get the rotamer library specified by the NCAA_ROTLIB flag in the residue type paramater file in the residue type paramater file if it exists.
References core::chemical::ResidueType::aa(), in::file::extra_rot_lib_path, basic::database::full_name(), core::chemical::ResidueType::get_ncaa_rotlib_n_bin_per_rot(), core::chemical::ResidueType::get_ncaa_rotlib_path(), core::chemical::ResidueType::n_proton_chi(), utility::options::PathVectorOption::name(), core::chemical::ResidueType::name3(), ncaa_rotlibs_, core::chemical::ResidueType::nchi(), utility::io::izstream::open(), option, r1, r2, core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::read_from_file(), core::pack::dunbrack::SingleResidueDunbrackLibrary::set_n_chi_bins(), utility::options::PathVectorOption::size(), core::pack::dunbrack::TR, and utility_exit_with_message.
Referenced by get_rsd_library().
| SingleResidueRotamerLibraryCAP core::pack::dunbrack::RotamerLibrary::get_peptoid_rotamer_library | ( | chemical::ResidueType const & | rsd_type | ) | const |
Get the rotamer library specified by the PEPTOID_ROTLIB flag in the residue type paramater file in the residue type paramater file if it exists.
DOUG DOUG DOUG a good bit of this will need to change for the new RT based system.
References in::file::extra_rot_lib_path, basic::database::full_name(), core::chemical::ResidueType::get_peptoid_rotlib_n_bin_per_rot(), core::chemical::ResidueType::get_peptoid_rotlib_path(), core::chemical::ResidueType::n_proton_chi(), utility::options::PathVectorOption::name(), core::chemical::ResidueType::name3(), core::chemical::ResidueType::nchi(), utility::io::izstream::open(), option, peptoid_rotlibs_, r1, r2, core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >::read_from_file(), core::pack::dunbrack::SingleResiduePeptoidLibrary::set_n_chi_bins(), utility::options::PathVectorOption::size(), core::pack::dunbrack::TR, and utility_exit_with_message.
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
References aa_libraries_, add_residue_library(), core::chemical::CENTROID, core::chemical::CENTROID_ROT, core::chemical::FA_STANDARD, core::chemical::get_L_equivalent(), get_NCAA_rotamer_library(), get_peptoid_rotamer_library(), core::chemical::ResidueType::get_RotamerLibraryName(), core::chemical::ResidueType::get_use_ncaa_rotlib(), core::chemical::ResidueType::get_use_peptoid_rotlib(), core::chemical::is_canonical_D_aa(), core::chemical::ResidueType::is_ligand(), key, libraries_, core::chemical::ResidueTypeSet::name(), core::chemical::ResidueType::name(), core::chemical::ResidueType::name3(), core::chemical::num_canonical_aas, core::chemical::ResidueType::residue_type_set(), reslibraries_, core::chemical::ResidueType::rotamer_aa(), and core::pack::dunbrack::TR.
Referenced by core::util::add_covalent_linkage_helper(), 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::cenrot::CenRotDunEnergy::eval_dof_derivative(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_derivatives(), core::pack::dunbrack::DunbrackEnergy::eval_residue_dof_derivative(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_dof_derivative(), core::pack::dunbrack::DunbrackEnergy::residue_energy(), core::pack::dunbrack::cenrot::CenRotDunEnergy::residue_energy(), rotamer_energy(), rotamer_energy_deriv(), and core::pack::dunbrack::rotamer_from_chi().
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References initialize_srsrdl(), and core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::read_from_files().
Referenced by create_semi_rotameric_dunlib().
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References chemical, and core::chemical::num_canonical_aas.
Referenced by create_fa_dunbrack_libraries_02_from_ASCII(), and create_srdl().
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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, core::chemical::aa_val, chemical, and core::chemical::num_canonical_aas.
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Hard code this data in a single place; adjust the booleans for the backbone independent
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, core::chemical::aa_val, and chemical.
Referenced by binary_is_up_to_date_10(), create_fa_dunbrack_libraries_10_from_ASCII(), create_srdl(), and write_binary_fa_dunbrack_libraries_10().
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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().
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References in::path::database, file, free, option, and core::pack::dunbrack::TR.
Referenced by write_binary_fa_dunbrack_libraries_02(), and write_binary_fa_dunbrack_libraries_10().
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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(), core::chemical::name_from_aa(), utility::io::izstream::read(), and utility_exit_with_message.
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 |
References get_rsd_library(), and core::conformation::Residue::type().
| Real core::pack::dunbrack::RotamerLibrary::rotamer_energy_deriv | ( | Residue const & | rsd, |
| RotamerLibraryScratchSpace & | scratch | ||
| ) | const |
| 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.
References aa_libraries_, core::chemical::CENTROID, core::chemical::FA_STANDARD, key, libraries_, core::chemical::ResidueTypeSet::name(), core::chemical::ResidueType::name(), core::chemical::ResidueType::name3(), ncaa_rotlibs_, core::chemical::num_canonical_aas, peptoid_rotlibs_, core::chemical::ResidueType::residue_type_set(), reslibraries_, and core::chemical::ResidueType::rotamer_aa().
Referenced by core::util::add_covalent_linkage_helper().
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References corrections::score::dun10, option, write_binary_fa_dunbrack_libraries_02(), and write_binary_fa_dunbrack_libraries_10().
Referenced by create_fa_dunbrack_libraries().
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References current_binary_format_version_id_02(), get_binary_name_02(), random_tempname(), rename, core::pack::dunbrack::TR, version, and write_to_binary().
Referenced by write_binary_fa_dunbrack_libraries().
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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 libraries_, and utility::io::ozstream::write().
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 |
References libraries_, and out.
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Map that associates three letter codes with SRRLCOPs for the noncanonical alpha-amino acid sidechain rotamer libraries.
DOUG DOUG DOUG Should this be done in the "threadsafe" way above?
Referenced by get_NCAA_rotamer_library(), and rsd_library_already_loaded().
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Map that associates three letter codes with SRRLCOPs for the peptoid sidechain rotamer libraries.
DOUG DOUG DOUG Should this be done in the "threadsafe" way above?
Referenced by get_peptoid_rotamer_library(), and rsd_library_already_loaded().
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Referenced by add_residue_library(), get_rsd_library(), and rsd_library_already_loaded().
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Referenced by get_instance().
1.8.7