core::chemical::rotamers::NCAARotamerLibrarySpecification Class Reference

#include <NCAARotamerLibrarySpecification.hh>

Inheritance diagram for core::chemical::rotamers::NCAARotamerLibrarySpecification:

Public Member Functions
	NCAARotamerLibrarySpecification ()
	NCAARotamerLibrarySpecification (std::string const &ncaa_rotlib_path)
	NCAARotamerLibrarySpecification (std::istream &)
virtual	~NCAARotamerLibrarySpecification ()
void	ncaa_rotlib_path (std::string const &path)
	Sets the path to the NCAA rotlib for the residue type. More...
void	ncaa_rotlib_n_bin_per_rot (utility::vector1< Size > const &n_bins_per_rot)
	Sets the number of rotamers for each rotatable bond described by the NCAA rotlib. More...
void	semirotameric_ncaa_rotlib (bool setting)
void	nrchi_symmetric (bool setting)
void	nrchi_start_angle (Real setting)
std::string const &	ncaa_rotlib_path () const
	Returns the path to the NCAA rotlib for the residue type. More...
core::Size	ncaa_rotlib_n_rotameric_bins () const
	Returns the number of rotatable bonds described by the NCAA rotlib (not nesesarily equal to nchi) More...
utility::vector1< Size > const &	ncaa_rotlib_n_bin_per_rot () const
	Returns the number of rotamers for each rotatable bond described by the NCAA rotlib for all bonds. More...
bool	semirotameric_ncaa_rotlib () const
bool	nrchi_symmetric () const
Real	nrchi_start_angle () const
virtual std::string	keyname () const
	Which type of SingleResidueRotamerLibrary does this specification sub-type correspond to? More...
virtual std::string	cache_tag (core::chemical::ResidueType const &) const
	How, if at all, should the corresponding SingleResidueRotamerLibrary be cached? More...
Public Member Functions inherited from core::chemical::rotamers::RotamerLibrarySpecification
	RotamerLibrarySpecification ()
virtual	~RotamerLibrarySpecification ()

Static Public Member Functions
static std::string	library_name ()

Private Attributes
std::string	ncaa_rotlib_path_
	path to the NCAA rotlib More...
utility::vector1< Size >	ncaa_rotlib_n_bins_per_rot_
	the number of rotamer bins for each chi angle in the NCAA rotlib More...
bool	semirotameric_ncaa_rotlib_
	whether or not the NCAA rotlib is semirotameric More...
bool	nrchi_symmetric_
Real	nrchi_start_angle_

Constructor & Destructor Documentation

core::chemical::rotamers::NCAARotamerLibrarySpecification::NCAARotamerLibrarySpecification

(

)

core::chemical::rotamers::NCAARotamerLibrarySpecification::NCAARotamerLibrarySpecification

(

std::string const &

ncaa_rotlib_path

)

core::chemical::rotamers::NCAARotamerLibrarySpecification::NCAARotamerLibrarySpecification

(

std::istream &

input

)

References ncaa_rotlib_n_bins_per_rot_, ncaa_rotlib_path_, and core::chemical::rotamers::TR().

core::chemical::rotamers::NCAARotamerLibrarySpecification::~NCAARotamerLibrarySpecification ( )

virtual

Member Function Documentation

std::string core::chemical::rotamers::NCAARotamerLibrarySpecification::cache_tag ( core::chemical::ResidueType const &  ) const

virtual

How, if at all, should the corresponding SingleResidueRotamerLibrary be cached?

The default is to return an empty string, which turns off caching.

The SingleResidueRotamerLibraries are cached in the SingleResidueRotamerLibraryFactory based on keyname() and cache_tag() (as keys in a map< string, map< string, SRRL > > ). Two RotamerLibrarySpecifications with identical return values for keyname() and cache_tag() should correspond to (functionally) identical SingleResidueRotamerLibraries.

This has to be in the RotamerLibrarySpecification, as when reading we need to know the cache string before creating the library.

A note on writing RotamerLibrarySpecifications and SingleResidueRotamerLibrarys: The functions of a SingleResidueRotamerLibrary will normally have access to the actual RotamerLibrarySpecification from the passed Residue/ResidueType. Therefore, you don't need to store all the information from a RLS in the SRRL. Not doing so allows you to have more general cache_tag(), as the cache_tag() function only needs to disambiguate RotamerLibrarySpecifications which result in different SingleResidueRotamerLibrarys. (That is, cache_tag() only needs to encapsulate data used by SingleResidueRotamerLibraryCreator to create the SingleResidueRotamerLibrary.)

The ResidueType is passed to cache_tag() so that if the SingleResidueRotamerLibraryCreator needs details from the ResidueType in order to correctly create the SingleResidueRotamerLibrary, that information can be extracted. In general, though, you want to avoid keying off of information in ResidueType as much as possible.

Reimplemented from core::chemical::rotamers::RotamerLibrarySpecification.

References core::chemical::ResidueType::mainchain_atoms(), core::chemical::ResidueType::name3(), ncaa_rotlib_n_bins_per_rot_, ncaa_rotlib_path_, nrchi_start_angle_, nrchi_symmetric_, and semirotameric_ncaa_rotlib_.

std::string core::chemical::rotamers::NCAARotamerLibrarySpecification::keyname ( ) const

virtual

Which type of SingleResidueRotamerLibrary does this specification sub-type correspond to?

Implements core::chemical::rotamers::RotamerLibrarySpecification.

References library_name().

std::string core::chemical::rotamers::NCAARotamerLibrarySpecification::library_name ( )

static

Referenced by core::pack::rotamers::SingleNCAARotamerLibraryCreator::keyname(), core::chemical::rotamers::NCAARotamerLibrarySpecificationCreator::keyname(), and keyname().

void core::chemical::rotamers::NCAARotamerLibrarySpecification::ncaa_rotlib_n_bin_per_rot ( utility::vector1< Size > const &  n_bins_per_rot )

inline

Sets the number of rotamers for each rotatable bond described by the NCAA rotlib.

References ncaa_rotlib_n_bins_per_rot_.

utility::vector1<Size> const& core::chemical::rotamers::NCAARotamerLibrarySpecification::ncaa_rotlib_n_bin_per_rot ( ) const

inline

Returns the number of rotamers for each rotatable bond described by the NCAA rotlib for all bonds.

References ncaa_rotlib_n_bins_per_rot_.

core::Size core::chemical::rotamers::NCAARotamerLibrarySpecification::ncaa_rotlib_n_rotameric_bins ( ) const

inline

Returns the number of rotatable bonds described by the NCAA rotlib (not nesesarily equal to nchi)

References ncaa_rotlib_n_bins_per_rot_.

void core::chemical::rotamers::NCAARotamerLibrarySpecification::ncaa_rotlib_path ( std::string const &  path )

inline

Sets the path to the NCAA rotlib for the residue type.

References ncaa_rotlib_path_, and protocols::hybridization::path.

std::string const& core::chemical::rotamers::NCAARotamerLibrarySpecification::ncaa_rotlib_path ( ) const

inline

Returns the path to the NCAA rotlib for the residue type.

References ncaa_rotlib_path_.

void core::chemical::rotamers::NCAARotamerLibrarySpecification::nrchi_start_angle ( Real  setting )

inline

References nrchi_start_angle_.

Real core::chemical::rotamers::NCAARotamerLibrarySpecification::nrchi_start_angle ( ) const

inline

References nrchi_start_angle_.

void core::chemical::rotamers::NCAARotamerLibrarySpecification::nrchi_symmetric ( bool  setting )

inline

References nrchi_symmetric_.

bool core::chemical::rotamers::NCAARotamerLibrarySpecification::nrchi_symmetric ( ) const

inline

References nrchi_symmetric_.

void core::chemical::rotamers::NCAARotamerLibrarySpecification::semirotameric_ncaa_rotlib ( bool  setting )

inline

References semirotameric_ncaa_rotlib_.

bool core::chemical::rotamers::NCAARotamerLibrarySpecification::semirotameric_ncaa_rotlib ( ) const

inline

References semirotameric_ncaa_rotlib_.

Member Data Documentation

utility::vector1< Size > core::chemical::rotamers::NCAARotamerLibrarySpecification::ncaa_rotlib_n_bins_per_rot_

private

the number of rotamer bins for each chi angle in the NCAA rotlib

Referenced by cache_tag(), ncaa_rotlib_n_bin_per_rot(), ncaa_rotlib_n_rotameric_bins(), and NCAARotamerLibrarySpecification().

std::string core::chemical::rotamers::NCAARotamerLibrarySpecification::ncaa_rotlib_path_

private

path to the NCAA rotlib

Referenced by cache_tag(), ncaa_rotlib_path(), and NCAARotamerLibrarySpecification().

Real core::chemical::rotamers::NCAARotamerLibrarySpecification::nrchi_start_angle_

private

Referenced by cache_tag(), and nrchi_start_angle().

bool core::chemical::rotamers::NCAARotamerLibrarySpecification::nrchi_symmetric_

private

Referenced by cache_tag(), and nrchi_symmetric().

bool core::chemical::rotamers::NCAARotamerLibrarySpecification::semirotameric_ncaa_rotlib_

private

whether or not the NCAA rotlib is semirotameric

Referenced by cache_tag(), and semirotameric_ncaa_rotlib().

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

• src/core/chemical/rotamers/NCAARotamerLibrarySpecification.hh
• src/core/chemical/rotamers/NCAARotamerLibrarySpecification.cc