core::import_pose::libraries Namespace Reference

Classes
class	BasePairStepLibrary
class	BasePairStepSequence
class	BasePairType
class	ChunkSet
class	RNA_ChunkLibrary
class	RNA_JumpLibrary
class	RNA_LibraryManager
	Holds all libraries relevant to FARFAR as CONST copies: More...
class	RNA_PairingTemplate

Typedefs
typedef utility::pointer::shared_ptr < BasePairStepLibrary >	BasePairStepLibraryOP
typedef utility::pointer::shared_ptr < BasePairStepLibrary const >	BasePairStepLibraryCOP
typedef utility::pointer::shared_ptr < ChunkSet >	ChunkSetOP
typedef utility::pointer::shared_ptr < ChunkSet const >	ChunkSetCOP
typedef utility::pointer::shared_ptr < RNA_ChunkLibrary >	RNA_ChunkLibraryOP
typedef utility::pointer::shared_ptr < RNA_ChunkLibrary const >	RNA_ChunkLibraryCOP
typedef utility::pointer::shared_ptr < RNA_JumpLibrary >	RNA_JumpLibraryOP
typedef utility::pointer::shared_ptr < RNA_JumpLibrary const >	RNA_JumpLibraryCOP
typedef utility::pointer::shared_ptr < RNA_PairingTemplate >	RNA_PairingTemplateOP
typedef utility::vector1 < RNA_PairingTemplateOP >	RNA_PairingTemplateList
typedef std::map< BasePairType, RNA_PairingTemplateList >	RNA_PairingTemplateMap
typedef utility::pointer::shared_ptr < RNA_LibraryManager >	RNA_LibraryManagerOP
typedef utility::pointer::shared_ptr < RNA_LibraryManager const >	RNA_LibraryManagerCOP

Functions
std::ostream &	operator<< (std::ostream &os, BasePairStepSequence const &bps)
utility::vector1< std::string >	remove_terminus_variant_types_for_rna (utility::vector1< std::string > const &types, char seq)
Size const	ROSETTA_LIBRARY_DOMAIN (1000)
bool	check_base_pair_step_availability (BasePairStepLibrary const &base_pair_step_library, BasePairStepSequence const &base_pair_step_sequence)
static basic::Tracer	tr ("protocols.rna.denovo.libraries.RNA_JumpLibrary")
char	one_letter_from_rt (chemical::ResidueType const &rt)

Variables
core::Size const	ROSETTA_LIBRARY_DOMAIN

Typedef Documentation

typedef utility::pointer::shared_ptr< BasePairStepLibrary const > core::import_pose::libraries::BasePairStepLibraryCOP

typedef utility::pointer::shared_ptr< BasePairStepLibrary > core::import_pose::libraries::BasePairStepLibraryOP

typedef utility::pointer::shared_ptr< ChunkSet const > core::import_pose::libraries::ChunkSetCOP

typedef utility::pointer::shared_ptr< ChunkSet > core::import_pose::libraries::ChunkSetOP

typedef utility::pointer::shared_ptr< RNA_ChunkLibrary const > core::import_pose::libraries::RNA_ChunkLibraryCOP

typedef utility::pointer::shared_ptr< RNA_ChunkLibrary > core::import_pose::libraries::RNA_ChunkLibraryOP

typedef utility::pointer::shared_ptr< RNA_JumpLibrary const > core::import_pose::libraries::RNA_JumpLibraryCOP

typedef utility::pointer::shared_ptr< RNA_JumpLibrary > core::import_pose::libraries::RNA_JumpLibraryOP

typedef utility::pointer::shared_ptr< RNA_LibraryManager const > core::import_pose::libraries::RNA_LibraryManagerCOP

typedef utility::pointer::shared_ptr< RNA_LibraryManager > core::import_pose::libraries::RNA_LibraryManagerOP

typedef utility::vector1< RNA_PairingTemplateOP > core::import_pose::libraries::RNA_PairingTemplateList

typedef std::map< BasePairType, RNA_PairingTemplateList > core::import_pose::libraries::RNA_PairingTemplateMap

typedef utility::pointer::shared_ptr< RNA_PairingTemplate > core::import_pose::libraries::RNA_PairingTemplateOP

Function Documentation

bool core::import_pose::libraries::check_base_pair_step_availability	(	BasePairStepLibrary const &	base_pair_step_library,
		BasePairStepSequence const &	base_pair_step_sequence
	)

References core::import_pose::libraries::BasePairStepLibrary::canonical(), core::import_pose::libraries::BasePairStepLibrary::database_dir(), core::import_pose::libraries::BasePairStepLibrary::has_value(), core::import_pose::libraries::BasePairStepSequence::tag(), and core::import_pose::TR().

Referenced by core::import_pose::libraries::RNA_ChunkLibrary::setup_base_pair_step_chunks().

char core::import_pose::libraries::one_letter_from_rt

(

chemical::ResidueType const &

rt

)

References core::chemical::ResidueTypeBase::aa(), core::chemical::na_ade, core::chemical::ResidueTypeBase::na_analogue(), core::chemical::na_cyt, core::chemical::na_gua, core::chemical::na_rad, core::chemical::na_rcy, core::chemical::na_rgu, core::chemical::na_ura, core::chemical::ResidueTypeBase::name(), and core::chemical::ResidueTypeBase::name1().

Referenced by core::import_pose::libraries::RNA_JumpLibrary::get_random_base_pair_jump().

std::ostream& core::import_pose::libraries::operator<<	(	std::ostream &	os,
		BasePairStepSequence const &	bps
	)

References core::import_pose::libraries::BasePairStepSequence::base_pair_step_sequence_, and core::import_pose::libraries::BasePairStepSequence::num_bulge_.

utility::vector1< std::string > core::import_pose::libraries::remove_terminus_variant_types_for_rna	(	utility::vector1< std::string > const &	types,
		char	seq
	)

References core::chemical::rna::rna_nts().

Referenced by core::import_pose::libraries::ChunkSet::filter_poses_have_same_sequence_and_variants().

Size const core::import_pose::libraries::ROSETTA_LIBRARY_DOMAIN

(

1000

)

static basic::Tracer core::import_pose::libraries::tr ( "protocols.rna.denovo.libraries.RNA_JumpLibrary"  )

static

Referenced by core::import_pose::libraries::RNA_JumpLibrary::get_random_base_pair_jump(), and core::import_pose::libraries::RNA_JumpLibrary::read_jumps_from_file().

Variable Documentation

core::Size const core::import_pose::libraries::ROSETTA_LIBRARY_DOMAIN

Referenced by protocols::rna::denovo::RNA_FragmentMonteCarlo::check_for_loop_modeling_case(), core::import_pose::libraries::ChunkSet::get_atom_id_domain_map_for_rosetta_library_chunk(), protocols::rna::movers::RNA_LoopCloser::get_cutpoints_closed(), core::import_pose::libraries::RNA_ChunkLibrary::setup_base_pair_step_chunks(), core::import_pose::libraries::RNA_ChunkLibrary::update_atom_level_domain_map(), protocols::rna::denovo::movers::RNA_Minimizer::update_atom_level_domain_map_to_move_rosetta_library_chunks(), and core::import_pose::libraries::RNA_ChunkLibrary::update_to_move_rosetta_library_chunks().