protocols::frags Namespace Reference

Classes
class	RMSVallData
class	TorsionFragment
	a class for single piece of torsion fragment More...
class	SingleResidueTorsionFragmentLibrary
	a class for collection of fragments for a single residue position More...
class	TorsionFragmentLibrary
	a class for classic Rosetta fragment library More...
class	FragLib
class	TorsionFragmentMover
class	VallData

Typedefs
using	Sizes = utility::vector1< core::Size >
typedef utility::pointer::shared_ptr< TorsionFragment >	TorsionFragmentOP
typedef utility::pointer::shared_ptr< SingleResidueTorsionFragmentLibrary >	SingleResidueTorsionFragmentLibraryOP
typedef utility::pointer::shared_ptr< TorsionFragmentLibrary >	TorsionFragmentLibraryOP
typedef utility::pointer::shared_ptr< TorsionFragmentLibrary const >	TorsionFragmentLibraryCOP
typedef utility::pointer::shared_ptr< FragLib >	FragLibOP
typedef utility::pointer::shared_ptr< FragLib const >	FragLibCOP
typedef utility::pointer::shared_ptr< TorsionFragmentMover >	TorsionFragmentMoverOP

Functions
void	heap_init (FArray1A_int heap, FArray1A_float coheap, int max_items)
	sets up an empty heap and stores the dimensioned size More...
void	heap_extract (FArray1A_int heap, FArray1A_float coheap, int &val, float &coval, bool &err)
	modifes heap and last_val return val and err. More...
void	heap_insert (FArray1A_int heap, FArray1A_float coheap, int val, float coval, bool &err)
	modifes heap and last_dummy, inserts val, returns err requires heap_max to be previously set via heap_init More...
void	heap_replace (FArray1A_int heap, FArray1A_float coheap, int val, float coval)
void	heap_down (FArray1A_int heap, FArray1A_float coheap, int index_in)
void	heap_up (FArray1A_int heap, FArray1A_float coheap, int &index_in)
void	heap_init (ObjexxFCL::FArray1A_int heap, ObjexxFCL::FArray1A_float coheap, int max_items)
void	heap_extract (ObjexxFCL::FArray1A_int heap, ObjexxFCL::FArray1A_float coheap, int &val, float &coval, bool &err)
void	heap_insert (ObjexxFCL::FArray1A_int heap, ObjexxFCL::FArray1A_float coheap, int val, float coval, bool &err)
void	heap_replace (ObjexxFCL::FArray1A_int heap, ObjexxFCL::FArray1A_float coheap, int val, float coval)
void	heap_down (ObjexxFCL::FArray1A_int heap, ObjexxFCL::FArray1A_float coheap, int index_in)
void	heap_up (ObjexxFCL::FArray1A_int heap, ObjexxFCL::FArray1A_float coheap, int &index_in)
static basic::Tracer	TR ("protocols.frags.TorsionFragment")
template<class T >
bool	has_element (utility::vector1< T > const &v, T const &t)
	these will go into a helper file soon More...
template<class T >
bool	has_element (T const &t, utility::vector1< T > const &v)
	never can remember the order... More...
bool	ss_length_check (core::Size const min_len_helix, core::Size const min_len_strand, core::pose::Pose const &pose)
void	add_vall_fragments (utility::vector1< core::Size > const &frag_sizes, core::Size const nfrags, pose::Pose const &pose, core::kinematics::MoveMap const &mm, std::string const &secstruct, Real const seq_weight, Real const ss_weight, FragLib &frag_lib, utility::vector1< core::Size > const &homs_to_exclude, Real const bb_weight, std::string const &bigbins, std::string const &inputseq)
void	add_vall_fragments (utility::vector1< core::Size > const &frag_sizes, core::Size const nfrags, pose::Pose const &pose, core::kinematics::MoveMap const &mm, utility::vector1< std::map< char, core::Real > > const &target_ss, Real const seq_weight, Real const ss_weight, FragLib &frag_lib, utility::vector1< core::Size > const &homs_to_exclude, Real const bb_weight, std::string const &bigbins, std::string const &inputseq)
FragLibOP	setup_vall_fragments (utility::vector1< core::Size > const &frag_sizes, core::Size const nfrags, pose::Pose const &pose, core::kinematics::MoveMap const &mm, std::string const &secstruct, Real const seq_weight, Real const ss_weight, utility::vector1< core::Size > const &homs_to_exclude)
void	add_vall_cheating_fragments (utility::vector1< core::Size > const &frag_sizes, core::Size const nfrags, pose::Pose const &pose, core::kinematics::MoveMap const &mm, std::string const &secstruct, Real const seq_weight, Real const ss_weight, Real const torsion_weight, Real const min_torsion_dev, Real const max_torsion_dev, FragLib &frag_lib, utility::vector1< core::Size > const &homs_to_exclude)
FragLibOP	setup_vall_cheating_fragments (utility::vector1< core::Size > const &frag_sizes, core::Size const nfrags, pose::Pose const &pose, core::kinematics::MoveMap const &mm, std::string const &secstruct, Real const seq_weight, Real const ss_weight, Real const torsion_weight, Real const min_torsion_dev, Real const max_torsion_dev, utility::vector1< core::Size > const &homs_to_exclude)
void	fill_in_gaps (core::Size const nfrags, pose::Pose const &pose, std::string const &secstruct, Real const seq_weight, Real const ss_weight, FragLib &frag_lib, utility::vector1< core::Size > const &homs_to_exclude, bool const allow_uninitialized_secstruct)
void	insert_fragment (core::Size const begin, core::Size const end, pose::Pose &pose, TorsionFragmentLibrary const &lib, core::Size const desired_insert_pos)
std::ostream &	operator<< (std::ostream &out, TorsionFragment const &f)
std::istream &	operator>> (std::istream &data, TorsionFragment &f)
std::ostream &	operator<< (std::ostream &out, SingleResidueTorsionFragmentLibrary const &lib)
std::istream &	operator>> (std::istream &data, SingleResidueTorsionFragmentLibrary &lib)
std::ostream &	operator<< (std::ostream &out, TorsionFragmentLibrary const &lib)
std::istream &	operator>> (std::istream &data, TorsionFragmentLibrary &lib)
std::ostream &	operator<< (std::ostream &out, FragLib const &lib)
std::istream &	operator>> (std::istream &data, FragLib &lib)
void	get_min_and_max_contigs (Sizes const &seg_in, core::Size &min_seg, core::Size &max_seg)
void	insert_random_fragments_in_flexible_protein_regions (Sizes const &flex_protein, FragLib const &frag_lib, pose::Pose &pose)
void	insert_random_fragments_in_flexible_protein_regions (utility::vector1< core::Size > const &flex_protein, FragLib const &frag_lib, core::pose::Pose &pose)
Real	torsion_dev_score (Real const frag_angle, Real const target_angle, Real const min_dev, Real const max_dev)
void	get_frags (core::Size const nfrags, std::string const &target_seq, std::string const &target_ss, core::Real const seq_weight, core::Real const ss_weight, bool const exclude_gly, bool const exclude_pro, bool const exclude_cis_peptides, utility::vector1< core::Size > const &homs_to_exclude, SingleResidueTorsionFragmentLibrary &library, core::Real const bb_weight=0.0, std::string const &target_bb=std::string())
	handles loading the vall if necessary More...
void	get_frags (core::Size const nfrags, std::string const &target_seq, utility::vector1< std::map< char, core::Real > > const &target_ss, core::Real const seq_weight, core::Real const ss_weight, bool const exclude_gly, bool const exclude_pro, bool const exclude_cis_peptides, utility::vector1< core::Size > const &homs_to_exclude, SingleResidueTorsionFragmentLibrary &library, core::Real const bb_weight=0.0, std::string const &target_bb=std::string())
	handles loading the vall if necessary More...
void	get_cheating_frags (core::Size const nfrags, std::string const &target_seq, std::string const &target_ss, utility::vector1< Real > const &target_phi, utility::vector1< Real > const &target_psi, utility::vector1< Real > const &target_omega, Real const seq_weight, Real const ss_weight, Real const torsion_weight, Real const min_torsion_dev, Real const max_torsion_dev, utility::vector1< core::Size > const &homs_to_exclude, SingleResidueTorsionFragmentLibrary &library)
void	dump_vall_fasta (std::string const &fasta_filename)
char	torsion2big_bin (core::Real const phi, core::Real const psi, core::Real const omega)
void	get_cheating_frags (core::Size const nfrags, std::string const &target_seq, std::string const &target_ss, utility::vector1< core::Real > const &target_phi, utility::vector1< core::Real > const &target_psi, utility::vector1< core::Real > const &target_omega, core::Real const seq_weight, core::Real const ss_weight, core::Real const torsion_weight, core::Real const min_torsion_dev, core::Real const max_torsion_dev, utility::vector1< core::Size > const &homs_to_exclude, SingleResidueTorsionFragmentLibrary &library)

Variables
utility::vector1< core::Size > const	empty_size_list

Typedef Documentation

FragLibCOP

typedef utility::pointer::shared_ptr< FragLib const > protocols::frags::FragLibCOP

FragLibOP

typedef utility::pointer::shared_ptr< FragLib > protocols::frags::FragLibOP

SingleResidueTorsionFragmentLibraryOP

typedef utility::pointer::shared_ptr< SingleResidueTorsionFragmentLibrary > protocols::frags::SingleResidueTorsionFragmentLibraryOP

Sizes

using protocols::frags::Sizes = typedef utility::vector1<core::Size>

TorsionFragmentLibraryCOP

typedef utility::pointer::shared_ptr< TorsionFragmentLibrary const > protocols::frags::TorsionFragmentLibraryCOP

TorsionFragmentLibraryOP

typedef utility::pointer::shared_ptr< TorsionFragmentLibrary > protocols::frags::TorsionFragmentLibraryOP

TorsionFragmentMoverOP

typedef utility::pointer::shared_ptr< TorsionFragmentMover > protocols::frags::TorsionFragmentMoverOP

TorsionFragmentOP

typedef utility::pointer::shared_ptr< TorsionFragment > protocols::frags::TorsionFragmentOP

Function Documentation

add_vall_cheating_fragments()

void protocols::frags::add_vall_cheating_fragments	(	utility::vector1< core::Size > const &	frag_sizes,
		core::Size const	nfrags,
		pose::Pose const &	pose,
		core::kinematics::MoveMap const &	mm,
		std::string const &	secstruct,
		Real const	seq_weight,
		Real const	ss_weight,
		Real const	torsion_weight,
		Real const	min_torsion_dev,
		Real const	max_torsion_dev,
		FragLib &	frag_lib,
		utility::vector1< core::Size > const &	homs_to_exclude
	)

References core::kinematics::MoveMap::get_bb(), get_cheating_frags(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_upper_terminus(), protocols::frags::FragLib::library(), core::pose::Pose::omega(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::Pose::residue(), protocols::frags::TorsionFragmentLibrary::resize(), core::pose::Pose::sequence(), and core::pose::Pose::size().

Referenced by setup_vall_cheating_fragments().

add_vall_fragments() [1/2]

void protocols::frags::add_vall_fragments	(	utility::vector1< core::Size > const &	frag_sizes,
		core::Size const	nfrags,
		pose::Pose const &	pose,
		core::kinematics::MoveMap const &	mm,
		std::string const &	secstruct,
		Real const	seq_weight,
		Real const	ss_weight,
		FragLib &	frag_lib,
		utility::vector1< core::Size > const &	homs_to_exclude,
		Real const	bb_weight,
		std::string const &	bigbins,
		std::string const &	inputseq
	)

References core::kinematics::MoveMap::get_bb(), get_frags(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_upper_terminus(), protocols::frags::FragLib::library(), core::pose::Pose::residue(), protocols::frags::TorsionFragmentLibrary::resize(), core::pose::Pose::sequence(), and core::pose::Pose::size().

Referenced by setup_vall_fragments().

add_vall_fragments() [2/2]

void protocols::frags::add_vall_fragments	(	utility::vector1< core::Size > const &	frag_sizes,
		core::Size const	nfrags,
		pose::Pose const &	pose,
		core::kinematics::MoveMap const &	mm,
		utility::vector1< std::map< char, core::Real > > const &	target_ss,
		Real const	seq_weight,
		Real const	ss_weight,
		FragLib &	frag_lib,
		utility::vector1< core::Size > const &	homs_to_exclude,
		Real const	bb_weight,
		std::string const &	bigbins,
		std::string const &	inputseq
	)

Parameters

seq_weight

/ THIS IS THE DIFFERENCE

References core::kinematics::MoveMap::get_bb(), get_frags(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_upper_terminus(), protocols::frags::FragLib::library(), core::pose::Pose::residue(), protocols::frags::TorsionFragmentLibrary::resize(), core::pose::Pose::sequence(), and core::pose::Pose::size().

dump_vall_fasta()

void protocols::frags::dump_vall_fasta

(

std::string const &

fasta_filename

)

References protocols::frags::VallData::chain(), core::conformation::membrane::out, and protocols::frags::VallData::sequence().

fill_in_gaps()

void protocols::frags::fill_in_gaps	(	core::Size const	nfrags,
		pose::Pose const &	pose,
		std::string const &	secstruct,
		Real const	seq_weight,
		Real const	ss_weight,
		FragLib &	frag_lib,
		utility::vector1< core::Size > const &	homs_to_exclude,
		bool const	allow_uninitialized_secstruct
	)

Fill in gaps in the FragLib with fragments chosen from the vall

Note

Does not change the size of any of the individual fragment libraries

References protocols::frags::FragLib::frag_sizes(), get_frags(), core::conformation::Residue::is_protein(), protocols::frags::FragLib::library(), core::pose::Pose::residue(), core::pose::Pose::sequence(), core::pose::Pose::size(), protocols::frags::TorsionFragmentLibrary::size(), and TR().

get_cheating_frags() [1/2]

void protocols::frags::get_cheating_frags	(	core::Size const	nfrags,
		std::string const &	target_seq,
		std::string const &	target_ss,
		utility::vector1< core::Real > const &	target_phi,
		utility::vector1< core::Real > const &	target_psi,
		utility::vector1< core::Real > const &	target_omega,
		core::Real const	seq_weight,
		core::Real const	ss_weight,
		core::Real const	torsion_weight,
		core::Real const	min_torsion_dev,
		core::Real const	max_torsion_dev,
		utility::vector1< core::Size > const &	homs_to_exclude,
		SingleResidueTorsionFragmentLibrary &	library
	)

References protocols::frags::VallData::get_cheating_frags().

Referenced by add_vall_cheating_fragments().

get_cheating_frags() [2/2]

void protocols::frags::get_cheating_frags	(	core::Size const	nfrags,
		std::string const &	target_seq,
		std::string const &	target_ss,
		utility::vector1< Real > const &	target_phi,
		utility::vector1< Real > const &	target_psi,
		utility::vector1< Real > const &	target_omega,
		Real const	seq_weight,
		Real const	ss_weight,
		Real const	torsion_weight,
		Real const	min_torsion_dev,
		Real const	max_torsion_dev,
		utility::vector1< core::Size > const &	homs_to_exclude,
		SingleResidueTorsionFragmentLibrary &	library
	)

References protocols::frags::VallData::get_cheating_frags().

Referenced by add_vall_cheating_fragments().

get_frags() [1/2]

void protocols::frags::get_frags	(	core::Size const	nfrags,
		std::string const &	target_seq,
		std::string const &	target_ss,
		Real const	seq_weight,
		Real const	ss_weight,
		bool const	exclude_gly,
		bool const	exclude_pro,
		bool const	exclude_cis_peptides,
		utility::vector1< core::Size > const &	homs_to_exclude,
		SingleResidueTorsionFragmentLibrary &	library,
		Real const	bb_weight,
		std::string const &	target_bb
	)

handles loading the vall if necessary

Handles loading default vall, then calls above routine

References protocols::frags::VallData::get_frags().

Referenced by add_vall_fragments(), and fill_in_gaps().

get_frags() [2/2]

void protocols::frags::get_frags	(	core::Size const	nfrags,
		std::string const &	target_seq,
		utility::vector1< std::map< char, core::Real > > const &	target_ss,
		Real const	seq_weight,
		Real const	ss_weight,
		bool const	exclude_gly,
		bool const	exclude_pro,
		bool const	exclude_cis_peptides,
		utility::vector1< core::Size > const &	homs_to_exclude,
		SingleResidueTorsionFragmentLibrary &	library,
		Real const	bb_weight,
		std::string const &	target_bb
	)

handles loading the vall if necessary

Handles loading default vall, then calls above routine

References protocols::frags::VallData::get_frags().

get_min_and_max_contigs()

void protocols::frags::get_min_and_max_contigs	(	Sizes const &	seg_in,
		core::Size &	min_seg,
		core::Size &	max_seg
	)

Determine length of shortest and longest contiguous segments

References protocols::splice::min_seg().

Referenced by insert_random_fragments_in_flexible_protein_regions().

has_element() [1/2]

template<class T >

bool protocols::frags::has_element	(	T const &	t,
		utility::vector1< T > const &	v
	)

never can remember the order...

References protocols::hybridization::t.

has_element() [2/2]

template<class T >

bool protocols::frags::has_element	(	utility::vector1< T > const &	v,
		T const &	t
	)

these will go into a helper file soon

References protocols::hybridization::t.

Referenced by insert_random_fragments_in_flexible_protein_regions().

heap_down() [1/2]

void protocols::frags::heap_down	(	FArray1A_int	heap,
		FArray1A_float	coheap,
		int	index_in
	)

Parameters

heap	- [in/out]? - convert to zero offset matrix
coheap	- [in/out]? -
index_in	- [in/out]? -

Global Read:

Global Write:

Remarks

References:

Author

Referenced by heap_extract(), and heap_replace().

heap_down() [2/2]

void protocols::frags::heap_down	(	ObjexxFCL::FArray1A_int	heap,
		ObjexxFCL::FArray1A_float	coheap,
		int	index_in
	)

heap_extract() [1/2]

void protocols::frags::heap_extract	(	FArray1A_int	heap,
		FArray1A_float	coheap,
		int &	val,
		float &	coval,
		bool &	err
	)

modifes heap and last_val return val and err.

Parameters

heap	- [in/out]? - convert to zero offset matrix
coheap	- [in/out]? -
val	- [in/out]? -
coval	- [in/out]? -
err	- [in/out]? -

Global Read:

Global Write:

Remarks

References:

Author

References heap_down(), and protocols::hybridization::val.

Referenced by protocols::frags::VallData::get_cheating_frags(), protocols::frags::VallData::get_frags(), and protocols::frags::RMSVallData::get_frags().

heap_extract() [2/2]

void protocols::frags::heap_extract	(	ObjexxFCL::FArray1A_int	heap,
		ObjexxFCL::FArray1A_float	coheap,
		int &	val,
		float &	coval,
		bool &	err
	)

heap_init() [1/2]

void protocols::frags::heap_init	(	FArray1A_int	heap,
		FArray1A_float	coheap,
		int	max_items
	)

sets up an empty heap and stores the dimensioned size

Parameters

heap	- [in/out]? -
coheap	- [in/out]? -
max_items	- [in/out]? -

Global Read:

Global Write:

Remarks

References:

Author

Referenced by protocols::frags::VallData::get_cheating_frags(), protocols::frags::VallData::get_frags(), and protocols::frags::RMSVallData::get_frags().

heap_init() [2/2]

void protocols::frags::heap_init	(	ObjexxFCL::FArray1A_int	heap,
		ObjexxFCL::FArray1A_float	coheap,
		int	max_items
	)

heap_insert() [1/2]

void protocols::frags::heap_insert	(	FArray1A_int	heap,
		FArray1A_float	coheap,
		int	val,
		float	coval,
		bool &	err
	)

modifes heap and last_dummy, inserts val, returns err requires heap_max to be previously set via heap_init

Parameters

heap	- [in/out]? - convert to zero offset matrix
coheap	- [in/out]? -
val	- [in/out]? -
coval	- [in/out]? -
err	- [in/out]? -

Global Read:

Global Write:

Remarks

References:

Author

References heap_replace(), heap_up(), and protocols::hybridization::val.

Referenced by protocols::frags::VallData::get_cheating_frags(), protocols::frags::VallData::get_frags(), and protocols::frags::RMSVallData::get_frags().

heap_insert() [2/2]

void protocols::frags::heap_insert	(	ObjexxFCL::FArray1A_int	heap,
		ObjexxFCL::FArray1A_float	coheap,
		int	val,
		float	coval,
		bool &	err
	)

heap_replace() [1/2]

void protocols::frags::heap_replace	(	FArray1A_int	heap,
		FArray1A_float	coheap,
		int	val,
		float	coval
	)

Parameters

heap	- [in/out]? - convert to zero offset matrix
coheap	- [in/out]? -
val	- [in/out]? -
coval	- [in/out]? -

Global Read:

Global Write:

Remarks

References:

Author

References heap_down(), and protocols::hybridization::val.

Referenced by heap_insert().

heap_replace() [2/2]

void protocols::frags::heap_replace	(	ObjexxFCL::FArray1A_int	heap,
		ObjexxFCL::FArray1A_float	coheap,
		int	val,
		float	coval
	)

heap_up() [1/2]

void protocols::frags::heap_up	(	FArray1A_int	heap,
		FArray1A_float	coheap,
		int &	index_in
	)

Parameters

heap	- [in/out]? - convert to zero offset matrix
coheap	- [in/out]? -
index_in	- [in/out]? -

Global Read:

Global Write:

Remarks

References:

Author

Referenced by heap_insert().

heap_up() [2/2]

void protocols::frags::heap_up	(	ObjexxFCL::FArray1A_int	heap,
		ObjexxFCL::FArray1A_float	coheap,
		int &	index_in
	)

insert_fragment()

void protocols::frags::insert_fragment	(	core::Size const	begin,
		core::Size const	end,
		pose::Pose &	pose,
		TorsionFragmentLibrary const &	lib,
		core::Size const	desired_insert_pos
	)

if desired_insert_pos is specified, the fragmnet will be inserted into that position. Otherwise, it will be randonly inserted into a region between "begin" and "end". The fragment insetion is done by changing according backbone torsions in the pose and "refolding" will be handled by the Pose before next time XYZ coordindates are being accessed. PBMOD: allow for cases where not all windows between begin and end have fragments by adding a while loop within which insert_pos is chosen and the frag depth is checked.

References core::sequence::end, core::pose::Pose::size(), protocols::frags::TorsionFragmentLibrary::size(), and TR().

Referenced by insert_random_fragments_in_flexible_protein_regions().

insert_random_fragments_in_flexible_protein_regions() [1/2]

void protocols::frags::insert_random_fragments_in_flexible_protein_regions	(	Sizes const &	flex_protein,
		FragLib const &	frag_lib,
		pose::Pose &	pose
	)

References core::pose::Pose::chain(), protocols::frags::FragLib::frag_sizes(), get_min_and_max_contigs(), has_element(), insert_fragment(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_upper_terminus(), protocols::frags::FragLib::library(), protocols::mean_field::min(), protocols::splice::min_seg(), core::pose::Pose::residue(), core::scoring::rg, core::pose::Pose::size(), protocols::frags::TorsionFragmentLibrary::size(), and TR().

insert_random_fragments_in_flexible_protein_regions() [2/2]

void protocols::frags::insert_random_fragments_in_flexible_protein_regions	(	utility::vector1< core::Size > const &	flex_protein,
		FragLib const &	frag_lib,
		core::pose::Pose &	pose
	)

operator<<() [1/4]

std::ostream & protocols::frags::operator<<	(	std::ostream &	out,
		FragLib const &	lib
	)

References protocols::frags::FragLib::frag_sizes(), protocols::frags::FragLib::library(), and core::conformation::membrane::out.

operator<<() [2/4]

std::ostream & protocols::frags::operator<<	(	std::ostream &	out,
		SingleResidueTorsionFragmentLibrary const &	lib
	)

References core::conformation::membrane::out, and protocols::frags::SingleResidueTorsionFragmentLibrary::size().

operator<<() [3/4]

std::ostream & protocols::frags::operator<<	(	std::ostream &	out,
		TorsionFragment const &	f
	)

References core::chemical::element::F, protocols::frags::TorsionFragment::get_secstruct(), protocols::frags::TorsionFragment::get_sequence(), protocols::frags::TorsionFragment::get_torsion(), protocols::frags::TorsionFragment::nbb(), core::conformation::membrane::out, and protocols::frags::TorsionFragment::size().

operator<<() [4/4]

std::ostream & protocols::frags::operator<<	(	std::ostream &	out,
		TorsionFragmentLibrary const &	lib
	)

References core::conformation::membrane::out, and protocols::frags::TorsionFragmentLibrary::size().

operator>>() [1/4]

std::istream & protocols::frags::operator>>	(	std::istream &	data,
		FragLib &	lib
	)

References protocols::frags::FragLib::clear(), and protocols::frags::FragLib::library().

operator>>() [2/4]

std::istream & protocols::frags::operator>>	(	std::istream &	data,
		SingleResidueTorsionFragmentLibrary &	lib
	)

References protocols::frags::SingleResidueTorsionFragmentLibrary::append_fragment(), and protocols::frags::SingleResidueTorsionFragmentLibrary::clear().

operator>>() [3/4]

std::istream & protocols::frags::operator>>	(	std::istream &	data,
		TorsionFragment &	f
	)

References protocols::cluster::calibur::aa, protocols::frags::TorsionFragment::set_secstruct(), protocols::frags::TorsionFragment::set_sequence(), protocols::frags::TorsionFragment::set_size_and_nbb(), and protocols::frags::TorsionFragment::set_torsion().

operator>>() [4/4]

std::istream & protocols::frags::operator>>	(	std::istream &	data,
		TorsionFragmentLibrary &	lib
	)

References protocols::frags::TorsionFragmentLibrary::clear(), and protocols::frags::TorsionFragmentLibrary::resize().

setup_vall_cheating_fragments()

FragLibOP protocols::frags::setup_vall_cheating_fragments	(	utility::vector1< core::Size > const &	frag_sizes,
		core::Size const	nfrags,
		pose::Pose const &	pose,
		core::kinematics::MoveMap const &	mm,
		std::string const &	secstruct,
		Real const	seq_weight,
		Real const	ss_weight,
		Real const	torsion_weight,
		Real const	min_torsion_dev,
		Real const	max_torsion_dev,
		utility::vector1< core::Size > const &	homs_to_exclude
	)

References add_vall_cheating_fragments().

setup_vall_fragments()

FragLibOP protocols::frags::setup_vall_fragments	(	utility::vector1< core::Size > const &	frag_sizes,
		core::Size const	nfrags,
		pose::Pose const &	pose,
		core::kinematics::MoveMap const &	mm,
		std::string const &	secstruct,
		Real const	seq_weight,
		Real const	ss_weight,
		utility::vector1< core::Size > const &	homs_to_exclude
	)

References add_vall_fragments().

ss_length_check()

bool protocols::frags::ss_length_check	(	core::Size const	min_len_helix,
		core::Size const	min_len_strand,
		core::pose::Pose const &	pose
	)

References core::pose::Pose::secstruct().

Referenced by protocols::frags::TorsionFragmentMover::pose_passes_ss_length_check().

torsion2big_bin()

char protocols::frags::torsion2big_bin ( core::Real const  phi, core::Real const  psi, core::Real const  omega  )

inline

References core::scoring::omega.

Referenced by protocols::frags::VallData::add_line().

torsion_dev_score()

Real protocols::frags::torsion_dev_score	(	Real const	frag_angle,
		Real const	target_angle,
		Real const	min_dev,
		Real const	max_dev
	)

Referenced by protocols::frags::VallData::get_cheating_frags().

TR()

static basic::Tracer protocols::frags::TR ( "protocols.frags.TorsionFragment"  )

static

Referenced by protocols::frags::TorsionFragmentMover::apply(), protocols::frags::TorsionFragmentLibrary::delete_residue(), fill_in_gaps(), protocols::frags::VallData::get_cheating_frags(), protocols::frags::VallData::get_frags(), insert_fragment(), insert_random_fragments_in_flexible_protein_regions(), protocols::frags::FragLib::library(), and protocols::frags::TorsionFragmentLibrary::read_file().

Variable Documentation

empty_size_list

utility::vector1< core::Size > const protocols::frags::empty_size_list