#include <VallData.hh>

Public Member Functions
	VallData ()
	default constructor More...

	VallData (std::string const &filename)
	constructor from input vall database file More...

void	shrink ()
	removes excess storage capacity to minimize memory usage More...

void	read_file (std::string const &filename)
	read from vall database file "filename" More...

void	add_line (const char sq, const char ss, const core::Real ph, const core::Real ps, const core::Real om)
	read in one more line from Vall input file More...

utility::vector1< char > const &	sequence () const

utility::vector1< char > const &	secstruct () const

utility::vector1< char > const &	bigbin () const

utility::vector1< core::Real > const &	phi () const

utility::vector1< core::Real > const &	psi () const

utility::vector1< core::Real > const &	omega () const

utility::vector1< core::Size > const &	chain () const

int	size () const
	number of lines in Vall database More...

core::Size	num_chains () const
	number of chains More...

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()) const
	pick fragments in a single window 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()) const

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) const

Private Attributes
utility::vector1< char >	sequence_

utility::vector1< char >	secstruct_

utility::vector1< char >	bigbin_

utility::vector1< core::Real >	phi_

utility::vector1< core::Real >	psi_

utility::vector1< core::Real >	omega_

utility::vector1< core::Size >	chain_

Constructor & Destructor Documentation

protocols::frags::VallData::VallData ( )

inline

default constructor

References bigbin_, omega_, phi_, psi_, secstruct_, and sequence_.

protocols::frags::VallData::VallData ( std::string const & filename )

inline

constructor from input vall database file

References bigbin_, omega_, phi_, psi_, read_file(), secstruct_, and sequence_.

Member Function Documentation

void protocols::frags::VallData::add_line	(	const char	sq,
		const char	ss,
		const core::Real	ph,
		const core::Real	ps,
		const core::Real	om
	)

inline

read in one more line from Vall input file

References bigbin_, chain_, omega_, phi_, psi_, secstruct_, sequence_, and protocols::frags::torsion2big_bin().

Referenced by read_file().

utility::vector1< char > const& protocols::frags::VallData::bigbin ( ) const

inline

References bigbin_.

utility::vector1< core::Size > const& protocols::frags::VallData::chain ( ) const

inline

References chain_.

Referenced by protocols::frags::dump_vall_fasta().

void protocols::frags::VallData::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
	)		const

References chain_, protocols::frags::heap_extract(), protocols::frags::heap_init(), protocols::frags::heap_insert(), protocols::frags::SingleResidueTorsionFragmentLibrary::insert_fragment(), protocols::mean_field::min(), omega(), omega_, phi(), phi_, psi(), psi_, protocols::hybridization::score, secstruct_, sequence_, size(), protocols::frags::torsion_dev_score(), and protocols::frags::TR().

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

void protocols::frags::VallData::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()`
	)		const

pick fragments in a single window

nfrags – number of fragment pieces to be picked
target_seq – query sequence and this also defines fragment length, such as 3mer or 9mer
target_ss – secondary structure of query sequence.
seq_weight and ss_weight – weight for sequence match and secstruct match
exclude_* – exclude such squence pattern when picking fragments
library – output as a collection of fragments for that residue window

scan through vall database, for each position within each window, if sequence does not match target sequence, penalize by seq_weight; if secstruct does not match target secstruct, penalize by ss_weight. In the end, picking top "nfrags" fragments with lowest penalty score (this internally uses a "heap" implementation). SEE ALSO THE DUPLICATE COPY BELOW WHICH INCLUDES FILTERING BY TARGET TORSION ANGLES IE, IF YOU FIX A BUG HERE FIX IT DOWN THERE AS WELL (THANKS)

References bigbin_, chain_, protocols::frags::heap_extract(), protocols::frags::heap_init(), protocols::frags::heap_insert(), protocols::frags::SingleResidueTorsionFragmentLibrary::insert_fragment(), protocols::mean_field::min(), omega(), omega_, phi(), phi_, psi(), psi_, protocols::hybridization::score, secstruct_, sequence_, size(), and protocols::frags::TR().

Referenced by protocols::frags::get_frags().

void protocols::frags::VallData::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()`
	)		const