protocols::frags::VallData Class Reference

#include <VallData.hh>

Collaboration diagram for protocols::frags::VallData:

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 Real ph, const Real ps, const 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< Real > const &	phi () const
utility::vector1< Real > const &	psi () const
utility::vector1< Real > const &	omega () const
int	size () const
	number of lines in Vall database More...
void	get_frags (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_cys_peptides, SingleResidueTorsionFragmentLibrary &library) const
	pick fragments in a single window More...

Private Attributes
utility::vector1< char >	sequence_
utility::vector1< char >	secstruct_
utility::vector1< Real >	phi_
utility::vector1< Real >	psi_
utility::vector1< Real >	omega_

Detailed Description

Definition at line 40 of file VallData.hh.

Constructor & Destructor Documentation

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

inline

default constructor

Definition at line 43 of file VallData.hh.

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

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

inline

constructor from input vall database file

Definition at line 54 of file VallData.hh.

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

Member Function Documentation

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

inline

read in one more line from Vall input file

Definition at line 83 of file VallData.hh.

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

void protocols::frags::VallData::get_frags	(	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_cys_peptides,
		SingleResidueTorsionFragmentLibrary &	library
	)		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).

Definition at line 128 of file VallData.cc.

References protocols::frags::heap_extract(), protocols::frags::heap_init(), protocols::frags::heap_insert(), protocols::frags::SingleResidueTorsionFragmentLibrary::insert_fragment(), core::scoring::omega, protocols::swa::phi(), protocols::swa::psi(), core::io::serialization::size(), and TR().

utility::vector1< Real > const& protocols::frags::VallData::omega ( ) const

inline

Definition at line 104 of file VallData.hh.

References omega_.

utility::vector1< Real > const& protocols::frags::VallData::phi ( ) const

inline

Definition at line 102 of file VallData.hh.

References phi_.

utility::vector1< Real > const& protocols::frags::VallData::psi ( ) const

inline

Definition at line 103 of file VallData.hh.

References psi_.

void protocols::frags::VallData::read_file

(

std::string const &

filename)

read from vall database file "filename"

support both old format and new format, i.e., with "trimmed" in filename

Definition at line 53 of file VallData.cc.

References core::scoring::omega, protocols::swa::phi(), and protocols::swa::psi().

Referenced by VallData().

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

inline

Definition at line 100 of file VallData.hh.

References secstruct_.

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

inline

Definition at line 99 of file VallData.hh.

References sequence_.

void protocols::frags::VallData::shrink ( )

inline

removes excess storage capacity to minimize memory usage

Definition at line 68 of file VallData.hh.

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

int protocols::frags::VallData::size ( ) const

inline

number of lines in Vall database

Definition at line 107 of file VallData.hh.

References sequence_.

Member Data Documentation

utility::vector1< Real > protocols::frags::VallData::omega_

private

Definition at line 129 of file VallData.hh.

Referenced by add_line(), omega(), shrink(), and VallData().

utility::vector1< Real > protocols::frags::VallData::phi_

private

Definition at line 127 of file VallData.hh.

Referenced by add_line(), phi(), shrink(), and VallData().

utility::vector1< Real > protocols::frags::VallData::psi_

private

Definition at line 128 of file VallData.hh.

Referenced by add_line(), psi(), shrink(), and VallData().

utility::vector1< char > protocols::frags::VallData::secstruct_

private

Definition at line 125 of file VallData.hh.

Referenced by add_line(), secstruct(), shrink(), and VallData().

utility::vector1< char > protocols::frags::VallData::sequence_

private

Definition at line 124 of file VallData.hh.

Referenced by add_line(), sequence(), shrink(), size(), and VallData().

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

• src/protocols/frags/VallData.hh
• src/protocols/frags/VallData.cc