#include <RMSVallData.hh>

Collaboration diagram for protocols::frags::RMSVallData:

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

	RMSVallData (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)

void	add_line (const char sq, const char ss, const Real x, const Real y, const Real z, 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 < numeric::xyzVector< Real > > const &	X () 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, utility::vector1< numeric::xyzVector< core::Real > > const &templ, std::string const &pref_seq, char const force_ss, core::fragment::FrameOP &frame, core::Real randomness=0.0, core::Real oversample=5.0) const

Private Attributes
utility::vector1< char >	sequence_

utility::vector1< char >	secstruct_

utility::vector1 < numeric::xyzVector< Real > >	X_

utility::vector1< Real >	phi_

utility::vector1< Real >	psi_

utility::vector1< Real >	omega_

bool	exclude_gly

bool	exclude_pro

bool	exclude_cys_peptides

Detailed Description

Definition at line 48 of file RMSVallData.hh.

Constructor & Destructor Documentation

protocols::frags::RMSVallData::RMSVallData ( )

inline

default constructor

Definition at line 51 of file RMSVallData.hh.

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

inline

constructor from input vall database file

Definition at line 65 of file RMSVallData.hh.

Member Function Documentation

void protocols::frags::RMSVallData::add_line	(	const char	sq,
		const char	ss,
		const Real	x,
		const Real	y,
		const Real	z,
		const Real	ph,
		const Real	ps,
		const Real	om
	)

inline

read in one more line from Vall input file

Definition at line 139 of file RMSVallData.hh.

void protocols::frags::RMSVallData::get_frags	(	Size const	nfrags,
		utility::vector1< numeric::xyzVector< core::Real > > const &	templ,
		std::string const &	pref_seq,
		char const	force_ss,
		core::fragment::FrameOP &	frame,
		core::Real	randomness = `0.0`,
		core::Real	oversample = `5.0`
	)		const

inline

Definition at line 166 of file RMSVallData.hh.

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

Referenced by protocols::rbsegment_relax::FragInsertAndAlignMover::initialize_rb_fragments().

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

inline

Definition at line 159 of file RMSVallData.hh.

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

inline

Definition at line 157 of file RMSVallData.hh.

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

inline

Definition at line 158 of file RMSVallData.hh.

void protocols::frags::RMSVallData::read_file ( std::string const & filename)

inline

Definition at line 94 of file RMSVallData.hh.

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

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

inline

Definition at line 153 of file RMSVallData.hh.

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

inline

Definition at line 152 of file RMSVallData.hh.

void protocols::frags::RMSVallData::shrink ( )

inline

removes excess storage capacity to minimize memory usage

Definition at line 83 of file RMSVallData.hh.

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

inline

number of lines in Vall database

Definition at line 162 of file RMSVallData.hh.

utility::vector1< numeric::xyzVector< Real > > const& protocols::frags::RMSVallData::X ( ) const

inline

Definition at line 155 of file RMSVallData.hh.

Member Data Documentation

bool protocols::frags::RMSVallData::exclude_cys_peptides

private

Definition at line 349 of file RMSVallData.hh.

bool protocols::frags::RMSVallData::exclude_gly

private

Definition at line 347 of file RMSVallData.hh.

bool protocols::frags::RMSVallData::exclude_pro

private

Definition at line 348 of file RMSVallData.hh.

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

private

Definition at line 345 of file RMSVallData.hh.

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

private

Definition at line 343 of file RMSVallData.hh.

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

private

Definition at line 344 of file RMSVallData.hh.

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

private

Definition at line 340 of file RMSVallData.hh.

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

private

Definition at line 339 of file RMSVallData.hh.

utility::vector1< numeric::xyzVector< Real > > protocols::frags::RMSVallData::X_

private

Definition at line 342 of file RMSVallData.hh.

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

src/protocols/frags/RMSVallData.hh

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation