protocols::frags::RMSVallData Class Reference

#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

Constructor & Destructor Documentation

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

inline

default constructor

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

inline

constructor from input vall database file

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

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

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

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

inline

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

inline

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

inline

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

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

inline

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

inline

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

inline

removes excess storage capacity to minimize memory usage

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

inline

number of lines in Vall database

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

inline

Member Data Documentation

bool protocols::frags::RMSVallData::exclude_cys_peptides

private

bool protocols::frags::RMSVallData::exclude_gly

private

bool protocols::frags::RMSVallData::exclude_pro

private

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

private

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

private

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

private

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

private

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

private

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

private

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

• src/protocols/frags/RMSVallData.hh