protocols::frags::RMSVallData Class Reference

#include <RMSVallData.hh>

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 core::Real x, const core::Real y, const core::Real z, 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 < numeric::xyzVector < core::Real > > const &	X () const
utility::vector1< core::Real > const &	phi () const
utility::vector1< core::Real > const &	psi () const
utility::vector1< core::Real > const &	omega () const
int	size () const
	number of lines in Vall database More...
void	get_frags (core::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 < core::Real > >	X_
utility::vector1< core::Real >	phi_
utility::vector1< core::Real >	psi_
utility::vector1< core::Real >	omega_
bool	exclude_gly
bool	exclude_pro
bool	exclude_cys_peptides

Constructor & Destructor Documentation

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

inline

default constructor

References exclude_cys_peptides, exclude_gly, exclude_pro, omega_, phi_, psi_, secstruct_, and sequence_.

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

inline

constructor from input vall database file

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

Member Function Documentation

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

inline

read in one more line from Vall input file

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

Referenced by read_file().

void protocols::frags::RMSVallData::get_frags ( core::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 exclude_cys_peptides, exclude_gly, exclude_pro, protocols::frags::heap_extract(), protocols::frags::heap_init(), protocols::frags::heap_insert(), omega(), omega_, phi(), phi_, psi(), psi_, protocols::hybridization::score, secstruct_, sequence_, size(), and X_.

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

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

inline

References omega_.

Referenced by get_frags(), and read_file().

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

inline

References phi_.

Referenced by get_frags(), and read_file().

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

inline

References psi_.

Referenced by get_frags(), and read_file().

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

inline

References add_line(), omega(), phi(), psi(), and shrink().

Referenced by RMSVallData().

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

inline

References secstruct_.

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

inline

References sequence_.

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

inline

removes excess storage capacity to minimize memory usage

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

Referenced by read_file().

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

inline

number of lines in Vall database

References sequence_.

Referenced by get_frags().

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

inline

References X_.

Member Data Documentation

bool protocols::frags::RMSVallData::exclude_cys_peptides

private

Referenced by get_frags(), and RMSVallData().

bool protocols::frags::RMSVallData::exclude_gly

private

Referenced by get_frags(), and RMSVallData().

bool protocols::frags::RMSVallData::exclude_pro

private

Referenced by get_frags(), and RMSVallData().

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

private

Referenced by add_line(), get_frags(), omega(), RMSVallData(), and shrink().

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

private

Referenced by add_line(), get_frags(), phi(), RMSVallData(), and shrink().

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

private

Referenced by add_line(), get_frags(), psi(), RMSVallData(), and shrink().

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

private

Referenced by add_line(), get_frags(), RMSVallData(), secstruct(), and shrink().

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

private

Referenced by add_line(), get_frags(), RMSVallData(), sequence(), shrink(), and size().

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

private

Referenced by add_line(), get_frags(), and X().

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

• src/protocols/frags/RMSVallData.hh