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Public Member Functions | Private Attributes | List of all members
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::Realphi_
 
utility::vector1< core::Realpsi_
 
utility::vector1< core::Realomega_
 
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
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
utility::vector1< core::Real > protocols::frags::RMSVallData::phi_
private
utility::vector1< core::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< core::Real > > protocols::frags::RMSVallData::X_
private

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


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