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Public Member Functions | Private Attributes | List of all members
protocols::frags::RMSVallData Class Reference

#include <RMSVallData.hh>

Collaboration diagram for protocols::frags::RMSVallData:
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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< Realphi_
 
utility::vector1< Realpsi_
 
utility::vector1< Realomega_
 
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
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
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

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