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

#include <VallData.hh>

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Public Member Functions

 VallData ()
 default constructor More...
 
 VallData (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)
 read from vall database file "filename" More...
 
void add_line (const char sq, const char ss, 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< 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, std::string const &target_seq, std::string const &target_ss, Real const seq_weight, Real const ss_weight, bool const exclude_gly, bool const exclude_pro, bool const exclude_cys_peptides, SingleResidueTorsionFragmentLibrary &library) const
 pick fragments in a single window More...
 

Private Attributes

utility::vector1< char > sequence_
 
utility::vector1< char > secstruct_
 
utility::vector1< Realphi_
 
utility::vector1< Realpsi_
 
utility::vector1< Realomega_
 

Constructor & Destructor Documentation

protocols::frags::VallData::VallData ( )
inline

default constructor

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

protocols::frags::VallData::VallData ( std::string const &  filename)
inline

constructor from input vall database file

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

Member Function Documentation

void protocols::frags::VallData::add_line ( const char  sq,
const char  ss,
const Real  ph,
const Real  ps,
const Real  om 
)
inline

read in one more line from Vall input file

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

void protocols::frags::VallData::get_frags ( Size const  nfrags,
std::string const &  target_seq,
std::string const &  target_ss,
Real const  seq_weight,
Real const  ss_weight,
bool const  exclude_gly,
bool const  exclude_pro,
bool const  exclude_cys_peptides,
SingleResidueTorsionFragmentLibrary library 
) const

pick fragments in a single window

  • nfrags – number of fragment pieces to be picked
  • target_seq – query sequence and this also defines fragment length, such as 3mer or 9mer
  • target_ss – secondary structure of query sequence.
  • seq_weight and ss_weight – weight for sequence match and secstruct match
  • exclude_* – exclude such squence pattern when picking fragments
  • library – output as a collection of fragments for that residue window

scan through vall database, for each position within each window, if sequence does not match target sequence, penalize by seq_weight; if secstruct does not match target secstruct, penalize by ss_weight. In the end, picking top "nfrags" fragments with lowest penalty score (this internally uses a "heap" implementation).

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

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

References omega_.

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

References phi_.

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

References psi_.

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

read from vall database file "filename"

support both old format and new format, i.e., with "trimmed" in filename

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

Referenced by VallData().

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

References secstruct_.

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

References sequence_.

void protocols::frags::VallData::shrink ( )
inline

removes excess storage capacity to minimize memory usage

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

int protocols::frags::VallData::size ( ) const
inline

number of lines in Vall database

References sequence_.

Member Data Documentation

utility::vector1< Real > protocols::frags::VallData::omega_
private

Referenced by add_line(), omega(), shrink(), and VallData().

utility::vector1< Real > protocols::frags::VallData::phi_
private

Referenced by add_line(), phi(), shrink(), and VallData().

utility::vector1< Real > protocols::frags::VallData::psi_
private

Referenced by add_line(), psi(), shrink(), and VallData().

utility::vector1< char > protocols::frags::VallData::secstruct_
private

Referenced by add_line(), secstruct(), shrink(), and VallData().

utility::vector1< char > protocols::frags::VallData::sequence_
private

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