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protocols::frags::VallData Class Reference

#include <VallData.hh>

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 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< char > const & bigbin () const
 
utility::vector1< core::Real >
const & 
phi () const
 
utility::vector1< core::Real >
const & 
psi () const
 
utility::vector1< core::Real >
const & 
omega () const
 
utility::vector1< core::Size >
const & 
chain () const
 
int size () const
 number of lines in Vall database More...
 
core::Size num_chains () const
 number of chains More...
 
void get_frags (core::Size const nfrags, std::string const &target_seq, std::string const &target_ss, core::Real const seq_weight, core::Real const ss_weight, bool const exclude_gly, bool const exclude_pro, bool const exclude_cis_peptides, utility::vector1< core::Size > const &homs_to_exclude, SingleResidueTorsionFragmentLibrary &library, core::Real const bb_weight=0.0, std::string const &target_bb=std::string()) const
 pick fragments in a single window More...
 
void get_frags (core::Size const nfrags, std::string const &target_seq, utility::vector1< std::map< char, core::Real > > const &target_ss, core::Real const seq_weight, core::Real const ss_weight, bool const exclude_gly, bool const exclude_pro, bool const exclude_cis_peptides, utility::vector1< core::Size > const &homs_to_exclude, SingleResidueTorsionFragmentLibrary &library, core::Real const bb_weight=0.0, std::string const &target_bb=std::string()) const
 
void get_cheating_frags (core::Size const nfrags, std::string const &target_seq, std::string const &target_ss, utility::vector1< core::Real > const &target_phi, utility::vector1< core::Real > const &target_psi, utility::vector1< core::Real > const &target_omega, core::Real const seq_weight, core::Real const ss_weight, core::Real const torsion_weight, core::Real const min_torsion_dev, core::Real const max_torsion_dev, utility::vector1< core::Size > const &homs_to_exclude, SingleResidueTorsionFragmentLibrary &library) const
 

Private Attributes

utility::vector1< char > sequence_
 
utility::vector1< char > secstruct_
 
utility::vector1< char > bigbin_
 
utility::vector1< core::Realphi_
 
utility::vector1< core::Realpsi_
 
utility::vector1< core::Realomega_
 
utility::vector1< core::Sizechain_
 

Constructor & Destructor Documentation

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

default constructor

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

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

constructor from input vall database file

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

Member Function Documentation

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

read in one more line from Vall input file

References bigbin_, chain_, omega_, phi_, psi_, secstruct_, sequence_, and protocols::frags::torsion2big_bin().

Referenced by read_file().

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

References bigbin_.

utility::vector1< core::Size > const& protocols::frags::VallData::chain ( ) const
inline

References chain_.

Referenced by protocols::frags::dump_vall_fasta().

void protocols::frags::VallData::get_cheating_frags ( core::Size const  nfrags,
std::string const &  target_seq,
std::string const &  target_ss,
utility::vector1< core::Real > const &  target_phi,
utility::vector1< core::Real > const &  target_psi,
utility::vector1< core::Real > const &  target_omega,
core::Real const  seq_weight,
core::Real const  ss_weight,
core::Real const  torsion_weight,
core::Real const  min_torsion_dev,
core::Real const  max_torsion_dev,
utility::vector1< core::Size > const &  homs_to_exclude,
SingleResidueTorsionFragmentLibrary library 
) const
void protocols::frags::VallData::get_frags ( core::Size const  nfrags,
std::string const &  target_seq,
std::string const &  target_ss,
core::Real const  seq_weight,
core::Real const  ss_weight,
bool const  exclude_gly,
bool const  exclude_pro,
bool const  exclude_cis_peptides,
utility::vector1< core::Size > const &  homs_to_exclude,
SingleResidueTorsionFragmentLibrary library,
core::Real const  bb_weight = 0.0,
std::string const &  target_bb = std::string() 
) 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). SEE ALSO THE DUPLICATE COPY BELOW WHICH INCLUDES FILTERING BY TARGET TORSION ANGLES IE, IF YOU FIX A BUG HERE FIX IT DOWN THERE AS WELL (THANKS)

References bigbin_, chain_, protocols::frags::heap_extract(), protocols::frags::heap_init(), protocols::frags::heap_insert(), protocols::frags::SingleResidueTorsionFragmentLibrary::insert_fragment(), protocols::mean_field::min(), omega(), omega_, phi(), phi_, psi(), psi_, protocols::hybridization::score, secstruct_, sequence_, size(), and protocols::frags::TR().

Referenced by protocols::frags::get_frags().

void protocols::frags::VallData::get_frags ( core::Size const  nfrags,
std::string const &  target_seq,
utility::vector1< std::map< char, core::Real > > const &  target_ss,
core::Real const  seq_weight,
core::Real const  ss_weight,
bool const  exclude_gly,
bool const  exclude_pro,
bool const  exclude_cis_peptides,
utility::vector1< core::Size > const &  homs_to_exclude,
SingleResidueTorsionFragmentLibrary library,
core::Real const  bb_weight = 0.0,
std::string const &  target_bb = std::string() 
) const
core::Size protocols::frags::VallData::num_chains ( ) const
inline

number of chains

References chain_.

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

References omega_.

Referenced by get_cheating_frags(), get_frags(), and read_file().

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

References phi_.

Referenced by get_cheating_frags(), get_frags(), and read_file().

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

References psi_.

Referenced by get_cheating_frags(), get_frags(), and read_file().

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

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_.

Referenced by protocols::frags::dump_vall_fasta().

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

removes excess storage capacity to minimize memory usage

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

Referenced by read_file().

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

number of lines in Vall database

References sequence_.

Referenced by get_cheating_frags(), and get_frags().

Member Data Documentation

utility::vector1< char > protocols::frags::VallData::bigbin_
private
utility::vector1< core::Size > protocols::frags::VallData::chain_
private
utility::vector1< core::Real > protocols::frags::VallData::omega_
private
utility::vector1< core::Real > protocols::frags::VallData::phi_
private
utility::vector1< core::Real > protocols::frags::VallData::psi_
private
utility::vector1< char > protocols::frags::VallData::secstruct_
private
utility::vector1< char > protocols::frags::VallData::sequence_
private

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