VallData.hh

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// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
// (c) This file is part of the Rosetta software suite and is made available under license.
// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
// (c) For more information, see http://www.rosettacommons.org. Questions about this can be
// (c) addressed to University of Washington UW TechTransfer, email: license@u.washington.edu.

#ifndef INCLUDED_protocols_frags_VallData_hh
#define INCLUDED_protocols_frags_VallData_hh


// Rosetta Headers

#include <core/types.hh>
#include <protocols/frags/VallData.fwd.hh>
#include <protocols/frags/TorsionFragment.fwd.hh>

// ObjexxFCL Headers
// AUTO-REMOVED #include <utility/vector1.hh>

// C++ Headers
// #include <cmath>
// #include <cstdlib>
// #include <iostream>
// #include <fstream>
// #include <sstream>
#include <string>

#include <utility/vector1_bool.hh>


namespace protocols {
namespace frags {

using core::Real;
using core::Size;

class VallData {
public:
  /// default constructor
  VallData ()
  {
    Size const big_size( 100000 ); // rough guess
    sequence_.reserve( big_size );
    secstruct_.reserve( big_size );
    phi_.reserve( big_size );
    psi_.reserve( big_size );
    omega_.reserve( big_size );
  }

  /// constructor from input vall database file
  VallData ( std::string const & filename )
  {
    Size const big_size( 100000 ); // rough guess
    // prevent lots of redimensioning as we read file? does this even matter?
    sequence_.reserve( big_size );
    secstruct_.reserve( big_size );
    phi_.reserve( big_size );
    psi_.reserve( big_size );
    omega_.reserve( big_size );
    read_file( filename );
  }

  /// removes excess storage capacity to minimize memory usage
  void
  shrink()
  {
    sequence_.shrink();
    secstruct_.shrink();
    phi_.shrink();
    psi_.shrink();
    omega_.shrink();
  }

  // read from vall database file "filename"
  void
  read_file( std::string const & filename );

  /// read in one more line from Vall input file
  void
  add_line(
    const char sq,
    const char ss,
    const Real ph,
    const Real ps,
    const Real om
  )
  {
    sequence_.push_back( sq );
    secstruct_.push_back( ss );

    phi_.push_back( ph );
    psi_.push_back( ps );
    omega_.push_back( om );
  }

  utility::vector1< char > const & sequence () const {return sequence_; }
  utility::vector1< char > const & secstruct() const {return secstruct_;}

  utility::vector1< Real > const & phi  () const {return phi_;}
  utility::vector1< Real > const & psi  () const {return psi_;}
  utility::vector1< Real > const & omega() const {return omega_;}

  /// number of lines in Vall database
  int size() const { return sequence_.size(); }

  // pick fragments for a single residue position from vall database
  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;

private:
  utility::vector1< char > sequence_;
  utility::vector1< char > secstruct_;

  utility::vector1< Real > phi_;
  utility::vector1< Real > psi_;
  utility::vector1< Real > omega_;

};

} // ns frags
} // ns protocols

#endif