vall_io.cc

Go to the documentation of this file.

// -*- 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.

/// @file   core/fragment/picking_old/vall/vall_io.hh
/// @brief  reading/writing of Vall libraries
/// @author Yih-En Andrew Ban (yab@u.washington.edu)

// AUTO-REMOVED #include <time.h>
// unit headers
#include <core/fragment/picking_old/vall/vall_io.hh>

// type headers
#include <core/types.hh>

// package headers
#include <core/fragment/picking_old/vall/VallLibrary.hh>

// project headers
#include <basic/Tracer.hh>

// utility headers
#include <utility/exit.hh>
#include <utility/io/izstream.hh>

// C++ headers
#include <sstream>
#include <string>

#include <utility/vector1.hh>


#ifdef WIN32
  #include <ctime>
#endif

namespace core {
namespace fragment {
namespace picking_old {
namespace vall {


// Tracer instance for this file
// Named after the original location of this code
static basic::Tracer TR( "core.fragment.picking_old.vall.vall_io" );


/// @brief load standard Vall library from file
/// @param[in] filename
/// @param[out] vall
/// @remarks Currently a difference in id (pdb name) or resi (residue sequence id)
///  will start a new stretch of lines defining a VallSection
void vall_library_from_file( std::string const & filename, VallLibrary & library, core::Size const preallocate ) {
  using core::Size;

  utility::io::izstream stream( filename );
  if ( !stream ) {
    utility_exit_with_message( "can't open file: " + filename );
  }

  // statistics
  Size n_lines = 0;
  Size prior_library_size = library.size();
  Size prior_n_residues = library.n_residues();

  TR << "Reading Vall library from " << filename << " ... " << std::endl;

  time_t time_start = time( NULL );

  std::string prior_id;
  Size prior_resi;
  VallResidue current_residue;
  VallSection section;

  // try to reduce number of allocation events if requested
  if ( preallocate > 0 ) {
    library.reserve( preallocate );
  }

  // parse Vall from file
  std::string line;
  while ( getline( stream, line ) ) {
    ++n_lines;
    prior_id = current_residue.id();
    prior_resi = current_residue.resi();

    current_residue.fill_from_string( line );

    // check for start of new continuous stretch
    if ( ( current_residue.resi() != prior_resi + 1 ) || ( current_residue.id() != prior_id ) ) {
      if ( section.size() > 0 ) {
        library.add_section( section );
      }
      section.clear(); // new section
    }

    section.append_residue( current_residue );

    if ( n_lines % 100000 == 0 ) {
      TR << "   " << n_lines << std::endl;
    }
  }

  if ( section.size() > 0 ) { // handle final set of entries
    library.add_section( section );
  }

  // free unused allocated memory
  if ( library.size() <= ( preallocate / 2 ) ) { // heuristic
    library.tighten_memory( false ); // entire library
  } else {
    library.tighten_memory(); // books only
  }

  time_t time_end = time( NULL );

  TR << "... done.  Read " << n_lines << " lines.  Time elapsed: " << ( time_end - time_start ) << " seconds." << std::endl;
  TR << "Prior library contained " << prior_library_size << " sections totaling " << prior_n_residues << " residues." << std::endl;
  TR << "Added " << library.size() << " sections to library totaling " << library.n_residues() << " residues." << std::endl;
}


} // vall
} // picking_old
} // fragment
} // core