VallResidue.cc

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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.

/// @file   core/fragment/picking_old/vall/VallResidue.cc
/// @brief  class for managing a line of the Vall fragment library
/// @author Yih-En Andrew Ban (yab@u.washington.edu)

// unit headers
#include <core/fragment/picking_old/vall/VallResidue.hh>

// project headers
#include <core/chemical/AA.hh>
#include <core/fragment/BBTorsionSRFD.hh>

// boost headers
#include <boost/type_traits.hpp>

// utility headers
#include <utility/pointer/owning_ptr.hh>

// C++ headers
// AUTO-REMOVED
#include <cstdio>
#include <iostream>
// AUTO-REMOVED #include <sstream>

#include <utility/vector1.hh>




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


// static initialization
utility::vector1< core::chemical::AA > VallResidue::order_ = order_vector();
VallResidue::String VallResidue::format_ = format_string();


/// @brief default constructor
VallResidue::VallResidue() :
  aa_( 0 ),
  ss_( 0 ),
  resi_( 0 ),
  x_( 0.0 ),
  y_( 0.0 ),
  z_( 0.0 ),
  phi_( 0.0 ),
  psi_( 0.0 ),
  omega_( 0.0 ),
  profile_( 20 ),
  position_index_( 0 ),
  section_index_( 0 )
{}


/// @brief string constructor
VallResidue::VallResidue( String const & line ) {
  fill_from_string( line );
}


/// @brief copy constructor
VallResidue::VallResidue( VallResidue const & rval ) :
  id_( rval.id_ ),
  aa_( rval.aa_ ),
  ss_( rval.ss_ ),
  resi_( rval.resi_ ),
  x_( rval.x_ ),
  y_( rval.y_ ),
  z_( rval.z_ ),
  phi_( rval.phi_ ),
  psi_( rval.psi_ ),
  omega_( rval.omega_ ),
  profile_( rval.profile_ ),
  position_index_( rval.position_index_ ),
  section_index_( rval.section_index_ )
{}


/// @brief default destructor
VallResidue::~VallResidue() {}


/// @brief copy assignment
VallResidue & VallResidue::operator =( VallResidue const & rval ) {
  if ( this != &rval ) {
    id_ = rval.id_;
    aa_ = rval.aa_;
    ss_ = rval.ss_;
    resi_ = rval.resi_;
    x_ = rval.x_;
    y_ = rval.y_;
    z_ = rval.z_;
    phi_ = rval.phi_;
    psi_ = rval.psi_;
    omega_ = rval.omega_;
    profile_ = rval.profile_;
    position_index_ = rval.position_index_;
    section_index_ = rval.section_index_;
  }
  return *this;
}


/// @brief build a BBTorsionSRFD of the given type from this page
/// @param[in] srfd_type BBTorsionSRFD::create() will be called from this object.
/// @return A BBTorsionSRFD of the given type initialized with the backbone
///  torsion information from this page.
VallResidue::BBTorsionSRFDOP VallResidue::bbtorsion_srfd( BBTorsionSRFD const & srfd_type ) const {
  BBTorsionSRFDOP srfd = static_cast< BBTorsionSRFD * >( srfd_type.create().get() );

  srfd->set_sequence( aa_ );
  srfd->set_secstruct( ss_ );

  // currently, phi = 1, psi = 2, omega = 3
  // see BBTorsionSRFD and Pose implemenations for details
  srfd->set_torsion( 1, phi_ );
  srfd->set_torsion( 2, psi_ );
  srfd->set_torsion( 3, omega_ );

  return srfd;
}


/// @brief fill internal data from string
/// @details Values are delimited by whitespace.  Ordering is:
///  <tt> id  aa  ss  resi  dummy  dummy  x  y  z  phi  psi  omega  dummy  dummy  dummy  dummy  (aa profile_info, 20 columns) </tt>
void VallResidue::fill_from_string( String const & line ) {

  char id[] = { '\0', '\0', '\0', '\0', '\0', '\0' }; // 5 char + 1 null termination

  // Use sscanf here; Vall is huge and istringstream is way too slow.
  // *One* sscanf call per line, multiple calls decreases performance!
  std::sscanf(
    line.c_str(),
    format_.c_str(),
    &id, &aa_, &ss_, &resi_,
    &x_, &y_, &z_,
    &phi_, &psi_, &omega_,
    &profile_[ order_[ 1 ] ],
    &profile_[ order_[ 2 ] ],
    &profile_[ order_[ 3 ] ],
    &profile_[ order_[ 4 ] ],
    &profile_[ order_[ 5 ] ],
    &profile_[ order_[ 6 ] ],
    &profile_[ order_[ 7 ] ],
    &profile_[ order_[ 8 ] ],
    &profile_[ order_[ 9 ] ],
    &profile_[ order_[ 10 ] ],
    &profile_[ order_[ 11 ] ],
    &profile_[ order_[ 12 ] ],
    &profile_[ order_[ 13 ] ],
    &profile_[ order_[ 14 ] ],
    &profile_[ order_[ 15 ] ],
    &profile_[ order_[ 16 ] ],
    &profile_[ order_[ 17 ] ],
    &profile_[ order_[ 18 ] ],
    &profile_[ order_[ 19 ] ],
    &profile_[ order_[ 20 ] ]
  );

  id_ = id;

}


/// @brief return a vector specifying the order of profile data in Vall
utility::vector1< core::chemical::AA > VallResidue::order_vector() {
  utility::vector1< core::chemical::AA > order( 20 );

  order[ 1] = core::chemical::aa_from_oneletter_code( 'A' );
  order[ 2] = core::chemical::aa_from_oneletter_code( 'C' );
  order[ 3] = core::chemical::aa_from_oneletter_code( 'D' );
  order[ 4] = core::chemical::aa_from_oneletter_code( 'E' );
  order[ 5] = core::chemical::aa_from_oneletter_code( 'F' );
  order[ 6] = core::chemical::aa_from_oneletter_code( 'G' );
  order[ 7] = core::chemical::aa_from_oneletter_code( 'H' );
  order[ 8] = core::chemical::aa_from_oneletter_code( 'I' );
  order[ 9] = core::chemical::aa_from_oneletter_code( 'K' );
  order[10] = core::chemical::aa_from_oneletter_code( 'L' );
  order[11] = core::chemical::aa_from_oneletter_code( 'M' );
  order[12] = core::chemical::aa_from_oneletter_code( 'N' );
  order[13] = core::chemical::aa_from_oneletter_code( 'P' );
  order[14] = core::chemical::aa_from_oneletter_code( 'Q' );
  order[15] = core::chemical::aa_from_oneletter_code( 'R' );
  order[16] = core::chemical::aa_from_oneletter_code( 'S' );
  order[17] = core::chemical::aa_from_oneletter_code( 'T' );
  order[18] = core::chemical::aa_from_oneletter_code( 'V' );
  order[19] = core::chemical::aa_from_oneletter_code( 'W' );
  order[20] = core::chemical::aa_from_oneletter_code( 'Y' );

  return order;
}


/// @brief return a formatting string for fill_from_string() dependent
///  upon actual type of core::Real and core::Size
/// @remarks This is necessary for sscanf; wrong type can give wrong
///  input.
VallResidue::String VallResidue::format_string() {
  using boost::is_same;

  // resolve types
  bool const is_ulong = is_same< Size, unsigned long >::value;
  bool const is_double = is_same< Real, double >::value;

  // format w/ the following order:
  std::ostringstream s;
  s << "%s" << " "; // (string) id
  s << "%c" << " "; // (char)   aa
  s << "%c" << " "; // (char)   ss
  s << ( is_ulong ? "%lu" : "%u" ) << " "; // (int)    resi
  s << "%*s" << " "; // (string) dummy
  s << "%*s" << " ";// (string) dummy
  s << ( is_double ? "%lf" : "%f" ) << " "; // (real)   x
  s << ( is_double ? "%lf" : "%f" ) << " "; // (real)   y
  s << ( is_double ? "%lf" : "%f" ) << " "; // (real)   z
  s << ( is_double ? "%lf" : "%f" ) << " "; // (real)   phi
  s << ( is_double ? "%lf" : "%f" ) << " "; // (real)   psi
  s << ( is_double ? "%lf" : "%f" ) << " "; // (real)   omega
  s << "%*s" << " "; // (string) dummy
  s << "%*s" << " "; // (string) dummy
  s << "%*s" << " "; // (string) dummy
  s << "%*s"; // (string) dummy

  // (real)   (aa profile_info, 20 columns)
  for ( Size i = 0; i < 20; ++i ) {
    s << " " << ( is_double ? "%lf" : "%f" );
  }

  return s.str();
}


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