Atom.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.
//////////////////////////////////////////////////////////////////////
/// @begin Atom.hh
///
/// @brief
/// The conformation class of the atom object
///
/// @detailed
/// This atom class differs from the AtomType/AtomTypeSet class in that it only contains the
/// information about the xyz coordinates, the index of the atom, and the index of the atomtype.
/// This information is generally initialized and set by conformation/Residue.hh.
/// Steven Combs - comments
///
/// @authors
/// Phil Bradley
///
///
///
/// @last_modified December 9 2010
/////////////////////////////////////////////////////////////////////////

#ifndef INCLUDED_core_conformation_Atom_hh
#define INCLUDED_core_conformation_Atom_hh


// Unit headers
#include <core/conformation/Atom.fwd.hh>

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

// Utility headers
#include <numeric/xyzVector.hh>

// C++ headers

namespace core {
namespace conformation {

/// A simple object with atom's position and its chemical type
class Atom {

public:
  /// @brief default constructor and set atom type number to 0 and place the
  /// atom at the origin
  Atom():
    xyz_( 0.0 ),
    type_( 0 ),
    mm_type_( 0 )
  {}

  /// @brief constructor with an atom type number
  // type is set at construction time -- atom is placed at the origin
  Atom( ShortSize const type_in, ShortSize const mm_type_in ):
    xyz_( 0.0 ),
    type_( type_in ),
    mm_type_( mm_type_in )
  {}

  /// @brief constructor with xyz and an atom type number
  // Atom( Vector const & xyz_in, int const type_in, Real temperature = 0.0 ):
  Atom( Vector const & xyz_in, ShortSize const type_in, ShortSize const mm_type_in ):
    xyz_( xyz_in ),
    type_( type_in ),
    mm_type_( mm_type_in )
  {}

  /// @brief destructor
  virtual
  ~Atom() {}

  /// @brief set the atom type number
  void type( ShortSize const type_in )
  {
    type_ = type_in;
  }

  /// @brief Returns the AtomType number
  ShortSize
  type() const
  {
    return type_;
  }

  /// @brief set the mm atom type number
  void mm_type( ShortSize const mm_type_in )
  {
    mm_type_ = mm_type_in;
  }

  /// @brief get the mm atom type number
  ShortSize
  mm_type() const
  {
    return mm_type_;
  }

  /// @brief Returns the atom coordinates as an xyzVector
  Vector const &
  xyz() const
  {
    return xyz_;
  }

  /// @brief Sets the atom coordinates using an xyzVector
  void
  xyz( Vector const & xyz_in )
  {
    xyz_ = xyz_in;
  }

  // /// @brief access temperature Real
  // Real temperature() const {
  //  return temperature_;
  // }
  //
  // /// @brief set temperature Real
  // void
  // temperature( Real temp ) {
  //  temperature_ = temp;
  // }

private:
#ifdef USEBOOSTSERIALIZE
  friend class boost::serialization::access;

  template<class Archive>
  void serialize(Archive & ar, const unsigned int version) {
      ar & xyz_;
      ar & type_;
      ar & mm_type_;
  }
#endif
  // data

  /// position
  Vector xyz_;

  /// rosetta atom_type
  ShortSize type_;

  /// mm_atom_type
  ShortSize mm_type_;

  /// b-factor from pdb file
  // Real temperature_;
};

std::ostream & operator << ( std::ostream & os, Atom const & atom );

} // pose
} // core



#endif // INCLUDED_core_pose_Residues_HH