ElementSet.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
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/// @file core/chemical/ElementSet.hh
/// @author P. Douglas Renfrew (renfrew@unc.edu)


#ifndef INCLUDED_core_chemical_ElementSet_hh
#define INCLUDED_core_chemical_ElementSet_hh


// Unit headers
#include <core/chemical/ElementSet.fwd.hh>
// AUTO-REMOVED #include <core/chemical/Element.hh>

// Project headers

// Utility headers
// AUTO-REMOVED #include <utility/vector1.hh>
#include <utility/exit.hh>
#include <utility/pointer/ReferenceCount.hh>

// C++ headers
// Commented by inclean daemon #include <string>
#include <map>

#include <utility/vector1_bool.hh>

#include <core/types.hh>
#include <core/chemical/Element.fwd.hh>




namespace core {
namespace chemical {


/// @brief A set of Elements
///
/// @details This class contains a vector of pointers each of which points to an
/// Element and the vector index is looked up by an element_name string
/// in a map.
///
class ElementSet : public utility::pointer::ReferenceCount {

public:
  ElementSet();
  virtual ~ElementSet();

  /// @brief Number of elements in the set
  Size
  n_elements() const
  {
    return elements_.size();
  }


  /// @brief Check if there is an element_type associated with an element_symbol string
  bool
  contains_element_type( std::string const & element_symbol ) const
  {
    std::map< std::string, int >::const_iterator
      iter( element_index_.find( element_symbol ) );
    return iter != element_index_.end();
  }


  /// @brief Lookup the element index by the element_symbol string
  int
  element_index( std::string const & element_symbol ) const
  {
    std::map< std::string, int >::const_iterator
      iter( element_index_.find( element_symbol ) );
    if ( iter == element_index_.end() ) {
      utility_exit_with_message("unrecognized element_symbol "+element_symbol);
    }
    return iter->second;
  }


  /// @brief Lookup an Element by 1-based indexing
  Element const &
  operator[] ( Size const index ) const
  {
    return *( elements_[ index ] );
  }


  /// @brief Load the ElementSet from a file
  void
  read_file( std::string const & filename );

  /// @brief Print all of the symbols of all of the Elements in the set. Usefull for debuging.
  void
  print_all_types();


  // data
private:

  /// @brief element_index_ lookup map
  ///
  /// @details element_index_ allows lookup of the element by its symbol
  std::map< std::string, int > element_index_;

  /// @brief a collection of Elements,
  ///
  /// @details Element has data of atom properties, and it can be
  /// looked up by element_index.
  utility::vector1< Element* > elements_;

};

} // chemical
} // core

#endif // INCLUDED_core_chemical_ElementSet_HH