OrbitalType.hh

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//
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//////////////////////////////////////////////////////////////////////
/// @begin OrbitalType.cc
///
/// @brief
/// A class that contains orbital parameters
///
/// @details
/// This class contains the "chemical" information for orbitals. This does not contain the actual
/// xyz coordinates of the class which is managed by the conformation/Residue.hh. The orbital_type properties
/// are assigned by the class OrbitalTypeSet which is initiated from the ChemicalManager. Orbital type properties
/// are currently are read in from the file located chemical/orbital_type_sets/fa_standard/orbital_properties.txt.
/// These properties contain the the parameters of distance, but can be modified. Currently this is a very small
/// class that will be added on as more and more properties are identified and added.
/// Note that information about the atomtype is stored along with the orbital type. This may or may not be useful
/// later. Just adding the functionality for shits and giggles.
///
/// Orbital type name: the orbital type name contains the hybridization, orbital name, and element associated with the orbital
///
/// Hybridization: the hybridiztion of the atom that the orbital is bonded to (sp, sp2, sp3)
///
/// Orbital Name: the name of the orbital. This usually is p, d, pi, sigma. The orbital name is different than the orbital type name
///
/// Atom Type Name: the type of atom associated with an orbital
///
/// Distance: distance the orbital comes off of the atom. Currently, for residues, the distance is the Bohr radius of Hydrogen+element
///
///
///
///
///
/// @author Steven Combs
///
///
/// @last_modified December 15 2010
/////////////////////////////////////////////////////////////////////////
#ifndef INCLUDED_core_chemical_orbitals_OrbitalType_hh
#define INCLUDED_core_chemical_orbitals_OrbitalType_hh

#include <utility/vector1.hh>
#include <core/types.hh>
#include <string>
#include <core/chemical/orbitals/OrbitalTypeMapper.fwd.hh>

namespace core{
namespace chemical{
namespace orbitals{

class OrbitalType {
public:


  OrbitalType(std::string & orbital_name, std::string & atom_type_name);

  ///@brief The parameters are the actual headings in the orbital_properties.txt. If you want to add more paramters,
  /// you must edit orbital_properties.txt and add another heading. You also need to edit AtomTypeSet.txt so that
  /// it recognizes that parameter and parses it. The parameters are different form the properties in that they
  /// are Reals/Size and properties are strings.
  void
  set_parameter(
    std::string const & param,
    core::Real const setting
  );

  ///@brief Currently, these properties are not actually in the orbital_properties.txt. I have them here
  /// as an example on how to add properties. This is also a place holder as the ligand code will
  /// soon be using these properties. The Acceptor/Donor could refer to orbitals that have a lone pair
  /// and are donating to a hydrogen, or an electron defficient region. In order to add properties, one
  /// must add the properties to the last line of orbital_properties.txt and make a private member variable
  /// for that property in the header file. Then do a string match comparision, like seen below. These properties
  /// are set via OrbitalTypeSet.hh
  void
  set_property(
    std::string const & property,
    bool const setting
  );

  ///@brief returns the name of the orbital type. defined in orbital_properties.txt
  std::string name() const;

  ///@brief returns the distance from the atom the orbital comes off. defined in orbital_properties.txt
  Real distance() const;

  ///@brief returns the atom_types associated with the orbital type. defined in orbital_properties.txt
  utility::vector1<std::string> atom_type_name() const;

  ///@brief returns hybrdiziation of atom the orbital is attached to
  std::string hybridization() const;

  ///@brief returns the orbital associated with the type
  std::string orbital_name() const;

  orbital_type_enum orbital_enum() const;


private:
  ///@brief is the orbital an acceptor?
  bool is_orbital_acceptor_;

  ///@brief is the orbital a donor?
  bool is_orbital_donor_;

  ///@brief the orbital type name
  std::string orbital_type_name_;

  ///@brief hybridization of atom the orbital is attached to
  std::string hybridization_;

  ///@brief orbital name associated with the orbital type
  std::string orbital_name_;

  ///@brief atom type associated with a given orbital type
  utility::vector1<std::string> atom_type_name_;


  ///@brief distance of orbital from center of atom
  core::Real distance_;

  orbital_type_enum orbital_type_enum_;


};

}
}
}



#endif /* ORBITALTYPE_HH_ */