AssignOrbitals.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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#ifndef INCLUDED_core_chemical_orbitals_AssignOrbitals_hh
#define INCLUDED_core_chemical_orbitals_AssignOrbitals_hh

#include <numeric/xyzVector.fwd.hh>
#include <core/chemical/ResidueType.fwd.hh>
#include <utility/vector1.hh>
// AUTO-REMOVED #include <core/chemical/AtomType.hh>

//Auto Headers
#include <core/chemical/AtomType.fwd.hh>


namespace core{
namespace chemical{
namespace orbitals{

/*struct OrbInfo{
  core::Size atom_index;
  core::Size hybridization;
  core::Size orbitaltypes;
  core::Real dist;
  utility::vector1<core::Size> bondedatoms;

};*/

class AssignOrbitals {
public:



  AssignOrbitals(core::chemical::ResidueTypeOP const restype);
  void assign_orbitals();

  void assign_only_pi_orbitals_to_atom(/*OrbInfo const & orbital_info,*/ core::chemical::AtomType const & atmtype);

  void assign_sp2_sp_orbitals_to_one_bonded_atom(/*OrbInfo const & orbital_info*/ core::chemical::AtomType const & atmtype);
  void add_orbitals_to_restype(
      core::Size const atm_index2,
      core::Size const atm_index3,
      //OrbInfo const & orbital_info,
      core::chemical::AtomType const & atmtype,
      std::string const atom_hybridization,
      utility::vector1< numeric::xyzVector<core::Real> > const orbital_xyz_vectors
  );

  void assign_sp2_orbitals_to_one_bonded_atom(/*OrbInfo const & orbital_info,*/ core::chemical::AtomType const & atmtype);


  utility::vector1< numeric::xyzVector<core::Real> > cross_product_helper(
      core::Size const atm_index1,
      core::Size const atm_index2,
      core::Size const atm_index3,
      core::Real const dist
  );

  void calculate_orbital_icoor(
      numeric::xyzVector<core::Real> const orbital_xyz,
      core::Size const atm_index1,
      core::Size const atm_index2,
      core::Size const atm_index3,
      std::string const orbital_element_name
  );

  utility::vector1< numeric::xyzVector<core::Real> >  Coordinates_TriganolPlanar_bondedto1atom_helper(
      core::Size const atm_index1,
      core::Size const atm_index2,
      core::Size const atm_index3,
      core::Real const dist

  );

  utility::vector1< numeric::xyzVector<core::Real> >  Coordinates_Tetrahedral_bondedto3atoms_helper(
      core::Size const atm_index1,
      core::Size const atm_index2,
      core::Size const atm_index3,
      core::Size const atm_index4,
      core::Real const dist

   );

private:

  core::Size Aindex_;
  core::Size AOhybridization_;
  core::Size Orbtype_;
  core::Real AOdist_;
  utility::vector1<core::Size> AObondedatoms_;

  core::chemical::ResidueTypeOP restype_;
  core::Size n_orbitals_;

  std::string make_orbital_type_name
  (
    AtomType const & atmtype,
    std::string const orbitaltype,
    core::Size const hybridization
  );

  std::string make_orbital_element_name();


  void set_orbital_type_and_bond(
    core::Size atom_index,
    std::string orbital_element_name,
    std::string orbital_type_full_name
  );

};


}
}
}



#endif /* INCLUDED_core_chemical_orbitals_AssignOrbitals_hh */