ICoorOrbitalData.cc

Go to the documentation of this file.

// -*- 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 AtomTypeSet
///
/// @brief
/// A class for reading in the orbital type properties
///
/// @detailed
/// This class contains the ORBITALS INTERNAL_ICOOR data that is read in from residue_io.cc. Actually,
/// the data is set when residue_io.cc calls the command from residuetype.cc set_orbital_icoor. The data
/// is set and chills out in memory until needed. The actual xyz coordinates are not stored at this point.
/// xyz coordinates are constructed when conformation/Residue.hh asks for the build function in this class.
/// At that point, the coordinates are built and returned.
///
/// But wait, you say, why do you store the names of the atoms instead of the index of the atoms!? Well, the
/// problem occurs when residuetype reorders the indices of the atoms. When this occurrs, the indices for the icoor
/// are not reordered here. Another problem ocurs because orbital indices are not reordered in this process because
/// orbital indices are seperate from the atom indices. Regardless, when you build the xyz coords, this step is transparent
/// because the function orbital_xyz() in residue.hh takes care of this conversion of indice to string.
///
/// @note NOTE!!!!!!!!!!! The internal coordinates cannot contain an orbital as the stub1, stub2, or stub3 atom.
/// This is because the xyz coordinates are not updated when the conformation changes. The stub1, stub2, stub2 atoms
/// must be actual atoms and not orbitals!!!!! (design feature or flaw? you decide)
///
///
/// @authors
/// Steven Combs
///
///
/// @last_modified December 12 2010
/////////////////////////////////////////////////////////////////////////



#include <core/chemical/orbitals/ICoorOrbitalData.hh>


#include <core/chemical/ResidueType.hh>
#include <core/conformation/Residue.hh>
// AUTO-REMOVED #include <core/conformation/Conformation.hh>
// AUTO-REMOVED #include <core/id/AtomID.hh>

// Utility headers
#include <utility/exit.hh>
#include <numeric/xyz.functions.hh>
#include <core/kinematics/Jump.hh>
#include <utility/vector1.hh>

//Auto Headers
namespace core{
namespace chemical{
namespace orbitals{

/// @brief construct ICoorOrbitalData.
ICoorOrbitalData::ICoorOrbitalData():
      phi_(0.0),
      theta_(0.0),
      distance_(0.0),
      stub1_(""),
      stub2_(""),
      stub3_("")

{}

/// @brief construct ICoorOrbitalData.
ICoorOrbitalData::ICoorOrbitalData(
    Real phi,
    Real theta,
    Real distance,
    std::string stub1,
    std::string stub2,
    std::string stub3

):
phi_(phi),
theta_(theta),
distance_(distance),
stub1_(stub1),
stub2_(stub2),
stub3_(stub3)
{}


//Testing size orbitals
ICoorOrbitalData::ICoorOrbitalData(
    Real phi,
    Real theta,
    Real distance,
    Size stub1,
    Size stub2,
    Size stub3
):
phi_(phi),
theta_(theta),
distance_(distance),
s_stub1_(stub1),
s_stub2_(stub2),
s_stub3_(stub3)
{

}



///@brief return the phi for a given orbital
Real ICoorOrbitalData::phi() const
{
  return phi_;
}

///@brief return the theta for a given orbital
Real ICoorOrbitalData::theta() const
{
  return theta_;
}

///@brief return the distance for a given orbital
Real ICoorOrbitalData::distance() const
{
  return distance_;
}

///@brief return the stub1 for a given orbital
std::string ICoorOrbitalData::stub1() const
{
  return stub1_;
}

///@brief return the stub2 for a given orbital
std::string ICoorOrbitalData::stub2() const
{
  return stub2_;
}

///@brief return the stub3 for a given orbital
std::string ICoorOrbitalData::stub3() const
{
  return stub3_;
}





///@brief build the xyz coordinates for an orbital based upon the stub1, stub2, stub3 xyz coordinates.
/// @note NOTE!!!!!!!!!!! The internal coordinates cannot contain an orbital as the stub1, stub2, or stub3 atom.
/// This is because the xyz coordinates are not updated when the conformation changes. The stub1, stub2, stub2 atoms
/// must be actual atoms and not orbitals!!!!11111!!!!!!!11111!(design feature or flaw? you decide)
Vector
ICoorOrbitalData::build(
    Vector stub1_xyz,
    Vector stub2_xyz,
    Vector stub3_xyz) const
{
  assert( kinematics::Stub( stub1_xyz,
      stub2_xyz,
      stub3_xyz).is_orthogonal( 0.001 ) );

  return kinematics::Stub(stub1_xyz, stub2_xyz, stub3_xyz).spherical(phi_, theta_, distance_);
}





}
}
}