Stub.cc

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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.
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// (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/kinematics/Stub.cc
/// @brief  Stub class
/// @author Phil Bradley


// Unit headers
#include <core/kinematics/Stub.hh>
#include <core/kinematics/RT.hh>

#include <utility/vector1.hh>
#include <numeric/xyz.functions.hh>



namespace core {
namespace kinematics {

Stub::Stub( RT const & rt ):
  M( rt.get_rotation() ),
  v( rt.get_translation() )
{}

/// @brief output operator, 3x3 matrix followd by an xyzVector
std::ostream &
operator<<( std::ostream & os, Stub const & a )
{
  os << "STUB";
  for ( int i=1; i<= 3; ++i ) {
    for ( int j=1; j<= 3; ++j ) {
      os << ' ' << a.M(i,j);
    }
  }
  for ( int i=1; i<= 3; ++i ) {
    os << ' ' << a.v(i);
  }
  return os;
}

/////////////////////////////////////////////////////////////////////////////
///@brief build a stub from a center points and other three points a, b, c
///
///@details orthogonal coord frame M contains three unit vectors by column,
///the first one is the unit vector from b pointing to a, the second one is the
///unit vector which is in the plane defined by vector b->a and b->c and
///perpendicular to b->a, the third one is the cross product of the first two.
void
Stub::from_four_points(
  Vector const & center,
  Vector const & a,
  Vector const & b,
  Vector const & c
)
{
  Vector e1( a - b);
  e1.normalize();

  Vector e3( cross( e1, c - b ) );
  e3.normalize();

  Vector e2( cross( e3,e1) );
  M.col_x( e1 ).col_y( e2 ).col_z( e3 );
  v = center;
}


Vector
Stub::build_fake_xyz( Size const index ) const
{
  Real const length( 1.4 );
  Real const angle( numeric::conversions::radians( 120.0 ) );
  Vector const xyz1( v );
  Vector const xyz2( xyz1 + length * M * Vector( -1, 0, 0 ) );
  Vector const xyz3( xyz2 + length * M * Vector( std::cos( angle ), std::sin( angle ), 0 ) );

  switch( index ) {
  case 1:
    return xyz1;
  case 2:
    return xyz2;
  case 3:
    return xyz3;
  default:
    utility_exit_with_message( "Stub::build_fake_xyz must be called with 1<= index <= 3" );
  }

  return Vector( 0.0 ); // wont get here

}


/// @brief Globals
///
/// @details a stub center at 0.0 with lab frame(identy matrix)
Stub /* const */ default_stub( Stub::Matrix::identity(), Stub::Vector( 0.0 ) );


} // namespace kinematics
} // namespace core