JumpEvaluator.cc

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// vi: set ts=2 noet:
//
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/// @file PoseEvaluator
/// @brief PoseEvaluator
/// @detailed
///
///
/// @author Oliver Lange



// Unit Headers
#include <protocols/simple_filters/JumpEvaluator.hh>

// Package Headers

// Project Headers
#include <core/conformation/Conformation.hh>
#include <core/io/silent/SilentStruct.hh>
#include <core/pose/Pose.hh>

// ObjexxFCL Headers
#include <ObjexxFCL/string.functions.hh>

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

//Auto Headers
#include <core/kinematics/AtomTree.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/tree/Atom.hh>


namespace protocols {
namespace simple_filters {

using namespace core;

/* It probably would be nice to change the interface away from using jump_nr towards
   explicit naming of the Stubs one wants to evaluate

   New interface would be :
   NamedStubID up_stub
   NamedStubID down_stub

   that would enable us to get rid of the current distinction ( is_protein() ) which
   switches between using the assumption that stub is N, CA, C or using the intrinsic atom-tree stubs

   using the atom-tree stubs is a bit against the philosophy of this evaluator since its existence was actually
   prompted by the problem that the atom-tree was using different atoms for the stub then expected and thus screwing
   up the simulation. An Evaluator using the atom-tree stubs would not have detected this problem.

*/

JumpEvaluator::JumpEvaluator( pose::Pose const& native_pose, Size jump_nr ) :
  evaluation::SingleValuePoseEvaluator< core::Real >( "RT_"+ObjexxFCL::string_of( jump_nr ) ),
  jump_nr_( jump_nr )
{
  using namespace kinematics;
  kinematics::Edge jump_edge = native_pose.fold_tree().jump_edge( jump_nr );
  Size res1=jump_edge.start();
  Size res2=jump_edge.stop();

  // work out the stubID
  chemical::ResidueType const& rt1 ( native_pose.residue_type ( res1 ) );
  chemical::ResidueType const& rt2 ( native_pose.residue_type ( res2 ) );

  if ( jump_edge.has_atom_info() && !(rt1.is_protein() && rt2.is_protein()) ) { // if jump_atoms defined, get stubs directly from atom_tree. temporary fix to pass unit test, but check with Oliver!
    up_jump_atom_   = id::AtomID( rt1.atom_index( jump_edge.start_atom() ), res1 );
    down_jump_atom_ = id::AtomID( rt2.atom_index( jump_edge.stop_atom() ),  res2 );
    native_up_ = native_pose.conformation().atom_tree().atom( up_jump_atom_ ).get_stub();
    native_down_ = native_pose.conformation().atom_tree().atom( down_jump_atom_ ).get_stub();
  } else { // otherwise assume standard protein residue to residue jump
    id::AtomID a1( rt1.atom_index ("N") , res1 );
    id::AtomID a2( rt1.atom_index ("CA") , res1 );
    id::AtomID a3( rt1.atom_index ("C") , res1 );
    down_stub_ = id::StubID( a1, a2, a3 );

    id::AtomID b1( rt2.atom_index ("N") , res2 );
    id::AtomID b2( rt2.atom_index ("CA") , res2 );
    id::AtomID b3( rt2.atom_index ("C") , res2 );
    up_stub_ = id::StubID(b1, b2, b3 );

    native_up_ = native_pose.conformation().atom_tree().stub_from_id( up_stub_ );
    native_down_ = native_pose.conformation().atom_tree().stub_from_id( down_stub_ );
  }
}


core::Real
JumpEvaluator::apply(
 pose::Pose& pose
) const {

  kinematics::Stub up, down;
  if ( up_jump_atom_.valid() && down_jump_atom_.valid() ) { // jump_atoms defined
    up = pose.conformation().atom_tree().atom( up_jump_atom_ ).get_stub();
    down = pose.conformation().atom_tree().atom( down_jump_atom_ ).get_stub();
  } else {
    up = pose.conformation().atom_tree().stub_from_id( up_stub_ );
    down = pose.conformation().atom_tree().stub_from_id( down_stub_ );
  }
  kinematics::RT rt(up, down);

  kinematics::Stub test_down;
  rt.make_jump( native_up_, test_down );

  Real rms( 0.0 );
  for ( Size i=1; i<=3; i++ ) {
      Vector tv = test_down.build_fake_xyz( i );
      Vector nv = native_down_.build_fake_xyz( i );
      Vector d = nv-tv;
      rms += d.length();
  }
  return rms;
}

core::Size
JumpNrEvaluator::apply(
 pose::Pose& pose
) const {
  return pose.num_jump();
}



}
}