CartesianMinimizerMap.hh

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// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
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/// @file   core/optimization/CartesianMinimizerMap.hh
/// @brief  Class for connecting DOFs in the atom tree to DOFs optimized by the AtomTreeMinimizer
/// @author Phil Bradley


#ifndef INCLUDED_core_optimization_CartesianMinimizerMap_hh
#define INCLUDED_core_optimization_CartesianMinimizerMap_hh

// Unit headers
#include <core/optimization/CartesianMinimizerMap.fwd.hh>

// Package headers
// AUTO-REMOVED #include <core/optimization/DOF_Node.hh>
#include <core/optimization/types.hh>

#include <core/id/TorsionID.hh>
#include <core/id/DOF_ID.hh>
#include <core/id/AtomID.hh>

// Project headers
#include <core/kinematics/MinimizerMapBase.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/kinematics/MoveMap.fwd.hh>
#include <core/id/AtomID_Map.hh>
// AUTO-REMOVED #include <core/id/DOF_ID_Map.hh>
#include <core/scoring/DerivVectorPair.hh>

// AUTO-REMOVED #include <list>

#include <utility/vector1.hh>
#include <ObjexxFCL/FArray1D.hh>



namespace core {
namespace optimization {

class CartesianMinimizerMap : public kinematics::MinimizerMapBase
{
public:

  ///
  CartesianMinimizerMap()
  {}

  ///
  ~CartesianMinimizerMap();

  ///
  virtual
  kinematics::DomainMap const &
  domain_map() const
  {
    return domain_map_;
  }

  virtual
  void
  add_torsion(
    DOF_ID const & new_torsion,
    DOF_ID const & parent
  );

  virtual
  void
  add_atom(
    AtomID const & AtomID,
    DOF_ID const & dof_id
  );

  ///
  void
  setup(
    pose::Pose & pose,
    kinematics::MoveMap const & move_map
  );

  /// clears old data+dimensions dof_node_pointer using size data from the pose
  void
  reset( pose::Pose const & pose );

  ///
  void
  copy_dofs_from_pose(
    pose::Pose const & pose,
    Multivec & dofs
  ) const;

  ///
  void
  copy_dofs_to_pose(
    pose::Pose & pose,
    Multivec const & dofs
  ) const;

  ///
  inline int
  ndofs() const { return 3*moving_atoms_.size(); }

  inline int
  ntorsions() const { return moving_dofids_.size(); }

  inline id::DOF_ID
  get_dof_id(Size n) const { return moving_dofids_[n]; }

  inline id::TorsionID
  get_TorsionID(Size n) const { return moving_torsionids_[n]; }

  inline int
  natoms() const  { return moving_atoms_.size(); }

  inline id::AtomID
  get_atom(Size n) const { return moving_atoms_[n]; }

  inline Size
  get_atom_index(id::AtomID x) const { return atom_indices_[x]; }

  utility::vector1< core::scoring::DerivVectorPair > &
  atom_derivatives( Size resid ) {
    return atom_derivatives_[ resid ];
  }

  void
  zero_stored_derivs();

private:

  // maps dofIDs->torsionIDs
  // removes dofIDs with no relevant atoms
  void
  assign_rosetta_torsions_and_trim( pose::Pose const & pose ); // part of setup


private:

  // map moving atoms->index
  id::AtomID_Map< core::Size > atom_indices_;

  /// list of all the moving atoms
  utility::vector1<id::AtomID> moving_atoms_;

  //
  utility::vector1< utility::vector1< core::scoring::DerivVectorPair > > atom_derivatives_;

  /// list of all moving torsions: dof ids and torsion ids
  /// we don't need all the info from dof_node, just this
  utility::vector1<id::DOF_ID> moving_dofids_;
  utility::vector1<id::TorsionID> moving_torsionids_;

  ///
  kinematics::DomainMap domain_map_;

}; // CartesianMinimizerMap


} // namespace kinematics
} // namespace core


#endif