UpstreamResTypeGeometry.hh

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/// @file   protocols/match/upstream/UpstreamResTypeGeometry.hh
/// @brief
/// @author Alex Zanghellini (zanghell@u.washington.edu)
/// @author Andrew Leaver-Fay (aleaverfay@gmail.com), porting to mini

#ifndef INCLUDED_protocols_match_upstream_UpstreamResTypeGeometry_hh
#define INCLUDED_protocols_match_upstream_UpstreamResTypeGeometry_hh

// Unit headers
#include <protocols/match/upstream/UpstreamResTypeGeometry.fwd.hh>

// Project headers
#include <core/chemical/ResidueType.fwd.hh>
#include <core/types.hh>

// Numeric headers
#include <numeric/HomogeneousTransform.hh>
#include <numeric/xyzVector.hh>

// Utility headers
// AUTO-REMOVED #include <utility/fixedsizearray1.hh>
#include <utility/pointer/ReferenceCount.hh>
// AUTO-REMOVED #include <utility/vector1.hh>

#include <utility/vector1.hh>


namespace protocols {
namespace match {
namespace upstream {

/// @brief A simple class that describes the geometry for a particular
/// residue type.  It describes the coordinate frame geometry for the
/// fourth atom defining each chi dihedral. The fourth atom is called
/// the "chi tip" atom, as it's at the tip of the growing kinematic chain
/// when building chi i. This class also describes the location
/// of the atoms controlled by each chi which are not the chi-tip atoms;
/// it measures their location in the coordinate frame of the chi-tip atom.
///
/// @details To generate the coordinate of the chi-tip atom, the
/// stored coordinate frame is multiplied
/// by the coordinate frame at the third atom after that coordinate frame
/// has been multipled by the chi-angle-z-axis rotation HT.
class UpstreamResTypeGeometry : public utility::pointer::ReferenceCount
{
public:
  ///@brief Automatically generated virtual destructor for class deriving directly from ReferenceCount
  virtual ~UpstreamResTypeGeometry();
  typedef core::Size                            Size;
  typedef core::Real                            Real;
  typedef core::Vector                          Vector;
  typedef numeric::HomogeneousTransform< Real > HTReal;

public:
  UpstreamResTypeGeometry();
  UpstreamResTypeGeometry( core::chemical::ResidueType const & );

  void initialize_from_residue_type( core::chemical::ResidueType const & );

public:

  /// @brief the name of the residue type used to generate this geometry
  std::string const & name() const {
    return restype_name_;
  }

  /// @brief the number of atoms in this residue type
  Size natoms() const {
    return controlling_chi_for_atom_.size();
  }

  Size nchi() const {
    return chitip_atoms_.size();
  }

  bool atom_controlled_by_any_chi( Size atomno ) const {
    return controlling_chi_for_atom_[ atomno ] != 0;
  }

  bool atom_is_chitip( Size atomno ) const {
    return controlling_chi_for_atom_[ atomno ] != 0 && which_point_for_atom_[ atomno ] == 0;
  }

  utility::vector1< Size > const &
  controlling_chi_for_atom() const { return controlling_chi_for_atom_; }

  utility::vector1< Size > const &
  which_point_for_atom() const { return which_point_for_atom_; }

  utility::vector1< Size > const &
  chitip_atoms() const { return chitip_atoms_; }

  Size
  chitip_atom( Size chi ) const {
    return chitip_atoms_[ chi ];
  }

  utility::vector1< HTReal > const &
  ht_for_chitip_atoms() const { return ht_for_chitip_atoms_; }

  HTReal const &
  ht_for_chitip_atom( Size chi ) const {
    return ht_for_chitip_atoms_[ chi ];
  }

  Size
  n_nonchitip_atoms_for_chi( Size chi ) const {
    return nonchitip_atoms_[ chi ].size();
  }

  utility::vector1< utility::vector1< Size > > const &
  nonchitip_atoms() const { return nonchitip_atoms_; }

  Size
  nonchitip_atom( Size chi, Size which_nonchitip_atom_for_chi ) const {
    return nonchitip_atoms_[ chi ][ which_nonchitip_atom_for_chi ];
  }

  utility::vector1< utility::vector1< Vector > > const &
  points_for_nonchitip_atoms() const { return points_for_nonchitip_atoms_; }

  utility::vector1< Vector > const &
  points_for_nonchitip_atoms( Size chi ) const {
    return points_for_nonchitip_atoms_[ chi ];
  }

  /// @brief Convenience function: get the coordinate in the chitip frame
  /// for a particular atom.  The atom must be a non-chitip atom that is
  /// not part of the backbone (it must be controlled by a chi angle).
  Vector const &
  point_for_nonchitip_atom( Size atom ) {
    assert( atom_controlled_by_any_chi( atom ) && !atom_is_chitip( atom ) );
    return points_for_nonchitip_atoms_[ controlling_chi_for_atom_[ atom ] ]
      [ which_point_for_atom_[ atom ] ];
  }


  Size N_atom_id() const { return N_atom_id_; }
  Size CA_atom_id() const { return CA_atom_id_; }
  Size C_atom_id() const { return C_atom_id_; }
  Size O_atom_id() const { return O_atom_id_; }
  Size CB_atom_id() const { return CB_atom_id_; }
  Size H_atom_id() const  { return H_atom_id_; }
  Size HA_atom_id() const  { return HA_atom_id_; }


  bool has_N_atom() const { return N_atom_id_ != 0; }
  bool has_CA_atom() const { return CA_atom_id_ != 0; }
  bool has_C_atom() const { return C_atom_id_ != 0; }
  bool has_O_atom() const { return O_atom_id_ != 0; }
  bool has_CB_atom() const { return CB_atom_id_ != 0; }
  bool has_H_atom() const  { return H_atom_id_ != 0; }
  bool has_HA_atom() const  { return HA_atom_id_ != 0; }

  bool
  atom_has_nonchi_coordinate( Size restype_atomid ) const;

  Vector const &
  coordinate_for_nonchi_atom_in_ideal_frame( Size restype_atomid ) const;


private:
  /// Data

  std::string restype_name_;

  utility::vector1< Size >   controlling_chi_for_atom_;
  utility::vector1< Size >   which_point_for_atom_;

  utility::vector1< Size >   chitip_atoms_;
  utility::vector1< HTReal > ht_for_chitip_atoms_;


  utility::vector1< utility::vector1< Size > >   nonchitip_atoms_;
  utility::vector1< utility::vector1< Vector > > points_for_nonchitip_atoms_;

  /// The ideal frame is defined at Calpha with the half point between N and C
  /// in the N plane-halfpoint-Calpha plane.
  /// i.g. HTReal( N, halfpoint, CAlpha);
  /// Non-chi dependendent atoms are measured from the ideal coordinate in this frame.
  /// This includes Cbeta and the Halphas.  It also includes O and H, but since their
  /// geometry depends on phi and psi, this data would be inappropriate for them.
  utility::vector1< Size   > restype_atom_id_2_nonchi_atom_id_;
  utility::vector1< Size   > nonchi_atom_id_2_restype_atom_id_;
  utility::vector1< Vector > nonchi_atoms_in_ideal_frame_;

  Size N_atom_id_;
  Size CA_atom_id_;
  Size C_atom_id_;
  Size O_atom_id_;
  Size CB_atom_id_;
  Size H_atom_id_;
  Size HA_atom_id_;

};



}
}
}

#endif