/*! \file minimol_utils.h
  Header file for minimol utils */

//C Copyright (C) 2000-2006 Kevin Cowtan and University of York
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#ifndef CLIPPER_MINIMOL_UTILS
#define CLIPPER_MINIMOL_UTILS


#include "minimol.h"


namespace clipper {


  //! Class for holding the indices of an atom within a MiniMol molecule class
  /*! The indices remain valid only while no changes are made to the
    MiniMol object. */
  class MAtomIndex {
  public:
    //! null constructor
    MAtomIndex() { p = -1; }
    //! constructor: from polymer, monomer and atom numbers.
    MAtomIndex( const int& polymer, const int& monomer, const int& atom ) : p(polymer), m(monomer), a(atom) {}
    //! test if object has been initialised
    bool is_null() const { return p >= 0; }
    const int& polymer() const { return p; }  //!< return polymer index
    const int& monomer() const { return m; }  //!< return monomer index
    const int& atom()    const { return a; }  //!< return atom index
    friend inline bool operator < ( MAtomIndex i1, MAtomIndex i2 ) { return ( i1.p < i2.p || ( i1.p == i2.p && ( i1.m < i2.m || ( i1.m == i2.m && i1.a < i2.a ) ) ) ); }
  private:
    int p, m, a;
  };

  //! Class for holding the indices of an atom within a MiniMol molecule class
  /*! The indices remain valid only while no changes are made to the
    MiniMol object. This class can also hold the number of a symmetry
    operator. */
  class MAtomIndexSymmetry : public MAtomIndex {
  public:
    //! null constructor
    MAtomIndexSymmetry() {}
    //! constructor: from polymer, monomer and atom numbers.
    MAtomIndexSymmetry( const int& polymer, const int& monomer, const int& atom , const int& symm ) : MAtomIndex(polymer,monomer,atom), s(symm) {}
    const int& symmetry() const { return s; }  //!< return symmetry index
  private:
    int s;
  };

  //! Find atoms in the vicinity of some coordinate in real space
  /*! Uses a fast non-bonded atom search. */
  class MAtomNonBond {
  public:
    //! null constructor
    MAtomNonBond() {}
    //! constructor: from MiniMol and grid radius
    MAtomNonBond( const clipper::MiniMol& mol, double rad = 5.0 );
    //! get a list of atoms in the rough vicinity of a coordinate
    std::vector<MAtomIndexSymmetry> atoms_near( const clipper::Coord_orth& co, double rad ) const;
    std::vector<MAtomIndexSymmetry> operator() ( const clipper::Coord_orth& co, double rad ) const;
    void debug() const;
  private:
    const MiniMol* mol_;
    double rad_;
    Spacegroup spgr;
    Cell cell;
    Grid_sampling grid;
    std::vector<int> lookup;
    std::vector<MAtomIndexSymmetry> atoms;
  };

} // namespace clipper

#endif