text: //
  //  Copyright (C) 2001-2017 Greg Landrum and Rational Discovery LLC
  //
  //   @@ All Rights Reserved @@
  //  This file is part of the RDKit.
  //  The contents are covered by the terms of the BSD license
  //  which is included in the file license.txt, found at the root
  //  of the RDKit source tree.
  //
  #include <RDGeneral/export.h>
  #ifndef _RD_BOND_H
  #define _RD_BOND_H
  
  // std stuff
  #include <iostream>
  
  // Ours
  #include <RDGeneral/Invariant.h>
  #include <Query/QueryObjects.h>
  #include <RDGeneral/types.h>
  #include <RDGeneral/RDProps.h>
  #include <GraphMol/details.h>
  #include <boost/foreach.hpp>
  
  namespace RDKit {
  class ROMol;
  class RWMol;
  class Atom;
  
  //! class for representing a bond
  /*!
  
    <b>Notes:</b>
      - many of the methods of Atom require that the Atom be associated
        with a molecule (an ROMol).
      - each Bond maintains a Dict of \c properties:
          - Each \c property is keyed by name and can store an
            arbitrary type.
          - \c Properties can be marked as \c calculated, in which case
            they will be cleared when the \c clearComputedProps() method
            is called.
          - Because they have no impact upon chemistry, all \c property
            operations are \c const, this allows extra flexibility for
            clients who need to store extra data on Bond objects.
  
  */
  class RDKIT_GRAPHMOL_EXPORT Bond : public RDProps {
    friend class RWMol;
    friend class ROMol;
  
   public:
    // FIX: grn...
    typedef Queries::Query<int, Bond const *, true> QUERYBOND_QUERY;
  
    //! the type of Bond
    typedef enum {
      UNSPECIFIED = 0,
      SINGLE,
      DOUBLE,
      TRIPLE,
      QUADRUPLE,
      QUINTUPLE,
      HEXTUPLE,
      ONEANDAHALF,
      TWOANDAHALF,
      THREEANDAHALF,
      FOURANDAHALF,
      FIVEANDAHALF,
      AROMATIC,
      IONIC,
      HYDROGEN,
      THREECENTER,
      DATIVEONE,  //!< one-electron dative (e.g. from a C in a Cp ring to a metal)
      DATIVE,     //!< standard two-electron dative
      DATIVEL,    //!< standard two-electron dative
      DATIVER,    //!< standard two-electron dative
      OTHER,
      ZERO  //!< Zero-order bond (from
      // http://pubs.acs.org/doi/abs/10.1021/ci200488k)
    } BondType;
  
    //! the bond's direction (for chirality)
    typedef enum {
      NONE = 0,    //!< no special style
      BEGINWEDGE,  //!< wedged: narrow at begin
      BEGINDASH,   //!< dashed: narrow at begin
      // FIX: this may not really be adequate
      ENDDOWNRIGHT,  //!< for cis/trans
      ENDUPRIGHT,    //!<  ditto
      EITHERDOUBLE,  //!< a "crossed" double bond
      UNKNOWN,       //!< intentionally unspecified stereochemistry
    } BondDir;
  
    //! the nature of the bond's stereochem (for cis/trans)
    typedef enum {     // stereochemistry of double bonds
      STEREONONE = 0,  // no special style
      STEREOANY,       // intentionally unspecified
      // -- Put any true specifications about this point so
      // that we can do comparisons like if(bond->getStereo()>Bond::STEREOANY)
      STEREOZ,     // Z double bond
      STEREOE,     // E double bond
      STEREOCIS,   // cis double bond
      STEREOTRANS  // trans double bond
    } BondStereo;
  
    Bond();
    //! construct with a particular BondType
    explicit Bond(BondType bT);
    Bond(const Bond &other);
    virtual ~Bond();
    Bond &operator=(const Bond &other);
  
    //! returns a copy
    /*!
      <b>Note:</b> the caller is responsible for <tt>delete</tt>ing
       the returned pointer.
    */
    virtual Bond *copy() const;
  
    //! returns our \c bondType
    BondType getBondType() const { return static_cast<BondType>(d_bondType); };
    //! sets our \c bondType
    void setBondType(BondType bT) { d_bondType = bT; };
    //! \brief returns our \c bondType as a double
    //!   (e.g. SINGLE->1.0, AROMATIC->1.5, etc.)
    double getBondTypeAsDouble() const;
  
    //! returns our contribution to the explicit valence of an Atom
    /*!
      <b>Notes:</b>
        - requires an owning molecule
    */
    double getValenceContrib(const Atom *at) const;
  
    //! sets our \c isAromatic flag
    void setIsAromatic(bool what) { df_isAromatic = what; };
    //! returns the status of our \c isAromatic flag
    bool getIsAromatic() const { return df_isAromatic; };
  
    //! sets our \c isConjugated flag
    void setIsConjugated(bool what) { df_isConjugated = what; };
    //! returns the status of our \c isConjugated flag
    bool getIsConjugated() const { return df_isConjugated; };
  
    //! returns whether or not this instance belongs to a molecule
    bool hasOwningMol() const { return dp_mol != nullptr; };
  
    //! returns a reference to the ROMol that owns this instance
    ROMol &getOwningMol() const {
      PRECONDITION(dp_mol, "no owner");
      return *dp_mol;
    };
    //! sets our owning molecule
    void setOwningMol(ROMol *other);
    //! sets our owning molecule
    void setOwningMol(ROMol &other) { setOwningMol(&other); };
  
    //! returns our index within the ROMol
    /*!
      <b>Notes:</b>
        - this makes no sense if we do not have an owning molecule
  
    */
    unsigned int getIdx() const { return d_index; };
    //! sets our index within the ROMol
    /*!
      <b>Notes:</b>
        - this makes no sense if we do not have an owning molecule
        - the index should be <tt>< this->getOwningMol()->getNumBonds()</tt>
    */
    void setIdx(unsigned int index) { d_index = index; };
  
    //! returns the index of our begin Atom
    /*!
      <b>Notes:</b>
        - this makes no sense if we do not have an owning molecule
    */
    unsigned int getBeginAtomIdx() const { return d_beginAtomIdx; };
  
    //! returns the index of our end Atom
    /*!
      <b>Notes:</b>
        - this makes no sense if we do not have an owning molecule
    */
    unsigned int getEndAtomIdx() const { return d_endAtomIdx; };
  
    //! given the index of one Atom, returns the index of the other
    /*!
      <b>Notes:</b>
        - this makes no sense if we do not have an owning molecule
    */
    unsigned int getOtherAtomIdx(unsigned int thisIdx) const;
  
    //! sets the index of our begin Atom
    /*!
      <b>Notes:</b>
        - requires an owning molecule
    */
    void setBeginAtomIdx(unsigned int what);
    //! sets the index of our end Atom
    /*!
      <b>Notes:</b>
        - requires an owning molecule
    */
    void setEndAtomIdx(unsigned int what);
  
    //! sets our begin Atom
    /*!
      <b>Notes:</b>
        - requires an owning molecule
    */
    void setBeginAtom(Atom *at);
    //! sets our end Atom
    /*!
      <b>Notes:</b>
        - requires an owning molecule
    */
    void setEndAtom(Atom *at);
  
    //! returns a pointer to our begin Atom
    /*!
      <b>Notes:</b>
        - requires an owning molecule
    */
    Atom *getBeginAtom() const;
    //! returns a pointer to our end Atom
    /*!
      <b>Notes:</b>
        - requires an owning molecule
    */
    Atom *getEndAtom() const;
    //! returns a pointer to the other Atom
    /*!
      <b>Notes:</b>
        - requires an owning molecule
    */
    Atom *getOtherAtom(Atom const *what) const;
  
    // ------------------------------------
    // Please see the note in Atom.h for some explanation
    // of these methods
    // ------------------------------------
  
    // This method can be used to distinguish query bonds from standard bonds
    virtual bool hasQuery() const { return false; };
  
    // FIX: the const crap here is all mucked up.
    //! NOT CALLABLE
    virtual void setQuery(QUERYBOND_QUERY *what);
    //! NOT CALLABLE
    virtual QUERYBOND_QUERY *getQuery() const;
  
    //! NOT CALLABLE
    virtual void expandQuery(
        QUERYBOND_QUERY *what,
        Queries::CompositeQueryType how = Queries::COMPOSITE_AND,
        bool maintainOrder = true);
  
    //! returns whether or not we match the argument
    /*!
        <b>Notes:</b>
          - for Bond objects, "match" means that either one of the Bonds
            has \c bondType Bond::UNSPECIFIED or both Bonds have the
            same \c bondType.
    */
    virtual bool Match(Bond const *what) const;
  
    //! sets our direction
    void setBondDir(BondDir what) { d_dirTag = what; };
    //! returns our direction
    BondDir getBondDir() const { return static_cast<BondDir>(d_dirTag); };
  
    //! sets our stereo code
    /*!
        STEREONONE, STEREOANY, STEREOE and STEREOZ can be set without
        neighboring atoms specified in getStereoAtoms since they are
        defined by the topology of the molecular graph. In order to set
        STEREOCIS or STEREOTRANS the neighboring atoms must be set first
        (using setStereoBonds()) to know what atoms are being considered.
  
        <b>Notes:</b>
          - MolOps::findPotentialStereoBonds can be used to set
            getStereoAtoms before setting CIS/TRANS
    */
    void setStereo(BondStereo what) {
      PRECONDITION(what <= STEREOE || getStereoAtoms().size() == 2,
                   "Stereo atoms should be specified before specifying CIS/TRANS "
                   "bond stereochemistry")
      d_stereo = what;
    };
    //! returns our stereo code
    BondStereo getStereo() const { return static_cast<BondStereo>(d_stereo); };
  
    //! sets the atoms to be considered as reference points for bond stereo
    /*!
        These do not necessarily need to be the highest 'ranking' atoms
        like CIP stereo requires. They can be any arbitrary atoms
        neighboring the begin and end atoms of this bond
        respectively. STEREOCIS or STEREOTRANS is then set relative to
        only these atoms.
  
        If CIP rankings are desired, use
        MolOps::findPotentialStereoBonds, but this is a more costly
        function as it takes the whole molecule topology into account.
    */
    void setStereoAtoms(unsigned int bgnIdx, unsigned int endIdx);
  
    //! returns the indices of our stereo atoms
    const INT_VECT &getStereoAtoms() const {
      if (!dp_stereoAtoms) {
        const_cast<Bond *>(this)->dp_stereoAtoms = new INT_VECT();
      }
      return *dp_stereoAtoms;
    };
    //! \overload
    INT_VECT &getStereoAtoms() {
      if (!dp_stereoAtoms) dp_stereoAtoms = new INT_VECT();
      return *dp_stereoAtoms;
    };
  
    //! calculates any of our lazy \c properties
    /*!
      <b>Notes:</b>
        - requires an owning molecule
    */
    void updatePropertyCache(bool strict = true) { (void)strict; }
  
   protected:
    //! sets our owning molecule
    // void setOwningMol(ROMol *other);
    //! sets our owning molecule
    // void setOwningMol(ROMol &other) {setOwningMol(&other);};
    bool df_isAromatic;
    bool df_isConjugated;
    std::uint8_t d_bondType;
    std::uint8_t d_dirTag;
    std::uint8_t d_stereo;
    atomindex_t d_index;
    atomindex_t d_beginAtomIdx, d_endAtomIdx;
    ROMol *dp_mol;
    INT_VECT *dp_stereoAtoms;
  
    void initBond();
  };
  
  //! returns twice the \c bondType
  //! (e.g. SINGLE->2, AROMATIC->3, etc.)
  uint8_t getTwiceBondType(const RDKit::Bond &b);
  
  };  // namespace RDKit
  
  //! allows Bond objects to be dumped to streams
  RDKIT_GRAPHMOL_EXPORT extern std::ostream &operator<<(std::ostream &target,
                                                        const RDKit::Bond &b);
  
  #endif
  