/**********************************************************************

atom.h - Handle OBAtom class.

Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.

Some portions Copyright (C) 2001-2006 by Geoffrey R. Hutchison

Some portions Copyright (C) 2003 by Michael Banck

This file is part of the Open Babel project.

For more information, see <http://openbabel.org/>

This program is free software; you can redistribute it and/or modify

it under the terms of the GNU General Public License as published by

the Free Software Foundation version 2 of the License.

This program is distributed in the hope that it will be useful,

but WITHOUT ANY WARRANTY; without even the implied warranty of

MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

GNU General Public License for more details.

***********************************************************************/

#ifndef OB_ATOM_H

#define OB_ATOM_H

#include <openbabel/babelconfig.h>

#ifndef OB_EXTERN

#  define OB_EXTERN extern

#endif

#include <vector>

#include <string>

#include <openbabel/base.h>

#include <openbabel/residue.h>

#include <openbabel/math/vector3.h>

namespace OpenBabel

{

  class OBBond;

  class OBMol;

  //! OBNodeBase is declared for backwards-compatibility with 2.0 and earlier code

  typedef OBAtom OBNodeBase;

  //! A standard iterator over a vector of bonds

  typedef std::vector<OBBond*>::iterator OBBondIterator;

  //! A standard iterator over a vector of atoms

  typedef std::vector<OBAtom*>::iterator OBAtomIterator;

  //ATOM Property Macros (flags)

  //! Atom is in a 4-membered ring

#define OB_4RING_ATOM     (1<<1)

  //! Atom is in a 3-membered ring

#define OB_3RING_ATOM     (1<<2)

  //! Atom is aromatic

#define OB_AROMATIC_ATOM  (1<<3)

  //! Atom is in a ring

#define OB_RING_ATOM      (1<<4)

  //! Atom is an electron donor

#define OB_DONOR_ATOM     (1<<7)

  //! Atom is an electron acceptor

#define OB_ACCEPTOR_ATOM  (1<<8)

#define SET_OR_UNSET_FLAG(X) \

  if (value) SetFlag(X); \

  else     UnsetFlag(X);

  // Class OBAtom

  // class introduction in atom.cpp

 #define OBATOM_TYPE_LEN 6

 class OBAPI OBAtom: public OBBase

    {

    protected:

      unsigned char                 _ele;       //!< atomic number (type unsigned char to minimize space -- allows for 0..255 elements)

      unsigned char                 _imph;      //!< number of implicit hydrogens

      char                          _type[OBATOM_TYPE_LEN];   //!< atomic type

      short                         _fcharge;   //!< formal charge

      unsigned short                _isotope;   //!< isotope (0 = most abundant)

      short                         _spinmultiplicity;//!< atomic spin, e.g., 2 for radical  1 or 3 for carbene

      unsigned int                  _idx;       //!< unique node index (GetIdx(), SetIdx())

      OBMol                        *_parent;    //!< parent molecule (if any)

      std::vector<OBBond*>          _vbond;     //!< bonds to this atom -- assumed to be one of the endpoints

      unsigned int                  _cidx;      //!< index into coordinate array

      unsigned short                _hyb;       //!< hybridization

      unsigned short                _flags;     //!< bitwise flags (e.g. aromaticity)

      double                        _pcharge;   //!< partial charge

      double                      **_c;         //!< coordinate array in double*

      mutable vector3               _v;         //!< coordinate vector

      OBResidue                    *_residue;   //!< parent residue (if applicable)

      unsigned long                 _id;        //!< unique id

      //! \return All flags

      int  GetFlag() const    {  return(_flags);  }

      //! Sets the bitwise @p flag

      void SetFlag(int flag)  { _flags |= flag;   }

      //! Unsets the bitwise @p flag

      void UnsetFlag(int flag) { _flags &= (~(flag)); }

      //! \return True of the atom has the @p flag

      bool HasFlag(int flag)  {  return((_flags & flag) ? true : false); }

    public:

      enum StereoFlag {

      };

       //! Used internally by graph traversal algorithms

      bool Visit;

      //! Constructor

      OBAtom();

      //! Destructor

      virtual ~OBAtom();

      //! Assignment

      OBAtom &operator = (OBAtom &);

      //! Equivalence

      bool operator==(const OBAtom * other) const {  return (GetIdx() == other->GetIdx()); }

      //! Duplicate another atom. Copies all information with the exception of index

      //! \since version 2.2

      void Duplicate(OBAtom *);

      //! Clear all data. Calls OBBase::Clear() to handle any generic data.

      //! \return True if successful.

      bool Clear();

      //! \name Methods to set atomic information

      //@{

      //! Set atom index (i.e., in an OBMol)

      void SetIdx(int idx)    { _idx = idx; _cidx = (idx-1)*3; }

      void SetId(unsigned long id) { _id = id; }

      //! Set atom hybridization (i.e., 1 = sp, 2 = sp2, 3 = sp3 ...)

      void SetHyb(int hyb)    { _hyb = hyb; }

      //! Set atomic number

      void SetAtomicNum(int atomicnum)    { _ele = (char)atomicnum; }

      //! Set isotope number (actual atomic weight is tabulated automatically, 0 = most abundant)

      void SetIsotope(unsigned int iso);

      //! Set the implicit hydrogen count to @p val

      void SetImplicitHCount(unsigned int val)    { _imph = (unsigned char)val; }

      //! Set the formal charge of the atom to @p fcharge

      void SetFormalCharge(int fcharge)   { _fcharge = fcharge; }

      //! Set the atomic spin to @p spin. See _spinmultiplicity

      void SetSpinMultiplicity(short spin){ _spinmultiplicity = spin; }

      //! Set the atomic type symbol (see OBTypeTable and OBAtomTyper for more)

      void SetType(const char *type);

      //! Set the atomic type symbol (see OBTypeTable and OBAtomTyper for more)

      void SetType(const std::string &type);

      //! Set the partial charge to @p pcharge

      void SetPartialCharge(double pcharge){ _pcharge = pcharge; }

      //! Set the coordinate vector for this atom to @p v as a vector3

      void SetVector(const vector3 &v);

      //! Set the coordinate vector for this atom based on @p x @p y & @p z

      void SetVector(const double x,const double y,const double z);

      //! Set the position of this atom from a pointer-driven array of coordinates

      void SetCoordPtr(double **c)        { _c = c; _cidx = (GetIdx()-1)*3; }

      //! Set the position of this atom based on the internal pointer array (i.e. from SetCoordPtr() )

      void SetVector();

      //! Attach an OBResidue @p res as containing this atom

      void SetResidue(OBResidue *res)     { _residue=res; }

      //! Attach an OBMol @p ptr as the parent container for this atom

      void SetParent(OBMol *ptr)          { _parent=ptr; }

      //! Mark atom as being aromatic

      void SetAromatic(bool value=true)                  { SET_OR_UNSET_FLAG(OB_AROMATIC_ATOM); }

      //! Mark an atom as belonging to at least one ring

      void SetInRing(bool value=true)         { SET_OR_UNSET_FLAG(OB_RING_ATOM); }

      //! Clear the internal coordinate pointer

      void ClearCoordPtr()     { _c = nullptr; _cidx=0; }

      //@}

      //! \name Methods to retrieve atomic information

      //@{

      //! \return the formal charge for this atom

      int          GetFormalCharge()  const { return(_fcharge);    }

      //! \return the atomic number for this atom

      unsigned int GetAtomicNum()     const { return((unsigned int)_ele); }

      //! \return the isotope for this atom, if specified, or 0 for unspecified

      unsigned short int GetIsotope() const { return(_isotope);    }

      //! \return the atomic spin, e.g., 0 (default) for normal atoms - note that this value is a convention,

      //!   2 for radical  1 or 3 for carbene

      int          GetSpinMultiplicity() const { return(_spinmultiplicity); }

      //! \return the atomic mass of this atom given by standard IUPAC

      //!  average molar mass

      double     GetAtomicMass()    const;

      //! \return the atomic mass of this atom given by the isotope

      //! (default of 0 gives the most abundant isotope)

      double     GetExactMass()     const;

      //! \return the internal atom index (e.g., inside an OBMol)

      unsigned int GetIdx()           const { return((int)_idx);  }

      unsigned int GetIndex() const { return _idx - 1; }

      unsigned long GetId() const { return _id; }

      //! \return the index into a pointer-driven array as used by

      //!   GetCoordPtr() or SetCoordPtr()

      unsigned int GetCoordinateIdx() const { return((int)_cidx); }

      //! \return The number of explicit bonds to this atom

      unsigned int GetExplicitDegree() const { return (unsigned int)_vbond.size(); }

      //! \return The total number of bonds to this atom including bonds to implicit hydrogens

      unsigned int GetTotalDegree() const { return (unsigned int)(_vbond.size() + _imph); }

      //! \return The sum of the bond orders of the explicit bonds to this atom

      unsigned int GetExplicitValence() const;

      //! \return The sum of the bond orders of all bonds to this atom including bonds to implicit hydrogens

      unsigned int GetTotalValence() const;

      //! \return The hybridization of this atom: 1 for sp, 2 for sp2, 3 for sp3, 4 for sq. planar, 5 for trig. bipy, 6 for octahedral

      unsigned int GetHyb()             const;

      //! \return The number of implicit hydrogens attached to this atom

      unsigned char GetImplicitHCount() const { return _imph; };

      //! \return The number of non-hydrogens connected to this atom

      unsigned int GetHvyDegree()      const;

      //! \return The number of heteroatoms connected to an atom

      unsigned int GetHeteroDegree()   const;

      //! \return the atomic type (e.g., for molecular mechanics)

      char        *GetType();

      //! \return the x coordinate

      double      GetX() const   {        return(x());    }

      //! \return the y coordinate

      double      GetY() const  {        return(y());    }

      //! \return the z coordinate

      double      GetZ() const  {        return(z());    }

      // These methods check to see if there is a coordinate pointer

      // or an internal vector (e.g., SetCoordPtr())

      //! \return the x coordinate

      double      x() const {

        if (_c)            return((*_c)[_cidx]);

        else               return _v.x();

      }

      //! \return the y coordinate

      double      y() const {

        if (_c)            return((*_c)[_cidx+1]);

        else               return _v.y();

      }

      //! \return the z coordinate

      double      z() const {

        if (_c)            return((*_c)[_cidx+2]);

        else               return _v.z();

      }

      //! \return the coordinates as a double* or NULL if none.

      //!

      //! See SetCoordPtr() for more. If no coordinate pointer is used

      //! (e.g., only vector3), NULL will be returned.

      double     *GetCoordinate(){

        if (_c)          return(&(*_c)[_cidx]);

        else             return nullptr;

      }

      //! \return the coordinates as a vector3 object

      vector3   &GetVector();

      //! \return the coordinates as a vector3 object

      const vector3   &GetVector() const;

      //! \return the partial charge of this atom, calculating a Gasteiger charge if needed

      double     GetPartialCharge();

      //! \return the residue which contains this atom, or NULL if none exists

      OBResidue *GetResidue();

      //! \return the molecule which contains this atom, or NULL if none exists

      OBMol     *GetParent()        {return((OBMol*)_parent);}

      //! Create a vector for a new bond from this atom, with length given by the supplied parameter

      //! \return success or failure

      bool       GetNewBondVector(vector3 &v,double length);

      //! \return the OBBond object between this atom and that supplied,

      //! or NULL if the two atoms are not bonded

      OBBond    *GetBond(OBAtom *);

      //@}

      //! \name Iterator methods

      //@{

      //! \return An iterator to the beginning of the bonds to this atom

      OBBondIterator BeginBonds()

        { return(_vbond.begin()); }

      //! \return An iterator to the end of the bonds to this atom

      OBBondIterator EndBonds()

        { return(_vbond.end());   }

      //! Set the iterator @p i to the beginning of the bonds

      //! \return The first bond to this atom (or NULL if none exist)

      OBBond *BeginBond(OBBondIterator &i);

      //! Increment the iterator @p i

      //! \return The next bond to this atom (or NULL if none exist)

      OBBond *NextBond(OBBondIterator &i);

      //! Set the iterator @p i to the beginning of the bonds

      //! \return The first neighboring atom (or NULL if none exist)

      OBAtom *BeginNbrAtom(OBBondIterator &i);

      //! Increment the iterator @p i

      //! \return The next neighboring atom (or NULL if none exist)

      OBAtom *NextNbrAtom(OBBondIterator &i);

      //@}

      //! \return the distance to the atom defined by OBMol::GetAtom()

      double GetDistance(int index);

      //! \return the distance to the supplied OBAtom

      double GetDistance(OBAtom*);

      //! \return the distance to the coordinates of the supplied vector3

      //! \since version 2.4

      double GetDistance(vector3* v);

      //! \return the angle defined by this atom -> b (vertex) -> c

      double GetAngle(int b, int c);

      //! \return the angle defined by this atom -> b (vertex) -> c

      double GetAngle(OBAtom *b, OBAtom *c);

      //! \name Addition of residue/bond info. for an atom

      //@{

      //! If no residue has been set for this atom, create a new one

      void NewResidue()

        {

          if (!_residue)

            _residue = new OBResidue;

        }

      //! Add (set) the residue for this atom

      void AddResidue(OBResidue *res) { SetResidue(res); }

      //! Delete any residue associated with this atom

      void DeleteResidue(){

        if (_residue) {

          delete _residue;

          _residue = nullptr; // Make sure to clear that a residue existed

        }

      }

      //! Add a bond to the internal list. Does not update the bond.

      void AddBond(OBBond *bond) { _vbond.push_back(bond); }

      //! \brief Insert @p bond into the internal list at the position from @p i

      //! Does not modify the bond

      void InsertBond(OBBondIterator &i, OBBond *bond)

        {

          _vbond.insert(i, bond);

        }

      //! Find @p bond and remove it from the internal list. Does not update the bond.

      bool DeleteBond(OBBond* bond);

      //! Clear all bonding information in this atom (does not delete them)

      void ClearBond() {_vbond.clear();}

      //@}

      //! \name Builder utilities

      //@{

      //! \brief If this is a hydrogen atom, transform into a methyl group

      //! \return success or failure

      bool HtoMethyl();

      //! Change the hybridization of this atom and modify the geometry accordingly

      //! \return success or failure

      //! \deprecated This will be removed in future versions of Open Babel

      OB_DEPRECATED bool SetHybAndGeom(int);

      //@}

      //! \name Property information

      //@{

      //! \return The number of oxygen atoms connected that only have one heavy valence

      unsigned int  CountFreeOxygens()      const;

      //! \return The number of sulfur atoms connected that only have one heavy valence

      //! \since version 2.4

      unsigned int  CountFreeSulfurs()      const;

      //! \return The number of hydrogens explicitly bound to this atom, optionally excluding D,T and isotope explicitly set to 1

      unsigned int  ExplicitHydrogenCount(bool ExcludeIsotopes=false) const;

      //! \return The number of rings that contain this atom

      unsigned int  MemberOfRingCount()     const;

      //! \return The size of the smallest ring that contains this atom (0 if not in a ring)

      unsigned int  MemberOfRingSize()    const;

      //! \return The number of explicit ring connections to this atom

      unsigned int  CountRingBonds() const;

      //! \return The smallest angle of bonds to this atom

      double    SmallestBondAngle();

      //! \return The average angle of bonds to this atom

      double    AverageBondAngle();

      /** Lewis acid/base vacancies for this atom

       *  \return A pair of integers, where first is acid count and second is base count

       *  \since version 2.3

       */

      std::pair<int, int> LewisAcidBaseCounts() const;

      //! \return Is there any residue information?

      bool HasResidue()    { return(_residue != nullptr);    }

      //! \return Is this a HETATM in a residue (returns false if not in a residue)

      //! \since version 2.4

      bool IsHetAtom() {

        if (_residue == nullptr)

          return false;

        else

          return _residue->IsHetAtom(this);

      }

      //! \return Is the specified element, as specified by atom number (see OBElement namespace)?

      bool IsElement(const unsigned int e) const {

           return e == _ele;

      }

      //! \return Is the atom aromatic?

      bool IsAromatic()      const;

      //! \return Is the atom in a ring?

      bool IsInRing()        const;

      //! \return Is the atom in a ring of a given size?

      bool IsInRingSize(int) const;

      //! \return Is this atom an element in the 15th or 16th main groups

      //!  (i.e., N, O, P, S ...) ?

      bool IsHeteroatom();

      //! \return Is this atom directly connected to the supplied OBAtom?

      bool IsConnected(OBAtom*);

      //! \return Is this atom related to the supplied OBAtom in

      //!  a 1,3 bonding pattern?

      bool IsOneThree(OBAtom*);

      //! \return Is this atom related to the supplied OBAtom in

      //!  a 1,4 bonding pattern?

      bool IsOneFour(OBAtom*);

      //! \return Is this atom an oxygen in a carboxyl (-CO2 or CO2H) group?

      bool IsCarboxylOxygen();

      //! \return Is this atom an oxygen in a phosphate (R-PO3) group?

      bool IsPhosphateOxygen();

      //! \return Is this atom an oxygen in a sulfate (-SO3) group?

      bool IsSulfateOxygen();

      //! \return Is this atom an oxygen in a nitro (-NO2) group?

      bool IsNitroOxygen();

      //! \return Is this atom a nitrogen in an amide (-C(=O)NR2) group?

      bool IsAmideNitrogen();

      //! \return Is this atom a hydrogen connected to a polar atom

      //!  (i.e., N, O, P, S)

      bool IsPolarHydrogen();

      //! \return Is this atom a hydrogen connected to a non-polar atom

      //!  (i.e., C)

      bool IsNonPolarHydrogen();

      //! \return Is this atom an aromatic nitrogen with at least one

      //!  double bond to an oxygen atom

      bool IsAromaticNOxide();

      //! \return Is this atom chiral?

      bool IsChiral();

      //! \return Is the atom part of a periodic unit cell?

      bool IsPeriodic() const;

      //! \return Is this atom an axial atom in a ring

      bool IsAxial();

      //! \return Is this atom a hydrogen-bond acceptor  (considering also atom surrounding)

      bool IsHbondAcceptor();

      //! \return Is this atom a hydrogen-bond acceptor (old function)?

      bool IsHbondAcceptorSimple();

            //! \return Is this atom a hydrogen-bond donor?

      bool IsHbondDonor();

      //! \return Is this a hydrogen atom attached to a hydrogen-bond donor?

      bool IsHbondDonorH();

      //! \return Is this atom a metal?

      //! \since version 2.4

      bool IsMetal();

      //! \return Whether a neighboring atom (alpha) has an unsaturated bond

      //!   to a third atom (beta).

      //! \param includePandS Whether to include phosphorus and sulfur neighbors

      //! in this determination (or to exclude them)

      bool HasAlphaBetaUnsat(bool includePandS=true);

      //! \return Whether this atom is connected to any bond with order == @p bo

      bool HasBondOfOrder(unsigned int bo);

      //! \return The count of bonds connected to this atom with order == @p bo

      int  CountBondsOfOrder(unsigned int bo);

      //! \return The maximum bond order for this atom

      int  HighestBondOrder();

      //! \return Whether this atom is connected to any bond with order >1

      bool HasNonSingleBond();

      //! \return Does this atom have a single bond

      bool HasSingleBond()    {        return(HasBondOfOrder(1));    }

      //! \return Does this atom have a double bond

      bool HasDoubleBond()    {        return(HasBondOfOrder(2));    }

      //! \return Does this atom have an aromatic bond

      bool HasAromaticBond()  {        return(HasBondOfOrder(5));    }

      //! \return Whether this atom matches the first atom in a given SMARTS pattern

      bool MatchesSMARTS(const char *);

      //@}

    }; // class OBAtom

}// namespace OpenBabel

#endif   // OB_ATOM_H

//! \file atom.h

//! \brief Handle atoms