/**********************************************************************
mol.h - Handle molecules. Declarations of OBMol, OBAtom, OBBond, OBResidue.
        (the main header for Open Babel)
 
Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
Some portions Copyright (C) 2001-2005 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.sourceforge.net/>
 
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_MOL_H
#define OB_MOL_H

#include <openbabel/babelconfig.h>

#ifndef EXTERN
#  define EXTERN extern
#endif

#include <math.h>

#include <algorithm>
#include <vector>
#include <string>
#include <map>

#if HAVE_IOSTREAM
#include <iostream>
#elif HAVE_IOSTREAM_H
#include <iostream.h>
#endif

#if HAVE_FSTREAM
#include <fstream>
#elif HAVE_FSTREAM_H
#include <fstream.h>
#endif

#include <openbabel/base.h>
#include <openbabel/data.h>
#include <openbabel/chains.h>
#include <openbabel/math/vector3.h>
#include <openbabel/bitvec.h>
#include <openbabel/ring.h>
#include <openbabel/generic.h>
#include <openbabel/typer.h>
#include <openbabel/oberror.h>
#include <openbabel/obiter.h>
#include <openbabel/reaction.h> //so it gets notices in DLL builds

namespace OpenBabel
{

class OBAtom;
class OBBond;
class OBMol;
class OBInternalCoord;

// Class OBResidue
// class introduction in residue.cpp
class OBAPI OBResidue
{
public:

    //! Constructor
    OBResidue(void);
    //! Copy constructor
    OBResidue(const OBResidue &);
    //! Destructor
    virtual ~OBResidue(void);

    OBResidue &operator=(const OBResidue &);

    void    AddAtom(OBAtom *atom);
    void    InsertAtom(OBAtom *atom);
    void    RemoveAtom(OBAtom *atom);
    void    Clear(void);

    void    SetName(const std::string &resname);
    void    SetNum(unsigned int resnum);
    void    SetChain(char chain);
    void    SetChainNum(unsigned int chainnum);
    void    SetIdx(unsigned int idx);

    void    SetAtomID(OBAtom *atom, const std::string &id);
    void    SetHetAtom(OBAtom *atom, bool hetatm);
    //! Set the atomic serial number for a given atom (see OBSerialNums)
    void    SetSerialNum(OBAtom *atom, unsigned int sernum);

    std::string    GetName(void)		const;
    unsigned int   GetNum(void)			const;
    unsigned int   GetNumAtoms()		const;
    char           GetChain(void)		const;
    unsigned int   GetChainNum(void)		const;
    unsigned int   GetIdx(void)			const;
    unsigned int   GetResKey(void)		const;

    std::vector<OBAtom*> GetAtoms(void)		const;
    std::vector<OBBond*> GetBonds(bool = true)	const;

    std::string    GetAtomID(OBAtom *atom)	const;
    //! \return the serial number of the supplied atom (uses OBSerialNums)
    unsigned       GetSerialNum(OBAtom *atom)	const;

    bool           GetAminoAcidProperty(int)      const;
    bool           GetAtomProperty(OBAtom *, int) const;
    bool           GetResidueProperty(int)        const;

    bool           IsHetAtom(OBAtom *atom)	const;
    bool	   IsResidueType(int)		const;

    //! \deprecated Use FOR_ATOMS_OF_RESIDUE and OBResidueAtomIter instead
    OBAtom *BeginAtom(std::vector<OBAtom*>::iterator &i);
    //! \deprecated Use FOR_ATOMS_OF_RESIDUE and OBResidueAtomIter instead
    OBAtom *NextAtom(std::vector<OBAtom*>::iterator &i);

    //! \name Methods for handling generic data
    //@{
    bool                              HasData(std::string &);
    bool                              HasData(const char *);
    bool                              HasData(unsigned int type);
    void                              DeleteData(unsigned int type);
    void                              DeleteData(OBGenericData*);
    void                              DeleteData(std::vector<OBGenericData*>&);
    void                              SetData(OBGenericData *d)
      { _vdata.push_back(d); }
    //! \return the number of OBGenericData items attached to this residue
    unsigned int                      DataSize()
      { return(_vdata.size()); }
    OBGenericData                    *GetData(unsigned int type);
    OBGenericData                    *GetData(std::string&);
    OBGenericData                    *GetData(const char *);
    std::vector<OBGenericData*>      &GetData()
      { return(_vdata); }
    std::vector<OBGenericData*>::iterator  BeginData()
      { return(_vdata.begin()); }
    std::vector<OBGenericData*>::iterator  EndData()
      { return(_vdata.end()); }
    //@}

protected: // members

    unsigned int	 	_idx;   //!< Residue index (i.e., internal index in an OBMol)
    char      	                _chain; //!< Chain ID
    unsigned int		_aakey; //!< Amino Acid key ID -- see SetResidueKeys()
    unsigned int	        _reskey;//!< Residue key ID -- see SetResidueKeys()
    unsigned int		_resnum;//!< Residue number (i.e., in file)
    std::string                 _resname;//!< Residue text name

    std::vector<bool>           _hetatm;//!< Is a given atom a HETAM
    std::vector<std::string>    _atomid;//!< Residue atom text IDs
    std::vector<OBAtom*>        _atoms; //!< List of OBAtom in this residue
    std::vector<unsigned int>   _sernum;//!< List of serial numbers
    std::vector<OBGenericData*> _vdata; //!< Custom data
}; // OBResidue


//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 has clockwise SMILES chiral stereochemistry (i.e., "@@")
#define OB_CSTEREO_ATOM   (1<<5)
//! Atom has anticlockwise SMILES chiral stereochemistry (i.e., "@")
#define OB_ACSTEREO_ATOM  (1<<6)
//! Atom is an electron donor
#define OB_DONOR_ATOM     (1<<7)
//! Atom is an electron acceptor
#define OB_ACCEPTOR_ATOM  (1<<8)
//! Atom is chiral
#define OB_CHIRAL_ATOM    (1<<9)
//! Atom has + chiral volume
#define OB_POS_CHIRAL_ATOM (1<<10)
//! Atom has - chiral volume
#define OB_NEG_CHIRAL_ATOM (1<<11)
// 12-16 currently unused

// Class OBAtom
// class introduction in atom.cpp
class OBAPI OBAtom : public OBNodeBase
{
protected:
    char                          _ele;		//!< atomic number (type char to minimize space -- allows for 0..255 elements)
    char                          _impval;	//!< implicit valence
    char                          _type[6];	//!< 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 short int          _idx;		//!< index in parent (inherited)
    unsigned short            _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*
    vector3                       _v;		//!< coordinate vector
    OBResidue                    *_residue;	//!< parent residue (if applicable)
    //OBMol                      *_parent;      //!< parent molecule (inherited)
    //vector<OBBond*>             _bond;	//!< connections (inherited)
    std::vector<OBGenericData*>   _vdata;	//!< custom data

    int  GetFlag() const    {  return(_flags);  }
    void SetFlag(int flag)  { _flags |= flag;   }
    bool HasFlag(int flag)  {  return((_flags & flag) ? true : false); }

public:

    //! Constructor
    OBAtom();
    //! Destructor
    virtual ~OBAtom();
    //! Assignment
    OBAtom &operator = (OBAtom &);
    //! Clear all data
    void 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; }
    //! 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);
    void SetImplicitValence(int val)    { _impval = (char)val; }
    void IncrementImplicitValence()     { _impval++; }
    void DecrementImplicitValence()     { _impval--; }
    void SetFormalCharge(int fcharge)   { _fcharge = fcharge; }
    void SetSpinMultiplicity(short spin){ _spinmultiplicity = spin; }
    void SetType(char *type);
    void SetType(std::string &type);
    void SetPartialCharge(double pcharge){ _pcharge = pcharge; }
    void SetVector(vector3 &v);
    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();
    void SetResidue(OBResidue *res)     { _residue=res; }
    //  void SetParent(OBMol *ptr)      { _parent=ptr; } // inherited
    void SetAromatic()                  { SetFlag(OB_AROMATIC_ATOM); }
    void UnsetAromatic()                { _flags &= (~(OB_AROMATIC_ATOM)); }
    //! Mark atom as having SMILES clockwise stereochemistry (i.e., "@@")
    void SetClockwiseStereo()           { SetFlag(OB_CSTEREO_ATOM|OB_CHIRAL_ATOM); }
    //! Mark atom as having SMILES anticlockwise stereochemistry (i.e., "@")
    void SetAntiClockwiseStereo()       { SetFlag(OB_ACSTEREO_ATOM|OB_CHIRAL_ATOM); }
    //! Mark an atom as having + chiral volume
    void SetPositiveStereo() { SetFlag(OB_POS_CHIRAL_ATOM|OB_CHIRAL_ATOM); }
    //! Mark an atom as having - chiral volume
    void SetNegativeStereo() { SetFlag(OB_NEG_CHIRAL_ATOM|OB_CHIRAL_ATOM); }
    //! Clear all stereochemistry information
    void UnsetStereo()
    {
        _flags &= ~(OB_ACSTEREO_ATOM);
        _flags &= ~(OB_CSTEREO_ATOM);
	_flags &= ~(OB_POS_CHIRAL_ATOM);
	_flags &= ~(OB_NEG_CHIRAL_ATOM);
        _flags &= ~(OB_CHIRAL_ATOM);
    }
    //! Mark an atom as belonging to at least one ring
    void SetInRing()         { SetFlag(OB_RING_ATOM); }
    //! Mark an atom as being chiral with unknown stereochemistry
    void SetChiral()         { SetFlag(OB_CHIRAL_ATOM); }
    //! Clear the internal coordinate pointer
    void ClearCoordPtr()     { _c = NULL; _cidx=0; }
    //@}

    //! \name Methods to retrieve atomic information
    //@{
    //int        GetStereo()        const { return((int)_stereo);}
    int          GetFormalCharge()  const { return(_fcharge);    }
    unsigned int GetAtomicNum()     const { return((unsigned int)_ele); }
    unsigned short int GetIsotope() const { return(_isotope);    }
    int          GetSpinMultiplicity() const { return(_spinmultiplicity); }
    //! The atomic mass of this atom given by standard IUPAC average molar mass
    double	 GetAtomicMass()    const;
    //! The atomic mass of given by the isotope (default of 0 s most abundant isotope)
    double	 GetExactMass()	    const;
    unsigned int GetIdx()           const { return((int)_idx);  }
    unsigned int GetCoordinateIdx() const { return((int)_cidx); }
    //! \deprecated Use GetCoordinateIdx() instead
    unsigned int GetCIdx()          const { return((int)_cidx); }
    //! The current number of explicit connections
    unsigned int GetValence()       const
    {
        return((_vbond.empty()) ? 0 : _vbond.size());
    }
    //! The hybridization of this atom (i.e. 1 for sp, 2 for sp2, 3 for sp3)
    unsigned int GetHyb()             const;
    //! The implicit valence of this atom type (i.e. maximum number of connections expected)
    unsigned int GetImplicitValence() const;
    //! The number of non-hydrogens connected to this atom
    unsigned int GetHvyValence()      const;
    //! The number of heteroatoms connected to an atom
    unsigned int GetHeteroValence()   const;
    char        *GetType();

    //! The x coordinate
    double      GetX()    {        return(x());    }
    //! The y coordinate
    double      GetY()    {        return(y());    }
    //! The z coordinate
    double      GetZ()    {        return(z());    }
    double      x()
    {
        if (_c)
            return((*_c)[_cidx]);
        else
            return _v.x();
    }
    double      y()
    {
        if (_c)
            return((*_c)[_cidx+1]);
        else
            return _v.y();
    }
    double      z()
    {
        if (_c)
            return((*_c)[_cidx+2]);
        else
            return _v.z();
    }
    //! \return the coordinates as a double*
    double     *GetCoordinate()
    {
        return(&(*_c)[_cidx]);
    }
    //! \return the coordinates as a vector3 object
    vector3   &GetVector();
    //! \return the partial charge of this atom, calculating a Gasteiger charge if needed
    double     GetPartialCharge();
    OBResidue *GetResidue();
    //OBMol   *GetParent()        {return((OBMol*)_parent);}
    //! Create a vector for a new bond from this atom, with length given by the supplied parameter
    bool       GetNewBondVector(vector3 &v,double length);
    OBBond    *GetBond(OBAtom *);
    OBAtom    *GetNextAtom();
    //@}

    //! \name Iterator methods
    //@{
    //! \deprecated Use FOR_BONDS_OF_ATOM and OBAtomBondIter instead
    std::vector<OBEdgeBase*>::iterator BeginBonds()
      { return(_vbond.begin()); }
    //! \deprecated Use FOR_BONDS_OF_ATOM and OBAtomBondIter instead
    std::vector<OBEdgeBase*>::iterator EndBonds()
      { return(_vbond.end());   }
    //! \deprecated Use FOR_BONDS_OF_ATOM and OBAtomBondIter instead
    OBBond *BeginBond(std::vector<OBEdgeBase*>::iterator &i);
    //! \deprecated Use FOR_BONDS_OF_ATOM and OBAtomBondIter instead
    OBBond *NextBond(std::vector<OBEdgeBase*>::iterator &i);
    //! \deprecated Use FOR_NBORS_OF_ATOM and OBAtomAtomIter instead
    OBAtom *BeginNbrAtom(std::vector<OBEdgeBase*>::iterator &);
    //! \deprecated Use FOR_NBORS_OF_ATOM and OBAtomAtomIter instead
    OBAtom *NextNbrAtom(std::vector<OBEdgeBase*>::iterator &);
    //@}

    //! \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 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
    //@{
    void NewResidue()
    {
        if (!_residue)
            _residue = new OBResidue;
    }
    void DeleteResidue()
    {
        if (_residue)
            delete _residue;
    }
    void AddBond(OBBond *bond)
    {
        _vbond.push_back((OBEdgeBase*)bond);
    }
    void InsertBond(std::vector<OBEdgeBase*>::iterator &i, OBBond *bond)
    {
        _vbond.insert(i, (OBEdgeBase*)bond);
    }
    bool DeleteBond(OBBond*);
	void ClearBond() {_vbond.clear();}
    //@}

    //! \name Requests for atomic property information
    //@{
    //! The number of oxygen atoms connected that only have one heavy valence
    unsigned int  CountFreeOxygens()      const;
    //! The number of hydrogens needed to fill the implicit valence of this atom
    unsigned int  ImplicitHydrogenCount() const;
    //! The number of hydrogens explicitly bound to this atom currently
    unsigned int  ExplicitHydrogenCount() const;
    //! The number of rings that contain this atom
    unsigned int  MemberOfRingCount()     const;
    //! The size of the smallest ring that contains this atom (0 if not in a ring)
    unsigned int  MemberOfRingSize()	  const;
    //! The smallest angle of bonds to this atom
    double	  SmallestBondAngle();
    //! The average angle of bonds to this atom
    double	  AverageBondAngle();
    //! The sum of the bond orders of the bonds to the atom (i.e. double bond = 2...)
    unsigned int  BOSum()                 const;
    //! The sum of the bond orders of bonds to the atom, considering only KDouble, KTriple bonds
    unsigned int  KBOSum()                const;
    //@}

    //! \name Builder utilities
    //@{
    //! If this is a hydrogen atom, transform into a methyl group
    bool HtoMethyl();
    //! Change the hybridization of this atom and modify the geometry accordingly
    bool SetHybAndGeom(int);
    //@}

    //! \name Property information
    //@{
    //! Is there any residue information?
    bool HasResidue()    { return(_residue != NULL);    }
    bool IsHydrogen()    { return(GetAtomicNum() == 1); }
    bool IsCarbon()      { return(GetAtomicNum() == 6); }
    bool IsNitrogen()    { return(GetAtomicNum() == 7); }
    bool IsOxygen()      { return(GetAtomicNum() == 8); }
    bool IsSulfur()      { return(GetAtomicNum() == 16);}
    bool IsPhosphorus()  { return(GetAtomicNum() == 15);}
    bool IsAromatic()      const;
    bool IsInRing()        const;
    bool IsInRingSize(int) const;
    //! Is this atom an element in the 15th or 16th main groups (i.e., N, O, P, S ...) ?
    bool IsHeteroatom();
    //! Is this atom any element except carbon or hydrogen?
    bool IsNotCorH();
    //! Is this atom connected to the supplied OBAtom?
    bool IsConnected(OBAtom*);
    //! Is this atom related to the supplied OBAtom in a 1,3 bonding pattern?
    bool IsOneThree(OBAtom*);
    //! Is this atom related to the supplied OBAtom in a 1,4 bonding pattern?
    bool IsOneFour(OBAtom*);
    //! Is this atom an oxygen in a carboxyl (-CO2 or CO2H) group?
    bool IsCarboxylOxygen();
    //! Is this atom an oxygen in a phosphate (R-PO3) group? 
    bool IsPhosphateOxygen();
    //! Is this atom an oxygen in a sulfate (-SO3) group?
    bool IsSulfateOxygen();
    //! Is this atom an oxygen in a nitro (-NO2) group?
    bool IsNitroOxygen();
    bool IsAmideNitrogen();
    bool IsPolarHydrogen();
    bool IsNonPolarHydrogen();
    bool IsAromaticNOxide();
    //! Is this atom chiral?
    bool IsChiral();
    bool IsAxial();
    //! Does this atom have SMILES-specified clockwise "@@" stereochemistry?
    bool IsClockwise()         { return(HasFlag(OB_CSTEREO_ATOM));  }
    //! Does this atom have SMILES-specified anticlockwise "@" stereochemistry?
    bool IsAntiClockwise()     { return(HasFlag(OB_ACSTEREO_ATOM)); }
    //! Does this atom have a positive chiral volume?
    bool IsPositiveStereo() { return(HasFlag(OB_POS_CHIRAL_ATOM)); }
    //! Does this atom have a negative chiral volume?
    bool IsNegativeStereo() { return(HasFlag(OB_NEG_CHIRAL_ATOM)); }
    //! Does this atom have SMILES-specified stereochemistry?
    bool HasChiralitySpecified()
      { return(HasFlag(OB_CSTEREO_ATOM|OB_ACSTEREO_ATOM)); }
    //! Does this atom have a specified chiral volume?
    bool HasChiralVolume()
      { return(HasFlag(OB_POS_CHIRAL_ATOM|OB_NEG_CHIRAL_ATOM)); }
    //! Is this atom a hydrogen-bond acceptor (receptor)?
    bool IsHbondAcceptor();
    //! Is this atom a hydrogen-bond donor?
    bool IsHbondDonor();
    //! Is this a hydrogen atom attached to a hydrogen-bond donor?
    bool IsHbondDonorH();
    bool HasAlphaBetaUnsat(bool includePandS=true);
    bool HasBondOfOrder(unsigned int);
    int  CountBondsOfOrder(unsigned int);
    bool HasNonSingleBond();
    bool HasSingleBond()    {        return(HasBondOfOrder(1));    }
    bool HasDoubleBond()    {        return(HasBondOfOrder(2));    }
    bool HasAromaticBond()  {        return(HasBondOfOrder(5));    }
    //! Determines if this atom matches the first atom in a given SMARTS pattern
    bool MatchesSMARTS(const char *);
    //@}

    //! \name Methods for handling generic data
    //@{
    bool                              HasData(std::string &);
    bool                              HasData(const char *);
    bool                              HasData(unsigned int type);
    void                              DeleteData(unsigned int type);
    void                              DeleteData(OBGenericData*);
    void                              DeleteData(std::vector<OBGenericData*>&);
    void                              SetData(OBGenericData *d)
    {        _vdata.push_back(d);    }
    //! \return the number of OBGenericData items attached to this atom
    unsigned int                      DataSize()
    {        return(_vdata.size());    }
    OBGenericData                    *GetData(unsigned int type);
    OBGenericData                    *GetData(std::string&);
    OBGenericData                    *GetData(const char *);
    std::vector<OBGenericData*>      &GetData() { return(_vdata); }
    std::vector<OBGenericData*>::iterator  BeginData()
    {        return(_vdata.begin());    }
    std::vector<OBGenericData*>::iterator  EndData()
    {        return(_vdata.end());      }
    //@}
}; // class OBAtom


// Class OBBond

//BOND Property Macros (flags)
//! An aromatic bond (regardless of bond order)
#define OB_AROMATIC_BOND  (1<<1)
//! A solid black wedge in 2D representations -- i.e., "up" from the 2D plane
#define OB_WEDGE_BOND     (1<<2)
//! A dashed "hash" bond in 2D representations -- i.e., "down" from the 2D plane
#define OB_HASH_BOND      (1<<3)
//! A bond in a ring
#define OB_RING_BOND      (1<<4)
//! The "upper" bond in a double bond cis/trans isomer (i.e., "/" in SMILES)
#define OB_TORUP_BOND     (1<<5)
//! The "down" bond in a double bond cis/trans isomer (i.e., "\" in SMILES)
#define OB_TORDOWN_BOND   (1<<6)
//! A Kekule single bond
#define OB_KSINGLE_BOND   (1<<7)
//! A Kekule double bond
#define OB_KDOUBLE_BOND   (1<<8)
//! A Kekule triple bond
#define OB_KTRIPLE_BOND   (1<<9)
#define OB_CLOSURE_BOND   (1<<10)
// 11-16 currently unused

// class introduction in bond.cpp
class OBAPI OBBond : public OBEdgeBase
{
protected:
    char                          _order; //!< Bond order (1, 2, 3, 5=aromatic)
    unsigned short int            _flags; //!< Any flags for this bond
    //OBAtom                     *_bgn;   //!< Not needed, inherited from OBEdgeBase
    //OBAtom                     *_end;   //!< Not needed, inherited from OBEdgeBase
    //OBMol                      *_parent;//!< Not needed, inherited from OBEdgeBase
    //unsigned short int          _idx;   //!< Not needed, inherited from OBEdgeBase
    std::vector<OBGenericData*>   _vdata; //!< Generic data for custom information

    bool HasFlag(int flag)    { return((_flags & flag) != 0); }
    void SetFlag(int flag)    { _flags |= flag;               }

public:
    //! Constructor
    OBBond();
    //! Destructor
    virtual ~OBBond();

    //! \name Bond modification methods
    //@{
    void SetIdx(int idx)
    {
        _idx = idx;
    }
    void SetBO(int order);
    void SetBegin(OBAtom *begin)
    {
        _bgn = begin;
    }
    void SetEnd(OBAtom *end)
    {
        _end = end;
    }
    // void SetParent(OBMol *ptr)               {_parent=ptr;} // (inherited)
    void SetLength(OBAtom*,double);
    void Set(int,OBAtom*,OBAtom*,int,int);
    void SetKSingle();
    void SetKDouble();
    void SetKTriple();
    void SetAromatic()    { SetFlag(OB_AROMATIC_BOND); }
    void SetHash()        { SetFlag(OB_HASH_BOND);     }
    void SetWedge()       { SetFlag(OB_WEDGE_BOND);    }
    void SetUp()          { SetFlag(OB_TORUP_BOND);    }
    void SetDown()        { SetFlag(OB_TORDOWN_BOND);  }
    void SetInRing()      { SetFlag(OB_RING_BOND);     }
    void SetClosure()     { SetFlag(OB_CLOSURE_BOND);  }

    void UnsetAromatic()  { _flags &= (~(OB_AROMATIC_BOND)); }
    void UnsetKekule()
    {
        _flags &= (~(OB_KSINGLE_BOND|OB_KDOUBLE_BOND|OB_KTRIPLE_BOND));
    }
    //@}

    //! \name bond data request methods
    //@{
    unsigned int     GetBO()            const { return((int)_order); }
    unsigned int     GetBondOrder()     const { return((int)_order); }
    unsigned int     GetFlags()         const { return(_flags);      }
    unsigned int     GetBeginAtomIdx()  const { return(_bgn->GetIdx()); }
    unsigned int     GetEndAtomIdx()    const { return(_end->GetIdx()); }
    OBAtom *GetBeginAtom()    { return((OBAtom*)_bgn);    }
    OBAtom *GetEndAtom()      { return((OBAtom*)_end);    }
    OBAtom *GetNbrAtom(OBAtom *ptr)
    {
        return((ptr != _bgn)? (OBAtom*)_bgn : (OBAtom*)_end);
    }
    // OBMol  *GetParent()                 {return(_parent);}  // (inherited)
    double   GetEquibLength();
    double   GetLength();
    int     GetNbrAtomIdx(OBAtom *ptr)
    {
        return((ptr!=_bgn)?_bgn->GetIdx():_end->GetIdx());
    }
    //@}

    //! \name property request methods
    //@{
    bool IsAromatic() const;
    bool IsInRing() const;
    bool IsRotor();
    bool IsAmide();
    bool IsPrimaryAmide();
    bool IsSecondaryAmide();
    bool IsEster();
    bool IsCarbonyl();
    bool IsSingle();
    bool IsDouble();
    bool IsTriple();
    bool IsKSingle();
    bool IsKDouble();
    bool IsKTriple();
    bool IsClosure();
    //! \return whether this is the "upper" bond in a double bond cis/trans
    //!   isomer (i.e., "/" in SMILES)
    bool IsUp()    {    return(HasFlag(OB_TORUP_BOND));    }
    //! \return whether this is the "lower" bond in a double bond cis/trans
    //!   isomer (i.e., "\" in SMILES)
    bool IsDown()  {    return(HasFlag(OB_TORDOWN_BOND));  }
    bool IsWedge() {    return(HasFlag(OB_WEDGE_BOND));    }
    bool IsHash()  {    return(HasFlag(OB_HASH_BOND));     }
    //! \return whether the geometry around this bond looks unsaturated
    bool IsDoubleBondGeometry();
    //@}

    //! \name Methods for handling generic data
    //@{
    bool                              HasData(std::string &);
    bool                              HasData(const char *);
    bool                              HasData(unsigned int type);
    void                              DeleteData(unsigned int type);
    void                              DeleteData(OBGenericData*);
    void                              DeleteData(std::vector<OBGenericData*>&);
    void                              SetData(OBGenericData *d)
    {
        _vdata.push_back(d);
    }
    //! \return the number of OBGenericData items attached to this bond
    unsigned int                      DataSize()
    {
        return(_vdata.size());
    }
    OBGenericData                    *GetData(unsigned int type);
    OBGenericData                    *GetData(std::string&);
    OBGenericData                    *GetData(const char *);
    std::vector<OBGenericData*>           &GetData()
    {
        return(_vdata);
    }
    std::vector<OBGenericData*>::iterator  BeginData()
    {
        return(_vdata.begin());
    }
    std::vector<OBGenericData*>::iterator  EndData()
    {
        return(_vdata.end());
    }
    //@}
}
; // class OBBond


// Class OBMol

//MOL Property Macros (flags) -- 32+ bits
#define OB_SSSR_MOL              (1<<1)
#define OB_RINGFLAGS_MOL         (1<<2)
#define OB_AROMATIC_MOL          (1<<3)
#define OB_ATOMTYPES_MOL         (1<<4)
#define OB_CHIRALITY_MOL         (1<<5)
#define OB_PCHARGE_MOL           (1<<6)
#define OB_HYBRID_MOL            (1<<8)
#define OB_IMPVAL_MOL            (1<<9)
#define OB_KEKULE_MOL            (1<<10)
#define OB_CLOSURE_MOL           (1<<11)
#define OB_H_ADDED_MOL           (1<<12)
#define OB_PH_CORRECTED_MOL      (1<<13)
#define OB_AROM_CORRECTED_MOL    (1<<14)
#define OB_CHAINS_MOL            (1<<15)
#define OB_TCHARGE_MOL		 (1<<16)
#define OB_TSPIN_MOL             (1<<17)
// flags 18-32 unspecified
#define OB_CURRENT_CONFORMER	 -1

// class introduction in mol.cpp
class OBAPI OBMol : public OBGraphBase
{
protected:
    int                           _flags;	//!< bitfield of flags
    bool                          _autoPartialCharge; //!< Assign partial charges automatically
    bool                          _autoFormalCharge; //!< Assign formal charges automatically
    std::string                   _title;	//!< Molecule title
    //vector<OBAtom*>             _atom;	//!< not needed (inherited)
    //vector<OBBond*>             _bond;	//!< not needed (inherited)
    unsigned short int            _dimension;   //!< Dimensionality of coordinates
    double                        _energy;      //!< Molecular heat of formation (if applicable)
    int				  _totalCharge; //!< Total charge on the molecule
    unsigned int                  _totalSpin;   //!< Total spin on the molecule (if not specified, assumes lowest possible spin)
    double                       *_c;	        //!< coordinate array
    std::vector<double*>          _vconf;       //!< vector of conformers
    unsigned short int            _natoms;      //!< Number of atoms
    unsigned short int            _nbonds;      //!< Number of bonds
    std::vector<OBResidue*>       _residue;     //!< Residue information (if applicable)
    std::vector<OBInternalCoord*> _internals;   //!< Internal Coordinates (if applicable)
    std::vector<OBGenericData*>   _vdata;       //!< Custom data -- see OBGenericData class for more
    unsigned short int            _mod;	        //!< Number of nested calls to BeginModify()

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

    //! \name Internal Kekulization routines -- see kekulize.cpp and NewPerceiveKekuleBonds()
    //@{
    void start_kekulize(std::vector <OBAtom*> &cycle, std::vector<int> &electron);
    int expand_kekulize(OBAtom *atom1, OBAtom *atom2, std::vector<int> &currentState, std::vector<int> &initState, std::vector<int> &bcurrentState, std::vector<int> &binitState, std::vector<bool> &mark);
    int getorden(OBAtom *atom);
    void expandcycle(OBAtom *atom, OBBitVec &avisit);
    //@}

public:

    //! \name Initialization and data (re)size methods
    //@{
    //! Constructor
    OBMol();
    //! Copy constructor
    OBMol(const OBMol &);
    //! Destructor
    virtual ~OBMol();
    //! Assignment
    OBMol &operator=(const OBMol &mol);
    OBMol &operator+=(const OBMol &mol);
    void ReserveAtoms(int natoms)
    {
        if (natoms && _mod)
            _vatom.reserve(natoms);
    }
    virtual OBAtom *CreateAtom(void);
    virtual OBBond *CreateBond(void);
    virtual void DestroyAtom(OBNodeBase*);
    virtual void DestroyBond(OBEdgeBase*);
    bool AddAtom(OBAtom&);
    bool AddBond(int,int,int,int flags=0,int insertpos=-1);
    bool AddBond(OBBond&);
    bool AddResidue(OBResidue&);
    bool InsertAtom(OBAtom &);
    bool DeleteAtom(OBAtom*);
    bool DeleteBond(OBBond*);
    bool DeleteResidue(OBResidue*);
    OBAtom    *NewAtom();
    OBResidue *NewResidue();
    //@}

    //! \name Molecule modification methods
    //@{
    //! Call when making many modifications -- clears conformer/rotomer data.
    virtual void BeginModify(void);
    //! Call when done with modificaions -- re-perceive data as needed.
    virtual void EndModify(bool nukePerceivedData=true);
    int GetMod()
    {
        return(_mod);
    }
    void IncrementMod()
    {
        _mod++;
    }
    void DecrementMod()
    {
        _mod--;
    }
    //@}

    //! \name Generic data handling methods (via OBGenericData)
    //@{
    //! \returns whether the generic attribute/value pair exists
    bool                              HasData(std::string &);
    //! \returns whether the generic attribute/value pair exists
    bool                              HasData(const char *);
    //! \returns whether the generic attribute/value pair exists
    bool                              HasData(unsigned int type);
    void                              DeleteData(unsigned int type);
    void                              DeleteData(OBGenericData*);
    void                              DeleteData(std::vector<OBGenericData*>&);
    void                              SetData(OBGenericData *d)
    {
        _vdata.push_back(d);
    }
    //! \return the number of OBGenericData items attached to this molecule.
    unsigned int                      DataSize(){ return(_vdata.size()); }
    OBGenericData                    *GetData(unsigned int type);
    OBGenericData                    *GetData(std::string&);
    OBGenericData                    *GetData(const char *);
    std::vector<OBGenericData*>      &GetData() { return(_vdata); }
    std::vector<OBGenericData*>::iterator  BeginData()
    {
        return(_vdata.begin());
    }
    std::vector<OBGenericData*>::iterator  EndData()
    {
        return(_vdata.end());
    }
    //@}

    //! \name Data retrieval methods
    //@{
    int          GetFlags()               { return(_flags); }
    //! \return the title of this molecule (often the filename)
    const char  *GetTitle() const         { return(_title.c_str()); }
    //! \return the number of atoms (i.e. OBAtom children)
    unsigned int NumAtoms() const         {  return(_natoms); }
    //! \return the number of bonds (i.e. OBBond children)
    unsigned int NumBonds() const         {  return(_nbonds); }
    //! \return the number of non-hydrogen atoms
    unsigned int NumHvyAtoms();
    //! \return the number of residues (i.e. OBResidue substituents)
    unsigned int NumResidues() const      { return(_residue.size()); }
    //! \return the number of rotatble bonds
    unsigned int NumRotors();
    
    OBAtom      *GetAtom(int);
    OBAtom      *GetFirstAtom();
    OBBond      *GetBond(int);
    OBBond      *GetBond(int, int);
    OBBond      *GetBond(OBAtom*,OBAtom*);
    OBResidue   *GetResidue(int);
    std::vector<OBInternalCoord*> GetInternalCoord();
    //! \return the dihedral angle between the four atoms supplied a1-a2-a3-a4)
    double       GetTorsion(int,int,int,int);
    //! \return the dihedral angle between the four atoms supplied a1-a2-a3-a4)
    double       GetTorsion(OBAtom*,OBAtom*,OBAtom*,OBAtom*);
    //! \return the stochoimetric formula (e.g., C4H6O)
    std::string  GetFormula();
    //! \return the heat of formation for this molecule (in kcal/mol)
    double       GetEnergy() const { return(_energy); }
    //! \return the standard molar mass given by IUPAC atomic masses (amu)
    double       GetMolWt();
    //! \return the mass given by isotopes (or most abundant isotope, if not specified)
    double	 GetExactMass();
    //! \return the total charge on this molecule (i.e., 0 = neutral, +1, -1...)
    int		 GetTotalCharge();
    //! \return the total spin on this molecule (i.e., 1 = singlet, 2 = doublet...)
    unsigned int GetTotalSpinMultiplicity();
    //! \return the dimensionality of coordinates (i.e., 0 = unknown or no coord, 2=2D, 3=3D)
    unsigned short int GetDimension() const { return _dimension; }
    double      *GetCoordinates() { return(_c); }
    //! \return the Smallest Set of Smallest Rings has been run (see OBRing class
    std::vector<OBRing*> &GetSSSR();
    //! Get the current flag for whether formal charges are set with pH correction
    bool AutomaticFormalCharge()   { return(_autoFormalCharge);  }
    //! Get the current flag for whether partial charges are auto-determined
    bool AutomaticPartialCharge()  { return(_autoPartialCharge); }
    //@}


    //! \name Data modification methods
    //@{
    void   SetTitle(const char *title);
    void   SetTitle(std::string &title);
    //! Set the stochiometric formula for this molecule
    void   SetFormula(std::string molFormula);
    //! Set the heat of formation for this molecule (in kcal/mol)
    void   SetEnergy(double energy) { _energy = energy; }
    //! Set the dimension of this molecule (i.e., 0, 1 , 2, 3)
    void   SetDimension(unsigned short int d) { _dimension = d; }
    void   SetTotalCharge(int charge);
    void   SetTotalSpinMultiplicity(unsigned int spin);
    void   SetInternalCoord(std::vector<OBInternalCoord*> int_coord)
      { _internals = int_coord; }
    //! Set the flag for determining automatic formal charges with pH (default=true)
    void SetAutomaticFormalCharge(bool val)
    { _autoFormalCharge=val;  }
    //! Set the flag for determining partial charges automatically (default=true)
    void SetAutomaticPartialCharge(bool val)
    { _autoPartialCharge=val; }

    //! Mark that aromaticity has been perceived for this molecule (see OBAromaticTyper)
    void   SetAromaticPerceived()    { SetFlag(OB_AROMATIC_MOL);    }
    //! Mark that Smallest Set of Smallest Rings has been run (see OBRing class)
    void   SetSSSRPerceived()        { SetFlag(OB_SSSR_MOL);        }
    //! Mark that rings have been perceived (see OBRing class for details)
    void   SetRingAtomsAndBondsPerceived(){SetFlag(OB_RINGFLAGS_MOL);}
    //! Mark that atom types have been perceived (see OBAtomTyper for details)
    void   SetAtomTypesPerceived()   { SetFlag(OB_ATOMTYPES_MOL);   }
    //! Mark that chains and residues have been perceived (see OBChainsParser)
    void   SetChainsPerceived()      { SetFlag(OB_CHAINS_MOL);      }
    //! Mark that chirality has been perceived
    void   SetChiralityPerceived()   { SetFlag(OB_CHIRALITY_MOL);   }
    //! Mark that partial charges have been assigned
    void   SetPartialChargesPerceived(){ SetFlag(OB_PCHARGE_MOL);   }
    void   SetHybridizationPerceived() { SetFlag(OB_HYBRID_MOL);    }
    void   SetImplicitValencePerceived(){ SetFlag(OB_IMPVAL_MOL);   }
    void   SetKekulePerceived()      { SetFlag(OB_KEKULE_MOL);      }
    void   SetClosureBondsPerceived(){ SetFlag(OB_CLOSURE_MOL);     }
    void   SetHydrogensAdded()       { SetFlag(OB_H_ADDED_MOL);     }
    void   SetCorrectedForPH()       { SetFlag(OB_PH_CORRECTED_MOL);}
    void   SetAromaticCorrected()    { SetFlag(OB_AROM_CORRECTED_MOL);}
    void   SetSpinMultiplicityAssigned(){ SetFlag(OB_TSPIN_MOL);    }
    void   SetFlags(int flags)       { _flags = flags;              }

    void   UnsetAromaticPerceived()  { _flags &= (~(OB_AROMATIC_MOL));   }
    void   UnsetPartialChargesPerceived(){ _flags &= (~(OB_PCHARGE_MOL));}
    void   UnsetImplicitValencePerceived(){_flags &= (~(OB_IMPVAL_MOL)); }
    void   UnsetFlag(int flag)       { _flags &= (~(flag));              }

    //! \name Molecule modification methods
    //@{
    // Description in transform.cpp
    virtual OBBase*    DoTransformations(const std::map<std::string,std::string>* pOptions);
    static const char* ClassDescription();
    //! Clear all information from a molecule
    bool Clear();
    //! Renumber the atoms of this molecule according to the order in the supplied vector
    void RenumberAtoms(std::vector<OBNodeBase*>&);
    //! Translate one conformer and rotate by a rotation matrix (which is returned) to the inertial frame-of-reference
    void ToInertialFrame(int conf, double *rmat);
    //! Translate all conformers to the inertial frame-of-reference
    void ToInertialFrame();
    //! Translates all conformers in the molecule by the supplied vector
    void Translate(const vector3 &v);
    //! Translates one conformer in the molecule by the supplied vector
    void Translate(const vector3 &v, int conf);
    void Rotate(const double u[3][3]);
    void Rotate(const double m[9]);
    void Rotate(const double m[9],int nconf);
    //! Translate to the center of all coordinates (for this conformer)
    void Center();
    //! Transform to standard Kekule bond structure (presumably from an aromatic form)
    bool Kekulize();
    bool PerceiveKekuleBonds();

    void NewPerceiveKekuleBonds();

    bool DeleteHydrogen(OBAtom*);
    bool DeleteHydrogens();
    bool DeleteHydrogens(OBAtom*);
    bool DeleteNonPolarHydrogens();
    bool AddHydrogens(bool polaronly=false,bool correctForPH=true);
    bool AddHydrogens(OBAtom*);
    bool AddPolarHydrogens();

    //! Deletes all atoms except for the largest contiguous fragment
    bool StripSalts();
    //! Converts the charged form of coordinate bonds, e.g.[N+]([O-])=O to N(=O)=O 
    bool ConvertDativeBonds();

    bool CorrectForPH();
    bool AssignSpinMultiplicity();
    vector3 Center(int nconf);
    //! Set the torsion defined by these atoms, rotating bonded neighbors
    void SetTorsion(OBAtom*,OBAtom*,OBAtom*,OBAtom*,double);
    //@}

    //! \name Molecule utilities and perception methods
    //@{
    //! Find Smallest Set of Smallest Rings (see OBRing class for more details)
    void FindSSSR();
    void FindRingAtomsAndBonds();
    void FindChiralCenters();
    void FindChildren(std::vector<int> &,int,int);
    void FindChildren(std::vector<OBAtom*>&,OBAtom*,OBAtom*);
    void FindLargestFragment(OBBitVec &);
    //! Sort a list of contig fragments by size from largest to smallest
    //! Each vector<int> contains the atom numbers of a contig fragment
    void ContigFragList(std::vector<std::vector<int> >&);
    //! Aligns atom a on p1 and atom b along p1->p2 vector
    void Align(OBAtom*,OBAtom*,vector3&,vector3&);
    //! Adds single bonds based on atom proximity
    void ConnectTheDots();
    //! Attempts to perceive multiple bonds based on geometries
    void PerceiveBondOrders();
    void FindTorsions();
    // documented in mol.cpp: graph-theoretical distance for each atom
    bool         GetGTDVector(std::vector<int> &);
    // documented in mol.cpp: graph-invariant index for each atom
    void         GetGIVector(std::vector<unsigned int> &);
    // documented in mol.cpp: calculate symmetry-unique identifiers
    void         GetGIDVector(std::vector<unsigned int> &);
    //@}

    //! \name Methods to check for existence of properties
    //@{
    //! Are there non-zero coordinates in two dimensions (i.e. X and Y)?
    bool Has2D();
    //! Are there non-zero coordinates in all three dimensions (i.e. X, Y, Z)?
    bool Has3D();
    //! Are there any non-zero coordinates?
    bool HasNonZeroCoords();
    bool HasAromaticPerceived()     { return(HasFlag(OB_AROMATIC_MOL)); }
    bool HasSSSRPerceived()         { return(HasFlag(OB_SSSR_MOL));     }
    bool HasRingAtomsAndBondsPerceived(){return(HasFlag(OB_RINGFLAGS_MOL));}
    bool HasAtomTypesPerceived()    { return(HasFlag(OB_ATOMTYPES_MOL));}
    bool HasChiralityPerceived()    { return(HasFlag(OB_CHIRALITY_MOL));}
    bool HasPartialChargesPerceived() { return(HasFlag(OB_PCHARGE_MOL));}
    bool HasHybridizationPerceived() { return(HasFlag(OB_HYBRID_MOL));  }
    bool HasImplicitValencePerceived() { return(HasFlag(OB_IMPVAL_MOL));}
    bool HasKekulePerceived() { return(HasFlag(OB_KEKULE_MOL));         }
    bool HasClosureBondsPerceived() { return(HasFlag(OB_CLOSURE_MOL));  }
    bool HasChainsPerceived() { return(HasFlag(OB_CHAINS_MOL));         }
    bool HasHydrogensAdded() { return(HasFlag(OB_H_ADDED_MOL));         }
    bool HasAromaticCorrected() { return(HasFlag(OB_AROM_CORRECTED_MOL));}
    bool IsCorrectedForPH() { return(HasFlag(OB_PH_CORRECTED_MOL));     }
    bool HasSpinMultiplicityAssigned() { return(HasFlag(OB_TSPIN_MOL)); }
    //! Is this molecule chiral?
    bool IsChiral();
    //! Are there any atoms in this molecule?
    bool Empty()                       { return(_natoms == 0);          }
    //@}

    //! \name Multiple conformer member functions
    //@{
    int     NumConformers()    { return((_vconf.empty())?0:_vconf.size()); }
    void    SetConformers(std::vector<double*> &v);
    void    AddConformer(double *f)    {  _vconf.push_back(f);    }
    void    SetConformer(int i)        {  _c = _vconf[i];         }
    void    CopyConformer(double*,int);
    void    DeleteConformer(int);
    double  *GetConformer(int i)       {  return(_vconf[i]);      }
    double  *BeginConformer(std::vector<double*>::iterator&i)
      { i = _vconf.begin();
        return((i == _vconf.end()) ? NULL:*i); }
    double  *NextConformer(std::vector<double*>::iterator&i)
      { i++;
        return((i == _vconf.end()) ? NULL:*i); }
    std::vector<double*> &GetConformers() {   return(_vconf);     }
    //@}

    //! \name Iterator methods
    //@{
    //! \deprecated Use FOR_ATOMS_OF_MOL and OBMolAtomIter instead
    OBAtom *BeginAtom(std::vector<OBNodeBase*>::iterator &i);
    //! \deprecated Use FOR_ATOMS_OF_MOL and OBMolAtomIter instead
    OBAtom *NextAtom(std::vector<OBNodeBase*>::iterator &i);
    //! \deprecated Use FOR_BONDS_OF_MOL and OBMolBondIter instead
    OBBond *BeginBond(std::vector<OBEdgeBase*>::iterator &i);
    //! \deprecated Use FOR_BONDS_OF_MOL and OBMolBondIter instead
    OBBond *NextBond(std::vector<OBEdgeBase*>::iterator &i);
    //! \deprecated Use FOR_RESIDUES_OF_MOL and OBResidueIter instead
    OBResidue *BeginResidue(std::vector<OBResidue*>::iterator &i)
    {
        i = _residue.begin();
        return((i == _residue.end()) ? NULL:*i);
    }
    //! \deprecated Use FOR_RESIDUES_OF_MOL and OBResidueIter instead
    OBResidue *NextResidue(std::vector<OBResidue*>::iterator &i)
    {
        i++;
        return((i == _residue.end()) ? NULL:*i);
    }
    OBInternalCoord *BeginInternalCoord(std::vector<OBInternalCoord*>::iterator &i)
    {
        i = _internals.begin();
        return((i == _internals.end()) ? NULL:*i);
    }
    OBInternalCoord *NextInternalCoord(std::vector<OBInternalCoord*>::iterator &i)
    {
        i++;
        return((i == _internals.end()) ? NULL:*i);
    }
    //@}

    //  Removed with OBConversion framework -- see OBConversion class instead
    //! \name Convenience functions for I/O
    //@{
    // friend std::ostream&       operator<< ( std::ostream&, OBMol& ) ;
    // friend std::istream&       operator>> ( std::istream&, OBMol& ) ;
    //@}
};

//! \brief Used to transform from z-matrix to cartesian coordinates.
class OBAPI OBInternalCoord
{
public:
    //class members
    OBAtom *_a,*_b,*_c;
    double   _dst,_ang,_tor;
    //! Constructor
    OBInternalCoord(OBAtom *a=(OBAtom*)NULL,
                    OBAtom *b=(OBAtom*)NULL,
                    OBAtom *c=(OBAtom*)NULL)
    {
        _a = a;
        _b = b;
        _c = c;
        _dst = _ang = _tor = 0.0;
    }
};

//function prototypes

OBAPI bool tokenize(std::vector<std::string>&, const char *buf, const char *delimstr=" \t\n");
OBAPI bool tokenize(std::vector<std::string>&, std::string&, const char *delimstr=" \t\n", int limit=-1);
//! remove leading and trailing whitespace from a string
OBAPI void Trim(std::string& txt);
//! \deprecated -- use OBMessageHandler class instead
OBAPI void ThrowError(char *str);
//! \deprecated -- use OBMessageHandler class instead
OBAPI void ThrowError(std::string &str);
OBAPI void CartesianToInternal(std::vector<OBInternalCoord*>&,OBMol&);
OBAPI void InternalToCartesian(std::vector<OBInternalCoord*>&,OBMol&);
OBAPI std::string NewExtension(std::string&,char*);
// Now handled by OBConversion class
// OBAPI bool SetInputType(OBMol&,std::string&);
// OBAPI bool SetOutputType(OBMol&,std::string&);

//global definitions
//! Global OBElementTable for element properties
EXTERN  OBElementTable   etab;
//! Global OBTypeTable for translating between different atom types
//! (e.g., Sybyl <-> MM2)
EXTERN  OBTypeTable      ttab;
//! Global OBIsotopeTable for isotope properties
EXTERN  OBIsotopeTable   isotab;
//! Global OBAromaticTyper for detecting aromatic atoms and bonds
EXTERN  OBAromaticTyper  aromtyper;
//! Global OBAtomTyper for marking internal valence, hybridization,
//!  and atom types (for internal and external use)
EXTERN  OBAtomTyper      atomtyper;
//! Global OBChainsParser for detecting macromolecular chains and residues
EXTERN  OBChainsParser   chainsparser;
//! Global OBMessageHandler error handler
EXTERN  OBMessageHandler obErrorLog;
//! Global OBResidueData biomolecule residue database
EXTERN  OBResidueData    resdat;

//Utility Macros

#ifndef BUFF_SIZE
#define BUFF_SIZE 32768
#endif

#ifndef EQ
#define EQ(a,b) (!strcmp((a), (b)))
#endif

#ifndef EQn
#define EQn(a,b,n) (!strncmp((a), (b), (n)))
#endif

#ifndef SQUARE
#define SQUARE(x) ((x)*(x))
#endif

#ifndef IsUnsatType
#define IsUnsatType(x)  (EQ(x,"Car") || EQ(x,"C2") || EQ(x,"Sox") || EQ(x,"Sac") || EQ(x,"Pac") || EQ(x,"So2"))
#endif

#ifndef __KCC
extern "C"
{
    OBAPI void  get_rmat(double*,double*,double*,int);
    OBAPI void  ob_make_rmat(double mat[3][3],double rmat[9]);
    OBAPI void  qtrfit (double *r,double *f,int size,double u[3][3]);
    OBAPI double superimpose(double*,double*,int);
}
#else
OBAPI void get_rmat(double*,double*,double*,int);
OBAPI void ob_make_rmat(double mat[3][3],double rmat[9]);
OBAPI void qtrfit (double *r,double *f,int size,double u[3][3]);
OBAPI double superimpose(double*,double*,int);
#endif // __KCC

} // end namespace OpenBabel

#endif // OB_MOL_H

//! \file
//! \brief Handle molecules. Declarations of OBMol, OBAtom, OBBond, OBResidue.
//!        (the main header for Open Babel)
