00001 /**********************************************************************
00002 bond.h - Handle OBBond class.
00003  
00004 Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
00005 Some portions Copyright (C) 2001-2006 by Geoffrey R. Hutchison
00006 Some portions Copyright (C) 2003 by Michael Banck
00007  
00008 This file is part of the Open Babel project.
00009 For more information, see <http://openbabel.sourceforge.net/>
00010  
00011 This program is free software; you can redistribute it and/or modify
00012 it under the terms of the GNU General Public License as published by
00013 the Free Software Foundation version 2 of the License.
00014  
00015 This program is distributed in the hope that it will be useful,
00016 but WITHOUT ANY WARRANTY; without even the implied warranty of
00017 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
00018 GNU General Public License for more details.
00019 ***********************************************************************/
00020 
00021 #ifndef OB_BOND_H
00022 #define OB_BOND_H
00023 
00024 #include <openbabel/babelconfig.h>
00025 
00026 #ifndef EXTERN
00027 #  define EXTERN extern
00028 #endif
00029 
00030 #include <openbabel/base.h>
00031 #include <openbabel/atom.h>
00032 
00033 namespace OpenBabel
00034 {
00035 
00036   class OBAtom;
00037 
00039   typedef OBBond OBEdgeBase;
00040 
00041   //BOND Property Macros (flags)
00043 #define OB_AROMATIC_BOND  (1<<1)
00045 #define OB_WEDGE_BOND     (1<<2)
00047 #define OB_HASH_BOND      (1<<3)
00049 #define OB_RING_BOND      (1<<4)
00051 #define OB_TORUP_BOND     (1<<5)
00053 #define OB_TORDOWN_BOND   (1<<6)
00055 #define OB_KSINGLE_BOND   (1<<7)
00057 #define OB_KDOUBLE_BOND   (1<<8)
00059 #define OB_KTRIPLE_BOND   (1<<9)
00061 #define OB_CLOSURE_BOND   (1<<10)
00062   // 11-16 currently unused
00063 
00064   // class introduction in bond.cpp
00065  class OBAPI OBBond: public OBBase
00066     {
00067     protected:
00068       unsigned int                _idx;   
00069       OBMol                      *_parent;
00070       OBAtom                     *_bgn;   
00071       OBAtom                     *_end;   
00072 
00073       char                        _order; 
00074       unsigned short int          _flags; 
00075 
00076       bool HasFlag(int flag)    { return((_flags & flag) != 0); }
00077       void SetFlag(int flag)    { _flags |= flag;               }
00078       void UnsetFlag(int flag)  { _flags &= (~(flag));          }
00079 
00080     public:
00082 
00083       bool Visit;
00084 
00086       OBBond();
00088       virtual ~OBBond();
00089 
00091 
00092 
00093 
00095       void SetIdx(int idx)        {          _idx = idx;        }
00097 
00098       void SetBO(int order);
00100       void SetBondOrder(int order);
00102       void SetBegin(OBAtom *begin){          _bgn = begin;      }
00104       void SetEnd(OBAtom *end)    {          _end = end;        }
00106       void SetParent(OBMol *ptr)  {        _parent= ptr;        }
00108       void SetLength(OBAtom *fixed,double length);
00111       void SetLength(double length);
00113       void Set(int index, OBAtom* begin,OBAtom* end,int order,int flags);
00115       void SetKSingle();
00117       void SetKDouble();
00119       void SetKTriple();
00121       void SetAromatic()    { SetFlag(OB_AROMATIC_BOND); }
00123       void SetHash()        { SetFlag(OB_HASH_BOND);     }
00125       void SetWedge()       { SetFlag(OB_WEDGE_BOND);    }
00127       void SetUp()          { SetFlag(OB_TORUP_BOND); UnsetFlag(OB_TORDOWN_BOND); }
00129       void SetDown()        { SetFlag(OB_TORDOWN_BOND); UnsetFlag(OB_TORUP_BOND);   }
00131       void SetInRing()      { SetFlag(OB_RING_BOND);     }
00133 
00136       void SetClosure()     { SetFlag(OB_CLOSURE_BOND);  }
00138       void UnsetHash()      { UnsetFlag(OB_HASH_BOND);    }
00140       void UnsetWedge()     { UnsetFlag(OB_WEDGE_BOND);   }
00142       void UnsetUp()        { UnsetFlag(OB_TORUP_BOND);   }
00144       void UnsetDown()      { UnsetFlag(OB_TORDOWN_BOND); }
00146       void UnsetAromatic()  { UnsetFlag(OB_AROMATIC_BOND);}
00148       void UnsetKekule()
00149         {
00150           _flags &= (~(OB_KSINGLE_BOND|OB_KDOUBLE_BOND|OB_KTRIPLE_BOND));
00151         }
00153 
00155 
00156 
00157       unsigned int     GetIdx()           const { return(_idx);  }
00159 
00160       unsigned int     GetBO()            const { return(_order); }
00162       unsigned int     GetBondOrder()     const { return(_order); }
00164       unsigned int     GetFlags()         const { return(_flags);      }
00166       unsigned int     GetBeginAtomIdx()  const 
00167         { return (_bgn ? _bgn->GetIdx() : 0); }
00169       unsigned int     GetEndAtomIdx()    const 
00170         { return (_end ? _end->GetIdx() : 0); }
00172       OBAtom *GetBeginAtom()    { return(_bgn);    }
00173       const OBAtom *GetBeginAtom() const 
00174         { return(_bgn);    }
00176       OBAtom *GetEndAtom()      { return(_end);    }
00177       const OBAtom *GetEndAtom() const
00178         { return(_end);    }
00180 
00182       OBAtom *GetNbrAtom(OBAtom *ptr)
00183         {
00184           return((ptr != _bgn)? _bgn : _end);
00185         }
00187       OBMol  *GetParent()                 {return(_parent);}
00189 
00190       double  GetEquibLength() const;
00192       double  GetLength() const;
00194 
00196       unsigned int     GetNbrAtomIdx(OBAtom *ptr)
00197         {
00198           if (ptr!=_bgn)
00199             return (_bgn ? _bgn->GetIdx() : 0); 
00200           else
00201             return (_end ? _end->GetIdx() : 0); 
00202         }
00204 
00206 
00207 
00208 
00209 
00210       bool IsAromatic() const;
00212       bool IsInRing() const;
00214 
00219       bool IsRotor();
00221       bool IsAmide();
00223       bool IsPrimaryAmide();
00225       bool IsSecondaryAmide();
00227       bool IsEster();
00229       bool IsCarbonyl();
00231       bool IsSingle();
00233       bool IsDouble();
00235       bool IsTriple();
00237       bool IsKSingle();
00239       bool IsKDouble();
00241       bool IsKTriple();
00243       bool IsClosure();
00246       bool IsUp()    {    return(HasFlag(OB_TORUP_BOND));    }
00249       bool IsDown()  {    return(HasFlag(OB_TORDOWN_BOND));  }
00252       bool IsWedge() {    return(HasFlag(OB_WEDGE_BOND));    }
00255       bool IsHash()  {    return(HasFlag(OB_HASH_BOND));     }
00257       bool IsDoubleBondGeometry();
00259 
00260     }; // class OBBond
00261 
00263   typedef std::vector<OBBond*>::iterator OBBondIterator;
00264 
00265 }// namespace OpenBabel
00266 
00267 #endif   // OB_BOND_H
00268