Stores information on rings in a molecule from SSSR perception. More...

#include <openbabel/ring.h>

Public Member Functions
size_t	Size () const
size_t	PathSize () const
bool	IsAromatic ()
void	SetType (char *type)
void	SetType (std::string &type)
char *	GetType ()
unsigned int	GetRootAtom ()
bool	IsMember (OBAtom *a)
bool	IsMember (OBBond *b)
bool	IsInRing (int i)
void	SetParent (OBMol *m)
OBMol *	GetParent ()
bool	findCenterAndNormal (vector3 &center, vector3 &norm1, vector3 &norm2)
Constructors
	OBRing ()
	OBRing (std::vector< int > &path, int size)
	OBRing (std::vector< int > &path, OBBitVec set)
	OBRing (const OBRing &src)
OBRing &	operator= (const OBRing &src)
Public Attributes
int	ring_id
std::vector< int >	_path
OBBitVec	_pathset

Detailed Description

Stores information on rings in a molecule from SSSR perception.

Ring information beyond atom and bond membership is usually not necessary, but more information can be had about the rings in a molecule. The OBRing class is used to store the information from a Smallest Set of Smallest Rings (SSSR) perception of a molecule. The OBMol member function OBMol::GetSSSR() stores the information it perceives in a vector<OBRing*> inside the molecule. Perception is only done once for a molecule unless the connection table is modified. The following code demonstrates how to extract the SSSR information:

    OBMol mol;

    vector<OBRing*> vr;
    vr = mol.GetSSSR();

OBRings store the atom numbers of the atoms in each of the smallest set of smallest rings in both a vector<int> and an OBBitVec. An example of how to print out the atom numbers present in all SSSR rings is show below:

    vector<OBRing*>::iterator i;
    vector<int>::iterator j;
    vector<OBRing*> *rlist = (vector<OBRing*>*)mol.GetData("RingList");
    for (i = rlist->begin();i != rlist->end();++i)
    {
       for(j = (*i)->_path.begin(); j != (*i)->_path.end(); ++j)
          cout << *j << ' ';
       cout << endl;
    }

will produce something like the following output for benzene:

    1 2 3 4 5 6

Ring information is automatically deleted from an OBMol when it goes out of scope or the OBMol::Clear() member function is called.

Implements blue-obelisk:findSmallestSetOfSmallestRings.

Constructor & Destructor Documentation

OBRing ( ) [inline]

OBRing	(	std::vector< int > &	path,
		int	size
	)

Initialize a ring from a set of atom indexes path and with size.

OBRing	(	std::vector< int > &	path,
		OBBitVec	set
	)		`[inline]`

OBRing ( const OBRing & src )

OBRing copy constructor.

Parameters:

src	reference to original OBRing object (rhs)

Member Function Documentation

OBRing & operator= ( const OBRing & src )

OBRing assignment operator.

Parameters:

src	reference to original OBRing object (rhs)

Returns:: reference to modified OBRing object (lhs)

size_t Size ( ) const [inline]

Returns:: the size of this ring (i.e., how many atoms in the cycle)

Referenced by OpenBabel::CompareRingSize(), and OBBond::FindSmallestRing().

size_t PathSize ( ) const [inline]

Returns:: the size of this ring (i.e., how many atoms in the cycle)

Deprecated:: Use Size() instead

bool IsAromatic ( )

Returns:: whether this ring is aromatic If all atoms in this ring are aromatic, the ring will be considered aromatic

Todo:: This method uses implicit bonding -- bond info is not stored in OBRing

void SetType ( char * type )

Set the ring type (see OBRingTyper for more)

void SetType ( std::string & type )

Set the ring type (see OBRingTyper for more)

char * GetType ( void )

Returns:: the ring type

unsigned int GetRootAtom ( )

Returns:: the index for the root atom. O for furan, S for thiazole, N for pyrrole. For 6 membered aromatic rings, the first non carbon atom is used for root. For 5 members rings the O, S or N (BOSum=3, valence=3) will be used for root

bool IsMember ( OBAtom * a )