OBRing Class Reference

#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() [1/4]

OBRing ( )

inline

OBRing() [2/4]

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

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

OBRing() [3/4]

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

inline

OBRing() [4/4]

OBRing

(

const OBRing &

src

)

OBRing copy constructor.

Parameters

src	reference to original OBRing object (rhs)

Member Function Documentation

operator=()

OBRing & operator=

(

const OBRing &

src

)

OBRing assignment operator.

Parameters

src	reference to original OBRing object (rhs)

Returns

reference to modified OBRing object (lhs)

Size()

size_t Size ( ) const

inline

Returns

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

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

PathSize()

size_t PathSize ( ) const

inline

Returns

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

Deprecated:

Use Size() instead

IsAromatic()

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

Referenced by OBDepict::DrawMolecule().

SetType() [1/2]

void SetType

(

char *

type

)

Set the ring type (see OBRingTyper for more)

SetType() [2/2]

void SetType

(

std::string &

type

)

Set the ring type (see OBRingTyper for more)

GetType()

char * GetType

(

)

Returns

the ring type

GetRootAtom()

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

IsMember() [1/2]

bool IsMember

(

OBAtom *

a

)

Returns

Whether atom a is a member of this ring

IsMember() [2/2]

bool IsMember

(

OBBond *

b

)

Returns

Whether both atoms in bond b are in this ring

Todo:

This method uses implicit bonding – bond info is not stored in OBRing

IsInRing()

bool IsInRing ( int  i )

inline

Returns

Whether i as an atom index is in this ring

Referenced by OBAromaticTyper::AssignAromaticFlags().

SetParent()

void SetParent ( OBMol *  m )

inline

Set the parent of this ring to m.

Referenced by OBMol::FindLSSR(), and OBMol::FindSSSR().

GetParent()

OBMol* GetParent ( )

inline

Returns

the parent of this ring, or NULL if none has been defined

findCenterAndNormal()

bool findCenterAndNormal	(	vector3 &	center,
		vector3 &	norm1,
		vector3 &	norm2
	)

Set the supplied vectors to the center of this ring, along with the normal (in both directions).

Parameters

center	The center of the ring
norm1	The normal of the best-fit plane for this ring
norm2	-1 * norm1 (i.e., the opposite direction of norm1)

Returns

True (success)

Member Data Documentation

ring_id

int ring_id

a unique id to ensure a stable sort in SSSR determination

Referenced by OpenBabel::CompareRingSize().

_path

std::vector<int> _path

the path of this ring (i.e., the atom indexes)

Referenced by OBDepict::AddAtomLabels(), OBAromaticTyper::AssignAromaticFlags(), OBDepict::DrawMolecule(), OBRing::findCenterAndNormal(), OBRing::OBRing(), OBRing::operator=(), and OpenBabel::visitRing().

_pathset

OBBitVec _pathset

the path of this ring as a redundant bit vector

Referenced by OpenBabel::ComparePairSecond(), OBRing::OBRing(), OBRing::operator=(), and OpenBabel::visitRing().

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The documentation for this class was generated from the following files:

• ring.h
• ring.cpp