OBRing Class Reference

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

#include <openbabel/ring.h>

List of all members.

Public Member Functions

int Size () const
int 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

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)

int Size (  )  const [inline]

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

Referenced by OpenBabel::CompareRingSize(), and OBRing::GetRootAtom().

int 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  ) 

Returns:
Whether atom a is a member of this ring

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

bool IsInRing ( int  i  )  [inline]

Returns:
Whether i as an atom index is in this ring

Referenced by OBAromaticTyper::SelectRootAtoms().

void SetParent ( OBMol *  m  )  [inline]

Set the parent of this ring to m.

Referenced by OBMol::FindSSSR().

OBMol* GetParent (  )  [inline]

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

Referenced by OBRing::GetRootAtom(), and OBRing::GetType().

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

std::vector<int> _path

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

Referenced by OBRing::findCenterAndNormal(), OBRing::GetRootAtom(), OBRing::IsAromatic(), OBRing::OBRing(), OBRing::operator=(), and OBAromaticTyper::SelectRootAtoms().

OBBitVec _pathset

the path of this ring as a redundant bit vector

Referenced by OpenBabel::FindRingAtoms(), OBRing::IsMember(), OBRing::OBRing(), and OBRing::operator=().

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