Open Babel: OBRing Class Reference

Public Member Functions | Public Attributes

# 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
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 ) |

Returns:
  Whether atom `a` is a member of this ring

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

OBMol* GetParent | ( | ) | `[inline]`

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

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

int ring_id

a unique id to ensure a stable sort in SSSR determination

Referenced by OpenBabel::CompareRingSize().

std::vector<int> _path

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

Referenced by OBDepict::DrawMolecule(), OBRing::findCenterAndNormal(), OpenBabel::get_bonds_of_ring(), OBRing::OBRing(), OBRing::operator=(), OBAromaticTyper::SelectRootAtoms(), OBMol::start_kekulize(), and OpenBabel::visitRing().

OBBitVec _pathset

the path of this ring as a redundant bit vector

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

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

- ring.h
- ring.cpp

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