Open Babel: atom.h File Reference

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# atom.h File Reference

Handle atoms. More...

`#include <openbabel/babelconfig.h>`
`#include <vector>`
`#include <string>`
`#include <openbabel/base.h>`
`#include <openbabel/residue.h>`
`#include <openbabel/math/vector3.h>`

Go to the source code of this file.

## Classes
class | OBAtom
| Atom class. More...
## Namespaces
namespace | OpenBabel
## Defines
#define | OB_4RING_ATOM (1<<1)
#define | OB_3RING_ATOM (1<<2)
#define | OB_AROMATIC_ATOM (1<<3)
#define | OB_RING_ATOM (1<<4)
#define | OB_CSTEREO_ATOM (1<<5)
#define | OB_ACSTEREO_ATOM (1<<6)
#define | OB_DONOR_ATOM (1<<7)
#define | OB_ACCEPTOR_ATOM (1<<8)
#define | OB_CHIRAL_ATOM (1<<9)
#define | OB_POS_CHIRAL_ATOM (1<<10)
#define | OB_NEG_CHIRAL_ATOM (1<<11)
#define | OB_ATOM_HAS_NO_H (1<<12)
#define | OB_ATOM_NOT_H_DEFICIENT (1<<13)
## Typedefs
typedef OBAtom | OBNodeBase
typedef std::vector< OBBond * > ::iterator | OBBondIterator
typedef std::vector< OBAtom * > ::iterator | OBAtomIterator

## Detailed Description

Handle atoms.

## Define Documentation

#define OB_4RING_ATOM (1<<1)

Atom is in a 4-membered ring.

#define OB_3RING_ATOM (1<<2)

Atom is in a 3-membered ring.

#define OB_AROMATIC_ATOM (1<<3)

Atom is aromatic.

Referenced by OBAtom::IsAromatic(), OBAtom::SetAromatic(), and OBAtom::UnsetAromatic().

#define OB_RING_ATOM (1<<4)

Atom is in a ring.

Referenced by OBAtom::IsInRing(), OBAtom::IsInRingSize(), and OBAtom::SetInRing().

#define OB_CSTEREO_ATOM (1<<5)

Atom has clockwise SMILES chiral stereochemistry (i.e., "@@")

Referenced by OBAtom::HasChiralitySpecified(), OBAtom::IsClockwise(), OBAtom::SetClockwiseStereo(), and OBAtom::UnsetStereo().

#define OB_ACSTEREO_ATOM (1<<6)

Atom has anticlockwise SMILES chiral stereochemistry (i.e., "@")

Referenced by OBAtom::HasChiralitySpecified(), OBAtom::IsAntiClockwise(), OBAtom::SetAntiClockwiseStereo(), and OBAtom::UnsetStereo().

#define OB_DONOR_ATOM (1<<7)

Atom is an electron donor.

#define OB_ACCEPTOR_ATOM (1<<8)

Atom is an electron acceptor.

#define OB_CHIRAL_ATOM (1<<9)

Atom is chiral.

Referenced by OBAtom::SetAntiClockwiseStereo(), OBAtom::SetChiral(), OBAtom::SetClockwiseStereo(), OBAtom::SetNegativeStereo(), OBAtom::SetPositiveStereo(), and OBAtom::UnsetStereo().

#define OB_POS_CHIRAL_ATOM (1<<10)

Atom has + chiral volume.

Referenced by OBAtom::HasChiralVolume(), OBAtom::IsPositiveStereo(), OBAtom::SetPositiveStereo(), and OBAtom::UnsetStereo().

#define OB_NEG_CHIRAL_ATOM (1<<11)

Atom has - chiral volume.

Referenced by OBAtom::HasChiralVolume(), OBAtom::IsNegativeStereo(), OBAtom::SetNegativeStereo(), and OBAtom::UnsetStereo().

#define OB_ATOM_HAS_NO_H (1<<12)

Atom has no hydrogen attached. Temporary use only during input of some formats.

Referenced by OBAtom::ForceNoH(), and OBAtom::HasNoHForced().

#define OB_ATOM_NOT_H_DEFICIENT (1<<13)

Atom is not hydrogen deficient. (for SMILES input)

Referenced by OBAtom::ForceImplH(), and OBAtom::HasImplHForced().

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