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>

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Namespaces
namespace	OpenBabel
Classes
class	OBAtom
	Atom class. More...
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::IsChiral(), 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().