Subsections

8.1 Stored Properties of Atoms

The OEAtomBase class is the work horse of the OEChem library, representing the atoms of a molecule. The following table shows the properties stored in each OEAtomBase along with the member methods to Set and Get that property.

Property Name	Type	Get Method	Set Method
Atomic Number	int	GetAtomicNum	SetAtomicNum
Formal Charge	int	GetFormalCharge	SetFormalCharge
Implicit Hydrogen Count	int	GetImplicitHCount	SetImplicitHCount
Isotopic Mass	int	GetIsotope	SetIsotope
Partial Charge	float	GetPartialCharge	SetPartialCharge
Atomic Hybridization	int GetHyb	SetHyb
Integer Atom Type	int	GetIntType	SetIntType
Atom Name	string	GetName	SetName
Atom Type Name	string	GetType	SetType
Radius	double	GetRadius	SetRadius
Reaction Role	int	GetRxnRole	SetRxnRole
Reaction Map Index	int	GetMapIdx	SetMapIdx
Ring Membership	0 or 1	IsInRing	SetInRing
Symmetry Class	int	GetSymmetryClass	SetSymmetryClass
Aromaticity	0 or 1	IsAromatic	SetAromatic

8.1.1 AtomicNum

The "atomic number" property of an atom is an unsigned integer representing the atomic number, or element, of that atom. The default value is zero.

8.1.2 FormalCharge

The "formal charge" property of an atom is an integer representing the formal charge on an atom. The default value is zero, indicating a neutral atom.

8.1.3 ImplicitHCount

The "implicit hydrogen count" property of an atom is an unsigned integer denoting the number of hydrogens implicitly attached to an atom. The default value is zero.

8.1.4 Isotope

The "isotope" property of an atom is an unsigned integer used to indicate whether the atom is mono-isotopic and if so the atomic mass of the relevant isotope. The default value is zero, indicating that the atom has a typical population of isotopes (based upon standard abundances) for that element.

8.1.5 PartialCharge

The "partial charge" property of an atom is a float used to hold the partial charge assigned to an atom. The default value is 0.0.

8.1.6 Hyb

The "hydridization" property of an atom is an unsigned int used to hold the atomic hybridization or geometry of an atom. The default value is OEHybridization_Unknown, which is zero.

8.1.7 IntType

The "integer type" property of an atom is an integer that holds the numeric atom type assigned to an atom. The default value is zero.

8.1.8 Name

The "name" property of an atom is a string used to record the atom name associated with an atom. The default value is the empty string.

8.1.9 Type

The "type" property of an atom is a string used to store the symbolic atom type assigned to an atom. The default value is the empty string.

8.1.10 Radius

The "radius" property of an atom is a float used to hold the radius assigned to an atom. The default value is 0.0.

8.1.11 RxnRole

The "reaction role" property of an atom is an unsigned integer used to record the role, if any, of an atom in a reaction or transform. The default value is OERxnRole_None, which is zero.

8.1.12 MapIdx

The "reaction map index" property of an atom is an unsigned used to represent the atom equivalences in reaction and transforms, or to label R-groups/attachment points in molecules. The default value is zero.

8.1.13 InRing

The "in ring" property of a atom is a boolean used to represent whether the atom is a member of a cycle/ring. The default value is false.

8.1.14 SymmetryClass

The "symmetry class" property of an atom is an unsigned integer used to represent the topological symmetry group of an atom. The default value is zero.

8.1.15 Aromatic

The "aromatic" property of an atom is a boolean used to represent whether the atom is considered a member of an aromatic ring/cycle. The default value is false.

				OEChem - Python Theory Manual

				OEChem - Python Theory Manual