Atom Properties

The OEAtomBase class is the workhorse of the OEChem TK library, representing the atoms of a molecule. This section details some of its important and often used properties and methods.

Read/Write Atom Properties

Property Name

Type

Get Method

Set Method

See Also

Atomic Number

unsigned int

GetAtomicNum

SetAtomicNum

Formal Charge

int

GetFormalCharge

SetFormalCharge

Formal Charges

Implicit Hyd. Count

unsigned int

GetImplicitHCount

SetImplicitHCount

Isotopic Mass

unsigned int

GetIsotope

SetIsotope

Partial Charge

double

GetPartialCharge

SetPartialCharge

Partial Charges

Atomic Hybridization

unsigned int

GetHyb

SetHyb

Integer Atom Type

int

GetIntType

SetIntType

Atom Name

string

GetName

SetName

Atom Type Name

string

GetType

SetType

Atom Radius

double

GetRadius

SetRadius

Reaction Role

unsigned int

GetRxnRole

SetRxnRole

Reactions

Reaction Map Index

unsigned int

GetMapIdx

SetMapIdx

Reactions

Ring Membership

bool

IsInRing

SetIsInRing

Ring Perception

Aromaticity

bool

IsAromatic

SetAromatic

Aromaticity

Atom Chirality

bool

IsChiral

SetChiral

Stereochemistry

Atom Stereo

unsigned int

GetStereo

SetStereo

Stereochemistry

Read Only Atom Properties

Property Name

Type

Get Method

See Also

Atom Degree

unsigned int

GetDegree

Explicit Atom Degree

unsigned int

GetExplicitDegree

Explicit Hydrogen Count

unsigned int

GetExplicitHCount

Explicit Valence

unsigned int

GetExplicitValence

Valence Models

Atom Heavy Degree

unsigned int

GetHvyDegree

Atom Heavy Valence

unsigned int

GetHvyValence

Valence Models

Atom Parent

OEMolBase

GetParent

Total Hydrogen Count

unsigned int

GetTotalHCount

Atom Valence

unsigned int

GetValence

Valence Models

Atom Index

unsigned int

GetIdx

Atom, Bond, and Conformer Indices

Atom Has Stereo

bool

HasStereoSpecified

Stereochemistry Perception

Atom Connection

bool

IsConnected

Attach Generic Data to Atoms

Generic data (see Generic Data) can be attached to any object that derives from the OEBase class. The following program shows an example where hydrogen bonding donor property is attached as a bool value to the corresponding OEAtomBase object.

Listing 2: Example of attaching generic data to atoms

from openeye import oechem

IsDonorAtom = oechem.OEMatchAtom("[!H0;#7,#8]")

mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol, "c1c(Cl)cncc1C(=O)O")

for atom in mol.GetAtoms():
    atom.SetData("isdonor", IsDonorAtom(atom))


class IsDonorAtomPred(oechem.OEUnaryAtomPred):
    def __call__(self, atom):
        return atom.GetData("isdonor")


print("Donor atoms:", end=" ")
for atom in mol.GetAtoms(IsDonorAtomPred()):
    print(atom.GetIdx(), oechem.OEGetAtomicSymbol(atom.GetAtomicNum()), end=" ")
print()

The OEAtomBase API provides the following methods, publicly inherited from OEBase, that allow the manipulation of generic data.

Methods to manipulate generic data

Method

Description

SetData

sets a generic data associating it with the given tag

AddData

adds a generic data associating it with the given tag

HasData

determines whether a molecule has any generic data with a given tag

GetData

returns the generic data associated with the given tag

DeleteData

deletes all generic data with the given tag

Clear

clears all stored generic data

Note

Generic data attached to a molecule or any of its atoms or bonds is automatically saved when the molecule is written into an .oeb file.