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

package openeye.docexamples.oechem;

import openeye.oechem.*;

public class GenericDataToAtom {
    private static class IsDonorAtomPred extends OEUnaryAtomPred {
        public boolean constCall(OEAtomBase atom) {
            return atom.GetBoolData("isdonor");
        }
        public OEUnaryAtomBoolFunc CreateCopy() {
            OEUnaryAtomBoolFunc copy = new IsDonorAtomPred();
            copy.swigReleaseOwnership();
            return copy;
        }
    }

    public static void main(String argv[]) {
        OEGraphMol mol = new OEGraphMol();
        oechem.OESmilesToMol(mol, "c1c(Cl)cncc1C(=O)O");

        OEMatchAtom IsDonorAtom = new OEMatchAtom("[!H0;#7,#8]");
        for (OEAtomBase atom : mol.GetAtoms()) {
            atom.SetBoolData("isdonor", IsDonorAtom.constCall(atom));
        }

        System.out.print("Donor atoms: ");
        for (OEAtomBase atom : mol.GetAtoms(new IsDonorAtomPred())) {
            System.out.print(atom.GetIdx() + " " +  oechem.OEGetAtomicSymbol(atom.GetAtomicNum()));
        }
        System.out.println("");
    }
}

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.