Molecule Properties¶

Molecules in OEChem TK are represented by OEMolBases. In addition to keeping track of the atoms and bonds that constitute a molecule, the OEMolBase is also used to store global information and Generic Data about the molecule.

Read/Write Molecule Properties¶

The OEMolBase API provides the following methods for storing common global information about the molecule.

Property Name	Type	Get Method	Set Method	See Also
Coordinates	`float` array	`GetCoords`	`SetCoords`	`ClearCoords`
Dimension	`unsigned int`	`GetDimension`	`SetDimension`
Energy	`float`	`GetEnergy`	`SetEnergy`
Perception	`bool`	`HasPerceived`	`SetPerceived`
Rxn	`bool`	`IsRxn`	`SetRxn`	Reactions
Title	`string`	`GetTitle`	`SetTitle`	Title

Title¶

The Title property is a string used to represent the name of the molecule. The default value is an empty string. This field may be used to store a registry number or other identifier, instead of a common name. The string is typically trimmed of white space by most file format readers.

The following code uses the GetTitle method to list the names of the molecules in a file. The input file is read and the list of identifiers (molecule names) are written to standard-out.

Listing 1: Printing molecule titles

package openeye.docexamples.oechem;

import openeye.oechem.*;

public class GetTitle {
    public static void main(String argv[]) {
        OEGraphMol mol = new OEGraphMol();
        oemolistream ifs = new oemolistream(argv[0]);

        while (oechem.OEReadMolecule(ifs, mol))
            System.out.println(mol.GetTitle());
        ifs.close();
    }
}

Atoms and Bonds¶

The OEMolBase API provides the following methods for accessing and altering the connection table of the molecule.

Description	Return Type	Method	See Also
Number of Atoms	`unsigned int`	`NumAtoms`
Number of Bonds	`unsigned int`	`NumBonds`
Maximum Atom Index	`unsigned int`	`GetMaxAtomIdx`	Atom, Bond, and Conformer Indices
Maximum Bond Index	`unsigned int`	`GetMaxBondIdx`	Atom, Bond, and Conformer Indices
Access to an Atom	`OEAtomBase`	`GetAtom`	Predicate Functors
Access to a Bond	`OEBondBase`	`GetBond`	Predicate Functors
Access to all Atoms	`OEIterBase<OEAtomBase>`	`GetAtoms`	Atom and Bond Traversal
Access to all Bonds	`OEIterBase<OEBondBase>`	`GetBonds`	Atom and Bond Traversal
Create a new Atom	OEAtomBase	`NewAtom`	Atom and Bond Creation
Create a new Bond	OEBondBase	`NewBond`	Atom and Bond Creation
Remove an Atom	`bool`	`DeleteAtom`
Remove a Bond	`bool`	`DeleteBond`
Rearrange Atoms	`bool`	`OrderAtoms`
Rearrange Bonds	`bool`	`OrderBonds`

Atom and Bond Creation¶

OEChem TK contains functions that allow molecules to be constructed from atoms and bonds explicitly. Listing 2 demonstrates how to create the water molecule.

Atoms are created by calling the OEMolBase.NewAtom method, and bonds are created by calling the OEMolBase.NewBond method. NewAtom takes the atomic number of the atom to create and returns the new OEAtomBase. NewBond takes two OEAtomBases and an integer bond order as arguments and returns the new OEBondBase.

Listing 2: Creating new atoms and bonds

package openeye.docexamples.oechem;

import openeye.oechem.*;

public class CreatingAtoms {
    public static void main(String argv[]) {
        OEGraphMol mol = new OEGraphMol();    

        OEAtomBase o  = mol.NewAtom(8);
        OEAtomBase h1 = mol.NewAtom(1);
        OEAtomBase h2 = mol.NewAtom(1);

        OEBondBase b1 = mol.NewBond(o,h1,1);
        OEBondBase b2 = mol.NewBond(o,h2,1);
    }
}

In Listing 2 the atomic numbers of oxygen, 8, and hydrogen, 1, are explicitly encoded in the program. To make code easier to read and less error prone, OEChem TK provides symbolic constants for the first 109 elements in the OEElemNo namespace. The OEElemNo namespace defines the atomic symbols with the appropriate atomic number.

Listing 3: Using OEElemNo namespace

package openeye.docexamples.oechem;

import openeye.oechem.*;

public class CreatingAtoms2 {
    public static void main(String argv[]) {
        OEGraphMol mol = new OEGraphMol();    

        OEAtomBase o  = mol.NewAtom(OEElemNo.O);
        OEAtomBase h1 = mol.NewAtom(OEElemNo.H);
        OEAtomBase h2 = mol.NewAtom(OEElemNo.H);

        OEBondBase b1 = mol.NewBond(o,h1,1);
        OEBondBase b2 = mol.NewBond(o,h2,1);
    }
}

Note

The atoms and bonds of a molecule are automatically deleted when their parent molecule is destroyed.

Attach Generic Data to Molecules¶

Generic data can be attached to any object that derives from the OEBase class. The following two snippets demonstrate how generic data (e.g. molecule weight) can be attached to a molecule:

int tag = oechem.OEGetTag("MolWeight");
mol.SetDoubleData(tag, oechem.OECalculateMolecularWeight(mol));

mol.SetDoubleData("MolWeight", oechem.OECalculateMolecularWeight(mol));

After annotation, the data can be accessed with the same integer or character string identifier:

tag = oechem.OEGetTag("MolWeight");
System.out.println(mol.GetDoubleData(tag));

System.out.println(mol.GetDoubleData("MolWeight"));

The OEMolBase 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.