Molecule Properties

Molecules in OEChem 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 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
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 from standard-in and the list of identifiers (molecule names) are written to standard-out.

Listing 1: Printing molecule titles

import openeye.oechem.*;

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

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

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 a Atom	OEAtomBase	GetAtom	Predicate Functors
Access to a Bond	OEBondBase	GetBond	Predicate Functors
Access to all Atoms	OEIterBase	GetAtoms	Atom and Bond Traversal
Access to all Bonds	OEIterBase	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 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 a integer bond order as arguments and returns the new OEBondBase.

Listing 2: Creating new atoms and bonds

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 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

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.