Periodic Table Functions

To simplify the task of dealing with the elements of the periodic table, OEChem contains several functions to obtain useful properties of the elements.

Atomic Symbol/Atomic Number

A common task is to obtain or display the atomic symbol of an atom represented by an OEAtomBase. To save space and reduce redundancy and consistency issues, the OEAtomBase class contains only an unsigned integer representing the atom’s atomic number. This value may be obtained using the OEAtomBase.GetAtomicNum method. This value can be converted into an atomic symbol using the OEGetAtomicSymbol function.

The example above uses the integer constant OEElemNo.C from the OEElemNo namespace. This namespace represents the atomic numbers of the 111 elements as their symbols as a convenience.

The inverse of OEGetAtomicSymbol, i.e. obtaining the atomic numbers from an atomic symbol, is performed by the OEGetAtomicNum function.

Element Properties

OEChem provides several functions for obtaining properties of the elements, all of which take an unsigned integer argument representing the element’s atomic number.

Property Name	Return Value	Function
Average Atomic Weight	double	OEGetAverageWeight
Most Abundant Isotope	unsigned int	OEGetDefaultMass

The OEChem library also provides the following two functions to deal with specific isotopes:

• OEGetIsotopicWeight
• OEIsCommonIsotope

Both functions take an unsigned integer representing the isotope’s atomic number (number of protons), and an unsigned integer representing the isotope’s mass (number of protons plus neutrons).

The following example shows how to calculate molecular weight (OECalculateMolecularWeight) :

    static double CalculateMolecularWeight(OEMolBase mol) {
        int elemno = 0;
        int mass = 0;
        int implicitH = 0;
        double weight = 0.0;

        for (OEAtomBase atom : mol.GetAtoms()) {
            elemno = atom.GetAtomicNum();
            mass = atom.GetIsotope();
            implicitH += atom.GetImplicitHCount();
            if ((elemno != 0) && (mass != 0) && oechem.OEIsCommonIsotope(elemno, mass)) {
                weight += oechem.OEGetIsotopicWeight(elemno, mass);
            } else {
                weight += oechem.OEGetAverageWeight(elemno);
            }
        }
        weight += implicitH * oechem.OEGetAverageWeight(OEElemNo.H);
        return weight;
    }

Atom Radius Functions

Property Name	Get Method	Applied on OEMolBase	Reference
Covalent Radius	OEGetCovalentRadius	OEAssignCovalentRadii
Default Radius used by DelPhi	OEGetDelphiRadius	OEAssignDelphiRadii	Accelrys
Effective Ionic Radius	OEGetHonigIonicCavityRadius	OEAssignHonigIonicCavityRadii	[Rashin-1985]
Van der Waals Radius	OEGetBondiVdWRadius	OEAssignBondiVdWRadii	[Bondi-1964]
Van der Waals Radius	OEGetPaulingVdWRadius	OEAssignPaulingVdWRadii	[Pauling-1960]
Van der Waals Radius	N/A [1]	OEAssignZap9Radii	[Nicholls-2008]

Table footnote:

[1] The get method is not available, since the radius value of OEElemNo.O and OEElemNo.N (defined in [Nicholls-2008]) depend on the chemical environment of the given atom.

The following snippet shows how to set and access the “Pauling” van der Waals radius in a given OEMolBase:

        oechem.OEAssignBondiVdWRadii(mol);
        for (OEAtomBase atom : mol.GetAtoms()) {
            System.out.println(atom.GetIdx() + " " + atom.GetRadius());
        }

Example of setting “Pauling” van der Waals radius