Periodic Table Functions¶

To simplify the task of dealing with the elements of the periodic table, OEChem TK 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.

const char *symb = OEGetAtomicSymbol(OEElemNo::C);
cout << "The atomic symbol for carbon is " << symb << endl;

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.

cout << "The atomic number for 'Cl' is " << OEGetAtomicNum("Cl") << endl;

Element Properties¶

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

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) :

double CalculateMolecularWeight(const OEMolBase &mol)
{
  unsigned int implicitH = 0u;
  double weight = 0.0;

  for (OEIter<const OEAtomBase> atom = mol.GetAtoms(); atom; ++atom)
  {
     const auto elemno = atom->GetAtomicNum();
     const auto mass = atom->GetIsotope();
     implicitH += atom->GetImplicitHCount();
     if ((elemno != 0u) && (mass != 0u) && OEIsCommonIsotope(elemno, mass))
        weight += OEGetIsotopicWeight(elemno, mass);
      else
        weight += OEGetAverageWeight(elemno);
  }
  weight += (implicitH * 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]
Van der Waals Radius		`OEAssignZap7Radii`	[Nicholls-2010]
Generic Assignment Function	N/A [2]	`OEAssignRadii`

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.

[2] Can be used to call any of the other methods to assign radii as well as to clear atomic radii.

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

OEGraphMol mol;
OESmilesToMol(mol, "c1ccncc1CF");
OEAssignPaulingVdWRadii(mol);
for (OEIter<const OEAtomBase> atom = mol.GetAtoms(); atom; ++atom)
  cout << atom->GetIdx() << ' ' << atom->GetRadius() << endl;

Example of setting “Pauling” van der Waals radius¶