/**
* Returns a set of nodes excluding all the hydrogens.
*
* @param formula The IMolecularFormula
* @return The heavyElements value into a List
* @cdk.keyword hydrogen, removal
*/
public static List<IElement> getHeavyElements(IMolecularFormula formula) {
List<IElement> newEle = new ArrayList<IElement>();
for (IElement element : elements(formula)) {
if (!element.getSymbol().equals("H")) {
newEle.add(element);
}
}
return newEle;
}
/**
* True, if the MolecularFormula contains the given element as IIsotope object.
*
* @param formula IMolecularFormula molecularFormula
* @param element The element this MolecularFormula is searched for
* @return True, if the MolecularFormula contains the given element object
*/
public static boolean containsElement(IMolecularFormula formula, IElement element) {
for (IIsotope isotope : formula.isotopes()) {
if (element.getSymbol().equals(isotope.getSymbol())) return true;
}
return false;
}
/**
* Get a list of IIsotope from a given IElement which is contained molecular. The search is based
* only on the IElement.
*
* @param formula The MolecularFormula to check
* @param element The IElement object
* @return The list with the IIsotopes in this molecular formula
*/
public static List<IIsotope> getIsotopes(IMolecularFormula formula, IElement element) {
List<IIsotope> isotopeList = new ArrayList<IIsotope>();
for (IIsotope isotope : formula.isotopes()) {
if (isotope.getSymbol().equals(element.getSymbol())) isotopeList.add(isotope);
}
return isotopeList;
}
/**
* Checks a set of Nodes for the occurrence of the isotopes in the molecular formula from a
* particular IElement. It returns 0 if the element does not exist. The search is based only on
* the IElement.
*
* @param formula The MolecularFormula to check
* @param element The IElement object
* @return The occurrence of this element in this molecular formula
*/
public static int getElementCount(IMolecularFormula formula, IElement element) {
int count = 0;
for (IIsotope isotope : formula.isotopes()) {
if (isotope.getSymbol().equals(element.getSymbol()))
count += formula.getIsotopeCount(isotope);
}
return count;
}
/**
* Returns the string representation of the molecule formula with numbers wrapped in
* <sub></sub> tags and the isotope of each Element in <sup></sup> tags
* and the total showCharge of IMolecularFormula in <sup></sup> tags. Useful for
* displaying formulae in Swing components or on the web.
*
* @param formula The IMolecularFormula object
* @param orderElements The order of Elements
* @param showCharge True, If it has to show the showCharge
* @param showIsotopes True, If it has to show the Isotope mass
* @return A HTML representation of the molecular formula
* @see #getHTML(IMolecularFormula)
*/
public static String getHTML(
IMolecularFormula formula, String[] orderElements, boolean showCharge, boolean showIsotopes) {
StringBuilder sb = new StringBuilder();
for (String orderElement : orderElements) {
IElement element = formula.getBuilder().newInstance(IElement.class, orderElement);
if (containsElement(formula, element)) {
if (!showIsotopes) {
sb.append(element.getSymbol());
int n = getElementCount(formula, element);
if (n > 1) {
sb.append("<sub>").append(n).append("</sub>");
}
} else {
for (IIsotope isotope : getIsotopes(formula, element)) {
Integer massNumber = isotope.getMassNumber();
if (massNumber != null) sb.append("<sup>").append(massNumber).append("</sup>");
sb.append(isotope.getSymbol());
int n = formula.getIsotopeCount(isotope);
if (n > 1) {
sb.append("<sub>").append(n).append("</sub>");
}
}
}
}
}
if (showCharge) {
Integer charge = formula.getCharge();
if (charge == CDKConstants.UNSET || charge == 0) {
return sb.toString();
} else {
sb.append("<sup>");
if (charge > 1 || charge < -1) sb.append(Math.abs(charge));
if (charge > 0) sb.append('+');
else sb.append(MINUS); // note, not a hyphen!
sb.append("</sup>");
}
}
return sb.toString();
}
@Test
public void testMassNumber() {
IElement chemObject = new NaturalElement("C", 12);
Assert.assertEquals(12, chemObject.getAtomicNumber().intValue());
}
@Test
public void testSymbol() {
IElement chemObject = new NaturalElement("C", 12);
Assert.assertEquals("C", chemObject.getSymbol());
}