/// <summary> Method that saturates an atom in a molecule by adding explicit hydrogens.
/// In order to get coordinates for these Hydrogens, you need to
/// remember the average bondlength of you molecule (coordinates for
/// all atoms should be available) by using
/// double bondLength = GeometryTools.getBondLengthAverage(atomContainer);
/// and then use this method here and then use
/// org.openscience.cdk.HydrogenPlacer(atomContainer, bondLength);
///
/// </summary>
/// <param name="atom"> Atom to saturate
/// </param>
/// <param name="container">AtomContainer containing the atom
/// </param>
/// <param name="totalContainer">In case you have a container containing multiple structures, this is the total container, whereas container is a partial structure
///
/// </param>
/// <cdk.keyword> hydrogen, adding </cdk.keyword>
/// <cdk.keyword> explicit hydrogen </cdk.keyword>
public virtual IAtomContainer addExplicitHydrogensToSatisfyValency(IAtomContainer container, IAtom atom, IAtomContainer totalContainer)
{
// set number of implicit hydrogens to zero
// add explicit hydrogens
//logger.debug("Start of addExplicitHydrogensToSatisfyValency(AtomContainer container, Atom atom)");
int missingHydrogens = valencyChecker.calculateNumberOfImplicitHydrogens(atom, container);
//logger.debug("According to valencyChecker, " + missingHydrogens + " are missing");
IAtomContainer changedAtomsAndBonds = addExplicitHydrogensToSatisfyValency(container, atom, missingHydrogens, totalContainer);
//logger.debug("End of addExplicitHydrogensToSatisfyValency(AtomContainer container, Atom atom)");
return(changedAtomsAndBonds);
}
