/// <summary> Removes the singly bonded oxygen from the acid group of the AminoAcid.
///
/// </summary>
/// <param name="acid">AminoAcid from which to remove the oxygen
/// </param>
/// <throws> CDKException when the C-terminus is not defined for the given AminoAcid </throws>
public static void removeAcidicOxygen(IAminoAcid acid)
{
if (acid.getCTerminus() == null)
{
throw new CDKException("Cannot remove oxygen: C-terminus is not defined!");
}
IBond[] bonds = acid.getConnectedBonds(acid.getCTerminus());
// ok, look for the oxygen which is singly bonded
for (int i = 0; i < bonds.Length; i++)
{
if (bonds[i].Order == CDKConstants.BONDORDER_SINGLE)
{
IAtom[] atoms = bonds[i].getAtoms();
for (int j = 0; j < atoms.Length; j++)
{
if (atoms[j].Symbol.Equals("O"))
{
// yes, we found a singly bonded oxygen!
acid.removeAtomAndConnectedElectronContainers(atoms[j]);
}
}
}
}
}
/// <summary> Removes the singly bonded oxygen from the acid group of the AminoAcid.
///
/// </summary>
/// <param name="acid">AminoAcid from which to remove the oxygen
/// </param>
/// <throws> CDKException when the C-terminus is not defined for the given AminoAcid </throws>
public static void removeAcidicOxygen(IAminoAcid acid)
{
if (acid.getCTerminus() == null)
throw new CDKException("Cannot remove oxygen: C-terminus is not defined!");
IBond[] bonds = acid.getConnectedBonds(acid.getCTerminus());
// ok, look for the oxygen which is singly bonded
for (int i = 0; i < bonds.Length; i++)
{
if (bonds[i].Order == CDKConstants.BONDORDER_SINGLE)
{
IAtom[] atoms = bonds[i].getAtoms();
for (int j = 0; j < atoms.Length; j++)
{
if (atoms[j].Symbol.Equals("O"))
{
// yes, we found a singly bonded oxygen!
acid.removeAtomAndConnectedElectronContainers(atoms[j]);
}
}
}
}
}
