public void TestFixedElementCounts()
{
var ifac = BODRIsotopeFactory.Instance;
IIsotope c = ifac.GetMajorIsotope("C");
IIsotope h = ifac.GetMajorIsotope("H");
IIsotope n = ifac.GetMajorIsotope("N");
IIsotope o = ifac.GetMajorIsotope("O");
MolecularFormulaRange mfRange = new MolecularFormulaRange();
mfRange.AddIsotope(c, 7, 7);
mfRange.AddIsotope(h, 15, 15);
mfRange.AddIsotope(o, 4, 4);
mfRange.AddIsotope(n, 2, 2);
double massMin = 10d;
double massMax = 1000d;
MolecularFormulaGenerator gen = new MolecularFormulaGenerator(builder, massMin, massMax, mfRange);
IMolecularFormulaSet mfSet = gen.GetAllFormulas();
Assert.IsNotNull(mfSet);
Assert.AreEqual(1, mfSet.Count);
Assert.AreEqual("C7H15N2O4", MolecularFormulaManipulator.GetString(mfSet[0]));
}
public void TestCompoundWith7Elements()
{
var ifac = BODRIsotopeFactory.Instance;
IIsotope c = ifac.GetMajorIsotope("C");
IIsotope h = ifac.GetMajorIsotope("H");
IIsotope n = ifac.GetMajorIsotope("N");
IIsotope o = ifac.GetMajorIsotope("O");
IIsotope s = ifac.GetMajorIsotope("S");
IIsotope p = ifac.GetMajorIsotope("P");
IIsotope cl = ifac.GetMajorIsotope("Cl");
MolecularFormulaRange mfRange = new MolecularFormulaRange();
mfRange.AddIsotope(c, 7, 9);
mfRange.AddIsotope(h, 8, 10);
mfRange.AddIsotope(o, 1, 3);
mfRange.AddIsotope(n, 0, 2);
mfRange.AddIsotope(s, 0, 2);
mfRange.AddIsotope(p, 0, 2);
mfRange.AddIsotope(cl, 2, 4);
double minMass = 318.915719 - 0.0001;
double maxMass = 318.915719 + 0.0001;
MolecularFormulaGenerator gen = new MolecularFormulaGenerator(builder, minMass, maxMass, mfRange);
IMolecularFormulaSet mfSet = gen.GetAllFormulas();
Assert.IsNotNull(mfSet);
Assert.AreEqual(1, mfSet.Count);
Assert.AreEqual("C8H9Cl3NO2PS", MolecularFormulaManipulator.GetString(mfSet[0]));
}
public void TestDifferentIsotopes()
{
var ifac = BODRIsotopeFactory.Instance;
IIsotope c = ifac.GetMajorIsotope("C");
var carbons = ifac.GetIsotopes("C");
IIsotope c13 = carbons.ElementAt(5); // 13
IIsotope h = ifac.GetMajorIsotope("H");
MolecularFormulaRange mfRange = new MolecularFormulaRange();
mfRange.AddIsotope(c, 0, 11);
mfRange.AddIsotope(c13, 0, 10);
mfRange.AddIsotope(h, 0, 10);
double minMass = 54.04193 - 0.001;
double maxMass = 54.04193 + 0.001;
MolecularFormulaGenerator gen = new MolecularFormulaGenerator(builder, minMass, maxMass, mfRange);
IMolecularFormulaSet mfSet = gen.GetAllFormulas();
Assert.IsNotNull(mfSet);
Assert.AreEqual(1, mfSet.Count);
IMolecularFormula trueFormula = new MolecularFormula(); // C3CH5
trueFormula.Add(c, 3);
trueFormula.Add(c13, 1);
trueFormula.Add(h, 5);
Assert.AreEqual(trueFormula.IsotopesCount, mfSet[0].IsotopesCount);
Assert.AreEqual(trueFormula.GetCount(c), mfSet[0].GetCount(c));
Assert.AreEqual(trueFormula.GetCount(c13), mfSet[0].GetCount(c13));
}
public void TestHighMass()
{
var ifac = BODRIsotopeFactory.Instance;
IIsotope c = ifac.GetMajorIsotope("C");
IIsotope h = ifac.GetMajorIsotope("H");
IIsotope n = ifac.GetMajorIsotope("N");
IIsotope o = ifac.GetMajorIsotope("O");
IIsotope s = ifac.GetMajorIsotope("S");
MolecularFormulaRange mfRange = new MolecularFormulaRange();
mfRange.AddIsotope(c, 350, 400);
mfRange.AddIsotope(h, 620, 650);
mfRange.AddIsotope(o, 100, 150);
mfRange.AddIsotope(n, 100, 150);
mfRange.AddIsotope(s, 0, 10);
double minMass = 8445.573784 - 0.00001;
double maxMass = 8445.573784 + 0.00001;
MolecularFormulaGenerator gen = new MolecularFormulaGenerator(builder, minMass, maxMass, mfRange);
IMolecularFormulaSet mfSet = gen.GetAllFormulas();
Assert.IsNotNull(mfSet);
Assert.AreEqual(1, mfSet.Count);
Assert.AreEqual("C374H623N103O116S", MolecularFormulaManipulator.GetString(mfSet[0]));
}
public void TestFormulaFoundInRange2()
{
var ifac = BODRIsotopeFactory.Instance;
IIsotope c = ifac.GetMajorIsotope("C");
IIsotope h = ifac.GetMajorIsotope("H");
IIsotope n = ifac.GetMajorIsotope("N");
IIsotope o = ifac.GetMajorIsotope("O");
MolecularFormulaRange mfRange = new MolecularFormulaRange();
mfRange.AddIsotope(c, 1, 50);
mfRange.AddIsotope(h, 1, 100);
mfRange.AddIsotope(o, 1, 50);
mfRange.AddIsotope(n, 1, 50);
double minMass = 187;
double maxMass = 189;
MolecularFormulaGenerator gen = new MolecularFormulaGenerator(builder, minMass, maxMass, mfRange);
IMolecularFormulaSet mfSet = gen.GetAllFormulas();
Assert.AreEqual(528, mfSet.Count);
bool found = false;
foreach (var formula in mfSet)
{
string mf = MolecularFormulaManipulator.GetString(formula);
if (mf.Equals("C11H10NO2"))
{
found = true;
break;
}
}
Assert.IsTrue(found, "The molecular formula C11H10NO2 should be found");
}
public void TestClone_Isotopes()
{
MolecularFormulaRange mfRange = new MolecularFormulaRange();
IIsotope carb = builder.NewIsotope("C");
IIsotope flu = builder.NewIsotope("F");
IIsotope h1 = builder.NewIsotope("H");
mfRange.AddIsotope(carb, 0, 5);
mfRange.AddIsotope(flu, 2, 8);
mfRange.AddIsotope(h1, 4, 10);
Assert.AreEqual(3, mfRange.Count);
Assert.AreEqual(0, mfRange.GetIsotopeCountMin(carb));
Assert.AreEqual(2, mfRange.GetIsotopeCountMin(flu));
Assert.AreEqual(4, mfRange.GetIsotopeCountMin(h1));
Assert.AreEqual(5, mfRange.GetIsotopeCountMax(carb));
Assert.AreEqual(8, mfRange.GetIsotopeCountMax(flu));
Assert.AreEqual(10, mfRange.GetIsotopeCountMax(h1));
object clone = mfRange.Clone();
Assert.IsTrue(clone is MolecularFormulaRange);
Assert.AreEqual(mfRange.Count, ((MolecularFormulaRange)clone).Count);
Assert.AreEqual(3, ((MolecularFormulaRange)clone).Count);
Assert.AreEqual(3, ((MolecularFormulaRange)clone).Count);
Assert.AreEqual(0, ((MolecularFormulaRange)clone).GetIsotopeCountMin(carb));
Assert.AreEqual(2, ((MolecularFormulaRange)clone).GetIsotopeCountMin(flu));
Assert.AreEqual(4, ((MolecularFormulaRange)clone).GetIsotopeCountMin(h1));
Assert.AreEqual(5, ((MolecularFormulaRange)clone).GetIsotopeCountMax(carb));
Assert.AreEqual(8, ((MolecularFormulaRange)clone).GetIsotopeCountMax(flu));
Assert.AreEqual(10, ((MolecularFormulaRange)clone).GetIsotopeCountMax(h1));
}
public void TestMiddleMass()
{
var ifac = BODRIsotopeFactory.Instance;
IIsotope c = ifac.GetMajorIsotope("C");
IIsotope h = ifac.GetMajorIsotope("H");
IIsotope n = ifac.GetMajorIsotope("N");
IIsotope o = ifac.GetMajorIsotope("O");
MolecularFormulaRange mfRange = new MolecularFormulaRange();
mfRange.AddIsotope(c, 0, 50);
mfRange.AddIsotope(h, 0, 100);
mfRange.AddIsotope(o, 0, 30);
mfRange.AddIsotope(n, 0, 10);
double minMass = 698.25879 - 0.0001;
double maxMass = 698.25879 + 0.0001;
MolecularFormulaGenerator gen = new MolecularFormulaGenerator(builder, minMass, maxMass, mfRange);
IMolecularFormulaSet mfSet = gen.GetAllFormulas();
Assert.IsNotNull(mfSet);
Assert.AreEqual(1, mfSet.Count);
Assert.AreEqual("C37H38N4O10", MolecularFormulaManipulator.GetString(mfSet[0]));
}
public void Main()
{
#region
var ifac = BODRIsotopeFactory.Instance;
IIsotope c = ifac.GetMajorIsotope("C");
IIsotope h = ifac.GetMajorIsotope("H");
IIsotope n = ifac.GetMajorIsotope("N");
IIsotope o = ifac.GetMajorIsotope("O");
IIsotope p = ifac.GetMajorIsotope("P");
IIsotope s = ifac.GetMajorIsotope("S");
MolecularFormulaRange mfRange = new MolecularFormulaRange();
mfRange.AddIsotope(c, 0, 50);
mfRange.AddIsotope(h, 0, 100);
mfRange.AddIsotope(o, 0, 50);
mfRange.AddIsotope(n, 0, 50);
mfRange.AddIsotope(p, 0, 10);
mfRange.AddIsotope(s, 0, 10);
var builder = Silent.ChemObjectBuilder.Instance;
double minMass = 133.003;
double maxMass = 133.005;
MolecularFormulaGenerator mfg = new MolecularFormulaGenerator(builder, minMass, maxMass, mfRange);
IMolecularFormulaSet mfSet = mfg.GetAllFormulas();
#endregion
}
public void TestMinCounts()
{
var ifac = BODRIsotopeFactory.Instance;
IIsotope c = ifac.GetMajorIsotope("C");
IIsotope h = ifac.GetMajorIsotope("H");
IIsotope n = ifac.GetMajorIsotope("N");
IIsotope o = ifac.GetMajorIsotope("O");
MolecularFormulaRange mfRange = new MolecularFormulaRange();
mfRange.AddIsotope(c, 5, 20);
mfRange.AddIsotope(h, 5, 20);
mfRange.AddIsotope(o, 5, 20);
mfRange.AddIsotope(n, 5, 20);
// The minimal formula MF=C5H5O5N5 MW=215.0290682825
double minMass = 100;
double maxMass = 250;
MolecularFormulaGenerator gen = new MolecularFormulaGenerator(builder, minMass, maxMass, mfRange);
IMolecularFormulaSet mfSet = gen.GetAllFormulas();
// Check that all element counts in the formula are >= 5
foreach (var f in mfSet)
{
foreach (var i in f.Isotopes)
{
int count = f.GetCount(i);
Assert.IsTrue(count >= 5);
}
}
}
public void TestNewIsotope_String_int()
{
IChemObjectBuilder builder = RootObject.Builder;
IIsotope isotope = builder.NewIsotope("C", 13);
Assert.IsNotNull(isotope);
}
public virtual void TestClone_IMolecualrFormula()
{
IMolecularFormulaSet mfS = Builder.NewMolecularFormulaSet();
IMolecularFormula mf1 = Builder.NewMolecularFormula();
IIsotope carb = Builder.NewIsotope("C");
IIsotope flu = Builder.NewIsotope("F");
IIsotope h1 = Builder.NewIsotope("H");
mf1.Add(carb);
mf1.Add(flu);
mf1.Add(h1, 3);
mfS.Add(mf1);
IMolecularFormula mf2 = Builder.NewMolecularFormula();
IIsotope carb2 = Builder.NewIsotope("C");
IIsotope iode = Builder.NewIsotope("I");
IIsotope h2 = Builder.NewIsotope("H");
mf2.Add(carb2);
mf2.Add(iode, 2);
mf2.Add(h2, 2);
mfS.Add(mf2);
object clone = mfS.Clone();
Assert.IsTrue(clone is IMolecularFormulaSet);
Assert.AreNotSame(mfS, clone);
Assert.AreEqual(mfS.Count(), ((IMolecularFormulaSet)clone).Count());
Assert.AreEqual(mfS[0].IsotopesCount, ((IMolecularFormulaSet)clone)
[0].IsotopesCount);
Assert.AreEqual(mfS[1].IsotopesCount, ((IMolecularFormulaSet)clone)
[1].IsotopesCount);
}
public void TestNewIsotope_IElement()
{
IChemObjectBuilder builder = RootObject.Builder;
IIsotope isotope = builder.NewIsotope(ChemicalElement.R);
Assert.IsNotNull(isotope);
}
public void TestNewIsotope_int_String_int_Double_double()
{
IChemObjectBuilder builder = RootObject.Builder;
IIsotope isotope = builder.NewIsotope("C", 13, 1.0, 1.0);
Assert.IsNotNull(isotope);
}
public virtual void TestNonclonable()
{
var isotope = new BODRIsotope("C", 6, 12, 12.0, 99.0);
IIsotope clone = (IIsotope)isotope.Clone();
Assert.AreEqual(isotope, clone);
}
public virtual void TestSetMassNumber_Integer()
{
IIsotope i = (IIsotope)NewChemObject();
i.MassNumber = 2;
Assert.AreEqual(2, i.MassNumber.Value);
}
public void TestMaxCounts()
{
var ifac = BODRIsotopeFactory.Instance;
IIsotope c = ifac.GetMajorIsotope("C");
IIsotope h = ifac.GetMajorIsotope("H");
IIsotope n = ifac.GetMajorIsotope("N");
IIsotope o = ifac.GetMajorIsotope("O");
MolecularFormulaRange mfRange = new MolecularFormulaRange();
mfRange.AddIsotope(c, 3, 7);
mfRange.AddIsotope(h, 3, 7);
mfRange.AddIsotope(o, 3, 7);
mfRange.AddIsotope(n, 3, 7);
// The maximal formula MF=C7H7O7N7 MW=301.0406955954
double minMass = 250;
double maxMass = 400;
MolecularFormulaGenerator gen = new MolecularFormulaGenerator(builder, minMass, maxMass, mfRange);
IMolecularFormulaSet mfSet = gen.GetAllFormulas();
// Check that all element counts in the formula are <= 7
foreach (var f in mfSet)
{
foreach (var i in f.Isotopes)
{
int count = f.GetCount(i);
Assert.IsTrue(count <= 7);
}
}
}
public void TestGetIsotopeCountMin_IIsotope4()
{
MolecularFormulaRange mfRange = new MolecularFormulaRange();
IIsotope carb1 = builder.NewIsotope("C");
IIsotope h1 = builder.NewIsotope("H");
IIsotope carb2 = builder.NewIsotope("C");
carb2.Abundance = 13.0876689;
IIsotope h2 = builder.NewIsotope("H");
h2.Abundance = 2.0968768;
mfRange.AddIsotope(carb1, 0, 10);
mfRange.AddIsotope(h1, 0, 10);
mfRange.AddIsotope(carb2, 5, 10);
mfRange.AddIsotope(h2, 5, 10);
Assert.AreEqual(4, mfRange.Count);
Assert.AreEqual(0, mfRange.GetIsotopeCountMin(carb1));
Assert.AreEqual(0, mfRange.GetIsotopeCountMin(h1));
Assert.AreEqual(5, mfRange.GetIsotopeCountMin(carb2));
Assert.AreEqual(5, mfRange.GetIsotopeCountMin(h2));
}
public void TestMatchAgainstItself()
{
var m_element1 = new Mock <IIsotope>(); IIsotope element1 = m_element1.Object;
string result = IsotopeDiff.Diff(element1, element1);
AssertZeroLength(result);
}
private IIsotope createIsotopeOfElement(System.String currentElement, SaxAttributesSupport atts)
{
IIsotope isotope = builder.newIsotope(currentElement);
for (int i = 0; i < atts.GetLength(); i++)
{
try
{
if ("id".Equals(atts.GetFullName(i)))
{
isotope.ID = atts.GetValue(i);
}
else if ("isotopeNumber".Equals(atts.GetFullName(i)))
{
isotope.MassNumber = System.Int32.Parse(atts.GetValue(i));
}
else if ("elementType".Equals(atts.GetFullName(i)))
{
isotope.Symbol = atts.GetValue(i);
}
}
catch (System.FormatException exception)
{
//logger.error("Value of isotope@", atts.GetFullName(i), " is not as expected.");
//logger.debug(exception);
}
}
return(isotope);
}
public virtual void TestSetExactMass_Double()
{
IIsotope i = (IIsotope)NewChemObject();
i.ExactMass = 12.03;
Assert.AreEqual(12.03, i.ExactMass.Value, 0.001);
}
public virtual void TestInstance_IIsotope()
{
IMolecularFormula mf = Builder.NewMolecularFormula();
IIsotope carb = Builder.NewIsotope("C");
IIsotope flu = Builder.NewIsotope("F");
IIsotope h1 = Builder.NewIsotope("H");
mf.Add(carb);
mf.Add(flu);
mf.Add(h1, 3);
IEnumerator <IIsotope> istoIter = mf.Isotopes.GetEnumerator();
Assert.IsNotNull(istoIter);
Assert.IsTrue(istoIter.MoveNext());
IIsotope next = istoIter.Current;
Assert.IsTrue(next is IIsotope);
// Assert.AreEqual(carb, next);
Assert.IsTrue(istoIter.MoveNext());
next = istoIter.Current;
Assert.IsTrue(next is IIsotope);
// Assert.AreEqual(flu, next);
Assert.IsTrue(istoIter.MoveNext());
next = istoIter.Current;
Assert.IsTrue(next is IIsotope);
// Assert.AreEqual(h1, next);
Assert.IsFalse(istoIter.MoveNext());
}
public override void startElement(System.String uri, System.String local, System.String raw, SaxAttributesSupport atts)
{
currentChars = "";
dictRef = "";
//logger.debug("startElement: ", raw);
//logger.debug("uri: ", uri);
//logger.debug("local: ", local);
//logger.debug("raw: ", raw);
if ("isotope".Equals(local))
{
workingIsotope = createIsotopeOfElement(currentElement, atts);
}
else if ("isotopeList".Equals(local))
{
currentElement = getElementSymbol(atts);
}
else if ("abundance".Equals(local))
{
//logger.warn("Disregarding dictRef for now...");
}
else if ("scalar".Equals(local))
{
for (int i = 0; i < atts.GetLength(); i++)
{
if ("dictRef".Equals(atts.GetFullName(i)))
{
dictRef = atts.GetValue(i);
}
}
}
}
public void TestGetMajorIsotopeInt()
{
var isofac = BODRIsotopeFactory.Instance;
IIsotope isotope = isofac.GetMajorIsotope(17);
Assert.AreEqual("Cl", isotope.Symbol);
}
public virtual void TestGetIsotope_Number_Clone()
{
IMolecularFormula mf = Builder.NewMolecularFormula();
IIsotope carb = Builder.NewIsotope("C");
IIsotope flu = Builder.NewIsotope("F");
IIsotope h1 = Builder.NewIsotope("H");
mf.Add(carb);
mf.Add(flu);
mf.Add(h1, 3);
object clone = mf.Clone();
Assert.IsTrue(clone is IMolecularFormula);
IMolecularFormula cloneFormula = (IMolecularFormula)clone;
Assert.AreEqual(1, cloneFormula.GetCount(carb));
Assert.AreEqual(1, cloneFormula.GetCount(flu));
Assert.AreEqual(3, cloneFormula.GetCount(h1));
// In a List the objects are not stored in the same order than called
// Assert.AreEqual("C", cloneFormula.Isotopes[0].Symbol);
// Assert.AreEqual("F", cloneFormula.Isotopes[1].Symbol);
// Assert.AreEqual("H", cloneFormula.Isotopes[2].Symbol);
}
public void TestGetMajorIsotopeNonelement()
{
var isofac = BODRIsotopeFactory.Instance;
IIsotope isotope = isofac.GetMajorIsotope("E");
Assert.IsNull(isotope);
}
public void TestGetMajorIsotopeString()
{
var isofac = BODRIsotopeFactory.Instance;
IIsotope isotope = isofac.GetMajorIsotope("Te");
Assert.AreEqual(129.9062244, isotope.ExactMass.Value, 0.0001);
}
/// <summary>
/// Returns the molecular weight (exact mass) of the major isotopes
/// of all heavy atoms of the given IAtomContainer.
/// </summary>
/// <param name="atomContainer">an IAtomContainer to calculate the mocular weight for</param>
/// <exception cref="CDKException">if an error occurs with the IsotopeFactory</exception>
/// <returns>the molecularweight (exact mass) of the major isotopes
/// of all heavy atoms of the given IAtomContainer</returns>
private static double GetMolecularWeight(T atomContainer)
{
double mw = 0.0;
try
{
var isotopeFactory = CDK.IsotopeFactory;
foreach (var atom in atomContainer.Atoms)
{
if (!atom.AtomicNumber.Equals(AtomicNumbers.H))
{
IIsotope majorIsotope = isotopeFactory.GetMajorIsotope(atom.Symbol);
if (majorIsotope != null && majorIsotope.ExactMass != null)
{
mw += majorIsotope.ExactMass.Value;
}
}
}
}
catch (IOException e)
{
throw new CDKException(e.Message, e);
}
return(mw);
}
/// <summary>
/// Adds an Isotope to this MolecularFormulaExpand in a number of
/// maximum and minimum occurrences allowed.
/// </summary>
/// <param name="isotope">The isotope to be added to this MolecularFormulaExpand</param>
/// <param name="countMax">The maximal number of occurrences to add</param>
/// <param name="countMin">The minimal number of occurrences to add</param>
public void AddIsotope(IIsotope isotope, int countMin, int countMax)
{
if (isotope == null)
{
throw new ArgumentNullException(nameof(isotope), "Isotope must not be null");
}
bool flag = false;
foreach (var thisIsotope in GetIsotopes())
{
if (IsTheSame(thisIsotope, isotope))
{
isotopesMax[thisIsotope] = countMax;
isotopesMin[thisIsotope] = countMin;
flag = true;
break;
}
}
if (!flag)
{
isotopesMax[isotope] = countMax;
isotopesMin[isotope] = countMin;
}
}
/// <summary>
/// Returns the most abundant (major) isotope with a given atomic number.
/// </summary>
/// <remarks>
/// The isotope's abundance is for atoms with atomic number 60 and smaller
/// defined as a number that is proportional to the 100 of the most abundant
/// isotope. For atoms with higher atomic numbers, the abundance is defined
/// as a percentage.
/// </remarks>
/// <param name="elem">The atomicNumber for which an isotope is to be returned</param>
/// <returns>The isotope corresponding to the given atomic number</returns>
/// <seealso cref="GetMajorIsotope(string)"/>
public IIsotope GetMajorIsotope(int elem)
{
IIsotope major = null;
if (this.majorIsotope[elem] != null)
{
return(Clone(this.majorIsotope[elem]));
}
var isotopes = this.isotopes[elem];
if (isotopes != null)
{
foreach (var isotope in isotopes)
{
if (isotope.Abundance <= 0)
{
continue;
}
if (major == null ||
isotope.Abundance > major.Abundance)
{
major = isotope;
}
}
if (major != null)
{
this.majorIsotope[elem] = major;
}
else
{
Trace.TraceError($"Could not find major isotope for: {elem}");
}
}
return(Clone(major));
}
private IMolecularFormula AsFormula(IIsotope isotope)
{
var mf = builder.NewMolecularFormula();
mf.Add(isotope);
return(mf);
}
public override void endElement(System.String uri, System.String local, System.String raw)
{
//logger.debug("end element: ", raw);
if ("isotope".Equals(local))
{
if (workingIsotope != null)
isotopes.Add(workingIsotope);
workingIsotope = null;
}
else if ("isotopeList".Equals(local))
{
currentElement = null;
}
else if ("abundance".Equals(local))
{
try
{
workingIsotope.NaturalAbundance = System.Double.Parse(currentChars);
}
catch (System.FormatException exception)
{
//logger.error("The abundance value is incorrect: ", currentChars);
//logger.debug(exception);
}
}
else if ("scalar".Equals(local))
{
try
{
if ("cdk:exactMass".Equals(dictRef))
{
workingIsotope.setExactMass(System.Double.Parse(currentChars));
}
else if ("cdk:atomicNumber".Equals(dictRef))
{
workingIsotope.AtomicNumber = System.Int32.Parse(currentChars);
}
}
catch (System.FormatException exception)
{
//logger.error("The ", dictRef, " value is incorrect: ", currentChars);
//logger.debug(exception);
}
}
}
public override void startElement(System.String uri, System.String local, System.String raw, SaxAttributesSupport atts)
{
currentChars = "";
dictRef = "";
//logger.debug("startElement: ", raw);
//logger.debug("uri: ", uri);
//logger.debug("local: ", local);
//logger.debug("raw: ", raw);
if ("isotope".Equals(local))
{
workingIsotope = createIsotopeOfElement(currentElement, atts);
}
else if ("isotopeList".Equals(local))
{
currentElement = getElementSymbol(atts);
}
else if ("abundance".Equals(local))
{
//logger.warn("Disregarding dictRef for now...");
}
else if ("scalar".Equals(local))
{
for (int i = 0; i < atts.GetLength(); i++)
{
if ("dictRef".Equals(atts.GetFullName(i)))
{
dictRef = atts.GetValue(i);
}
}
}
}
/// <summary> Configures an atom to have all the data of the
/// given isotope.
///
/// </summary>
/// <param name="atom"> The atom to be configure
/// </param>
/// <param name="isotope"> The isotope to read the data from
/// </param>
/// <returns> The configured atom
/// </returns>
public virtual IAtom configure(IAtom atom, IIsotope isotope)
{
atom.MassNumber = isotope.MassNumber;
atom.Symbol = isotope.Symbol;
atom.setExactMass(isotope.getExactMass());
atom.AtomicNumber = isotope.AtomicNumber;
atom.NaturalAbundance = isotope.NaturalAbundance;
return atom;
}
