public void TestIsotope_IElement()
{
var element = ChemicalElement.C;
IIsotope i = new Isotope(element);
Assert.AreEqual("C", i.Symbol);
}
/// <summary>
/// Comparison method to sort the isotopes by natural abundance
/// Sorts largest to smallest
/// </summary>
/// <param name="x"></param>
/// <param name="y"></param>
/// <returns></returns>
private int CompareNaturalAbundance(Isotope x, Isotope y)
{
if (x == null)
{
if (y == null)
{
return(0);
}
return(-1);
}
if (y == null)
{
return(1);
}
var returnValue = y.NaturalAbundance.CompareTo(x.NaturalAbundance);
if (returnValue != 0)
{
return(returnValue);
}
return(y.Mass.CompareTo(x.Mass));
}
public double CalculateMassSums()
{
double mass_sum = 0;
for (Isotope iso = Isotope.pu238; iso <= Isotope.am241; iso++)
{
currentMassSum[(int)iso].v = 0;
}
foreach (CompositeIsotopic ci in isotopicComponents)
{
if (ci.pu_mass == 0.0f)
{
continue;
}
for (Isotope iso = Isotope.pu238; iso <= Isotope.am241; iso++)
{
currentMassSum[(int)iso].v += ci.CurrentMass[(int)iso].v;
}
}
for (Isotope iso = Isotope.pu238; iso <= Isotope.pu242; iso++)
{
mass_sum += currentMassSum[(int)iso].v;
}
return(mass_sum);
}
//draws the isotope label at ten-o-clock
private LabelMetrics DrawIsotopeLabel(DrawingContext drawingContext, AtomTextMetrics mainAtomMetrics, AtomTextMetrics hMetrics)
{
Debug.Assert(Isotope != null);
string isoLabel = Isotope.ToString();
var isotopeText = new IsotopeLabelText(isoLabel, PixelsPerDip());
Vector isotopeOffsetVector = BasicGeometry.ScreenNorth * GlyphText.SymbolSize;
Matrix rotator = new Matrix();
double angle = -60;
//avoid overlap of label and hydrogens
if (hMetrics != null && ParentAtom.GetDefaultHOrientation() == CompassPoints.West)
{
angle = -35;
}
rotator.Rotate(angle);
isotopeOffsetVector = isotopeOffsetVector * rotator;
Point isoCenter = mainAtomMetrics.Geocenter + isotopeOffsetVector;
isotopeText.MeasureAtCenter(isoCenter);
isotopeText.Fill = Fill;
isotopeText.DrawAtBottomLeft(isotopeText.TextMetrics.BoundingBox.BottomLeft, drawingContext);
return(isotopeText.TextMetrics);
}
/// <summary>
/// Parse isotopic envelope string for feature.
/// </summary>
/// <param name="env">Isotopic envelope string.</param>
/// <returns>Array of isotopes.</returns>
private static Isotope[] ReadIsotopicEnvelope(string env)
{
var isotopePeaks = env.Split(';');
if (isotopePeaks.Length == 0)
{
return(null);
}
var isotopes = new Isotope[isotopePeaks.Length];
for (int i = 0; i < isotopePeaks.Length; i++)
{
var parts = isotopePeaks[i].Split(',');
if (parts.Length < 2)
{
continue;
}
int index;
double relativeIntensity;
if (!int.TryParse(parts[0], out index) || !double.TryParse(parts[1], out relativeIntensity))
{
continue;
}
isotopes[i] = new Isotope(index, relativeIntensity);
}
return(isotopes);
}
/// <summary>
/// Compares the isotopicNumber for sorting purposes. Sorts smallest to largest
/// </summary>
/// <param name="x"></param>
/// <param name="y"></param>
/// <returns></returns>
private int CompareNumber(Isotope x, Isotope y)
{
if (x == null)
{
if (y == null)
{
return(0);
}
else
{
return(-1);
}
}
else
{
if (y == null)
{
return(1);
}
else
{
return(x.IsotopeNumber.CompareTo(y.IsotopeNumber));
}
}
}
/// <summary>
/// Comparison method to sort the isotopes by natural abundance
/// Sorts largest to smallest
/// </summary>
/// <param name="x"></param>
/// <param name="y"></param>
/// <returns></returns>
private int CompareNaturalAbundance(Isotope x, Isotope y)
{
if (x == null)
{
if (y == null)
{
return(0);
}
else
{
return(-1);
}
}
else
{
if (y == null)
{
return(1);
}
else
{
var retval = y.NaturalAbundance.CompareTo(x.NaturalAbundance);
if (retval != 0)
{
return(retval);
}
else
{
return(y.Mass.CompareTo(x.Mass));
}
}
}
}
public void TestIsotope_String_int()
{
IIsotope i = new Isotope("C", 12);
Assert.AreEqual(12, i.MassNumber.Value);
Assert.AreEqual("C", i.Symbol);
}
public void TestIsotope_Transmute()
{
int z1 = 1, a1 = 4;
var iso1 = new Isotope(z1, a1, null, Decay.NEmit, 0.001, 's');
int z1p = iso1.Transmute(Decay.NEmit, out int a1p);
Assert.AreEqual(a1 - 1, a1p);
Assert.AreEqual(z1, z1p);
int z2 = 118, a2 = 300;
var iso2 = new Isotope(z: z2, a: a2, abundance: null, decayMode: Decay.Alpha, halflife: 0.02, timeUnit: 's');
int z2p = iso2.Transmute(Decay.Alpha, out int a2p);
Assert.AreEqual(a2 - 4, a2p);
Assert.AreEqual(z2 - 2, z2p);
int z3 = 3, a3 = 8;
var iso3 = new Isotope(z3, a3, null, Decay.BetaMinus, 0.03, 's');
int z3p = iso3.Transmute(Decay.BetaMinus, out int a3p);
Assert.AreEqual(a3, a3p);
Assert.AreEqual(z3 + 1, z3p);
int z4 = 4, a4 = 11;
var iso4 = new Isotope(z4, a4, null, Decay.BetaPlus, 0.04, 's');
int z4p = iso4.Transmute(Decay.BetaPlus, out int a4p);
Assert.AreEqual(a4, a4p);
Assert.AreEqual(z4 - 1, z4p);
int z5 = 6, a5 = 15;
var iso5 = new Isotope(z5, a5, null, Decay.Beta2, 0.05, 's');
int z5p = iso5.Transmute(Decay.Beta2, out int a5p);
Assert.AreEqual(a5, a5p);
Assert.AreEqual(z5 + 2, z5p);
int z6 = 6, a6 = 15;
var iso6 = new Isotope(z6, a6, null, Decay.ECap1, 0.06, 's');
int z6p = iso6.Transmute(Decay.ECap1, out int a6p);
Assert.AreEqual(a6, a6p);
Assert.AreEqual(z6 - 1, z6p);
int z7 = 7, a7 = 17;
var iso7 = new Isotope(z7, a7, null, Decay.ECap2, 0.07, 's');
int z7p = iso7.Transmute(Decay.ECap2, out int a7p);
Assert.AreEqual(a7, a7p);
Assert.AreEqual(z7 - 2, z7p);
int z8 = 8, a8 = 18;
var iso8 = new Isotope(z8, a8, null, Decay.Gamma, 0.08, 's');
int z8p = iso8.Transmute(Decay.Gamma, out int a8p);
Assert.AreEqual(a8, a8p);
Assert.AreEqual(z8, z8p);
}
public void TestIsotope_int_String_double_double()
{
IIsotope i = new Isotope("C", 12.001, 80.0);
Assert.AreEqual("C", i.Symbol);
Assert.AreEqual(6, i.AtomicNumber);
Assert.AreEqual(12.001, i.ExactMass.Value, 0.001);
Assert.AreEqual(80.0, i.Abundance.Value, 0.001);
}
public bool check_grid(int n, Isotope.Drawing.Size s, int dcols, int drows)
{
int r, c;
GridLayout.GetSquarestGrid(n, s, out c, out r);
Assert.AreEqual(drows, r);
Assert.AreEqual(dcols, c);
return true;
}
public void AddLargeIsotopeToFormula()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
ChemicalFormula formulaB = new ChemicalFormula("C2H3NOFe");
Isotope fe = PeriodicTable.GetElement("Fe").PrincipalIsotope;
formulaA.Add(fe, 1);
Assert.AreEqual(formulaA, formulaB);
}
public void AddZeroIsotopeToFormula()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
ChemicalFormula formulaB = new ChemicalFormula("C2H3NO");
Isotope h1 = PeriodicTable.GetElement("H")[1];
formulaA.Add(h1, 0);
Assert.AreEqual(formulaA, formulaB);
}
public void AddNegativeIsotopeToFormula()
{
ChemicalFormula formulaA = new ChemicalFormula("C2HH{1}2NO");
ChemicalFormula formulaB = new ChemicalFormula("C2HNO");
Isotope h1 = PeriodicTable.GetElement("H")[1];
formulaA.Add(h1, -2);
Assert.AreEqual(formulaA, formulaB);
}
public static void AddIsotopeToFormula()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("C2H3NO");
ChemicalFormula formulaB = ChemicalFormula.ParseFormula("C2H3H{1}NO");
Isotope h1 = PeriodicTable.GetElement("H")[1];
formulaA.Add(h1, 1);
Assert.AreEqual(formulaA, formulaB);
}
/// <summary>
/// Removes an isotope.
/// </summary>
/// <param name="isotope">The isotope to remove.</param>
/// <returns>true if exists; otherwise, false.</returns>
public bool RemoveIsotope(Isotope isotope)
{
if (!isotopes.Remove(isotope))
{
return(false);
}
if (isotopes.Remove(isotope))
{
isotopes.Remove(isotope);
}
return(true);
}
public void AddIsotopeWithExistingMassNumber()
{
var elementC = new Element("C", 6, 12.0106);
elementC.AddIsotope(12, 12, 0.9893);
elementC.AddIsotope(13, 13.00335483507, 0.0107);
Isotope isotope = elementC[13];
Assert.AreEqual("C{13}", isotope.ToString());
Assert.AreEqual(6, isotope.Protons);
Assert.AreEqual(7, isotope.Neutrons);
}
public int SpecificIsotopeCount(Isotope isotope)
{
// Residues count
int count = residues.Sum(aar => aar.ThisChemicalFormula.CountSpecificIsotopes(isotope));
// Modifications count (if the mod is a IHasChemicalFormula)
if (_modifications != null)
{
count += _modifications.Where(mod => mod is IHasChemicalFormula).Cast <IHasChemicalFormula>().Sum(mod => mod.ThisChemicalFormula.CountSpecificIsotopes(isotope));
}
return(count);
}
public void TestCompare_NaturalAbundance()
{
Isotope iso = new Isotope("C")
{
Abundance = 12.000000
};
Isotope iso2 = new Isotope("C")
{
Abundance = 12.0
};
Assert.IsTrue(iso.Compare(iso2));
}
public void TestCompare_ExactMass()
{
Isotope iso = new Isotope("C")
{
ExactMass = 12.000000
};
Isotope iso2 = new Isotope("C")
{
ExactMass = 12.0
};
Assert.IsTrue(iso.Compare(iso2));
}
public void TestCompare_MassNumber()
{
Isotope iso = new Isotope("C")
{
MassNumber = 12
};
Isotope iso2 = new Isotope("C")
{
MassNumber = (int)12.0
};
Assert.IsTrue(iso.Compare(iso2));
}
public Isotopics CreateIsotopicsFromSums(DateTime ref_date, bool INCCParity, double mass_sum)
{
Isotopics isor = new Isotopics();
isor.pu_date = new DateTime(ref_date.Ticks);
isor.am_date = new DateTime(ref_date.Ticks);
isor.source_code = source_code;
isor.id = string.Copy(id);
for (Isotope iso = Isotope.pu238; iso <= Isotope.am241; iso++)
{
isor.SetVal(iso, 100.0 * currentMassSum[(int)iso].v / mass_sum);
}
return(isor);
}
private IElement GetFixedIsotopeElement(IElement element, int?fixedIsotopeNumber)
{
if (fixedIsotopeNumber == null)
{
return(element);
}
IIsotope oldIsotope = element.Isotopes
.Single(x => x.NeutronCount == fixedIsotopeNumber - element.AtomicNumber);
IIsotope newIsotope = new Isotope(element.AtomicNumber, oldIsotope.NeutronCount, 1.0);
return(new Element(element.AtomicNumber, element.Symbol,
new ReadOnlyCollection <IIsotope>(new[] { newIsotope })));
}
protected void InitializeIsotopes()
{
var elements = GetAllElements(Constants.FILETYP.DECAY);
foreach (var element in elements)
{
var isotope = new Isotope(element.Z, element.A);
foreach (var data in NuclearData)
{
var fn = GetIsotopeFile(element.Z, element.A, data.ReactionType);
isotope = data.Read(isotope, element.Z, element.A, fn);
}
Isotopes.Add(isotope);
}
}
public void TestIsotope_Ctor()
{
var iso1 = new Isotope(2, 5, 0.0);
Assert.AreEqual(2, iso1.Z);
Assert.AreEqual(5, iso1.A);
Assert.AreEqual(Decay.None, iso1.DecayMode);
Assert.AreEqual(0, iso1.StabilityIndex);
Assert.IsTrue(iso1.IsStable);
var iso2 = new Isotope(z: 118, a: 300, abundance: null, decayMode: Decay.Alpha, halflife: 0.01, timeUnit: 's');
Assert.AreEqual(300, iso2.A);
Assert.AreEqual(Decay.Alpha, iso2.DecayMode);
Assert.AreEqual(5, iso2.StabilityIndex);
}
public static void FillIsotopes()
{
DataTable dt = iRadiate.Common.IO.TextFileReader.ReadCSVFile("Isotopes.csv", true);
foreach (DataRow r in dt.Rows)
{
Isotope iso = new Isotope();
iso.Element = lib.GetItems(typeof(Element), new List <RetrievalCriteria>()).Where(x => (x as Element).Symbol == r["AtomicSymbol"].ToString()).First() as Element;
iso.Weight = Convert.ToInt32(r["Weight"].ToString());
iso.Metastable = Convert.ToBoolean(r["Metastable"].ToString());
iso.HalfLife = Convert.ToDouble(r["HalfLife"].ToString());
lib.SaveItem(iso);
DumpDataStoreItem(iso);
}
}
private Geometry DrawIsotopeLabel(Atom parentAtom, Geometry symbolGeometry)
{
Point startingPoint = parentAtom.Position;
Point nextPos;
if (parentAtom.IsotopeNumber == null)
{
return(symbolGeometry);
}
else
{
Geometry atomGeo = null;
string isoLabel = Isotope.ToString();
if (!(symbolGeometry is EllipseGeometry)) //that is, weve got an explcit, non carbon element
{
var atomText = BuildSymbolLabel(parentAtom.SymbolText, ref startingPoint, out nextPos);
atomGeo = atomText.BuildGeometry(startingPoint);
}
else //its a vertex carbon
{
atomGeo = symbolGeometry;
}
//have a stab at placing the isotope label.
//placementvector gives the CENTRE of the charge text!
//first generate a vector pointing straight up
Vector placementVector = new Vector(0.0, -Math.Max(atomGeo.Bounds.Width, atomGeo.Bounds.Height));
Matrix rotator = new Matrix();
//isotope labels always go in at 10-o-clock from the atom.
rotator.Rotate(-60);
placementVector *= rotator;
//Point firstPlacementPoint = new Point(atomGeo.Bounds.Right, atomGeo.Bounds.Top - chargeText.Height/2);
FormattedText isoText = GetSubscriptText(isoLabel);
Point firstPlacementPoint = parentAtom.Position + placementVector -
new Vector(isoText.Width / 2, isoText.Height / 2);
System.Windows.Media.Geometry isoGeo = isoText.BuildGeometry(firstPlacementPoint);
return(new CombinedGeometry(symbolGeometry, isoGeo));
}
}
public static void FillRadiopharmaceuticals()
{
DataTable dt = iRadiate.Common.IO.TextFileReader.ReadCSVFile("Radiopharmacueticals.csv", true);
foreach (DataRow r in dt.Rows)
{
Console.WriteLine(r["AtomicSymbol"].ToString() + " " + r["AtomicWeight"].ToString());
Chemical rp = new Chemical();
List <RetrievalCriteria> rcList = new List <RetrievalCriteria>();
RetrievalCriteria rc1 = new RetrievalCriteria("Abbreviation", CriteraType.ExactTextMatch, r["AtomicSymbol"].ToString() + "-" + r["AtomicWeight"].ToString());
rcList.Add(rc1);
Isotope iso = lib.GetItems(typeof(Isotope), rcList).First() as Isotope;
rp.Isotope = iso;
rp.LigandAbbreviation = r["Ligand"].ToString();
lib.SaveItem(rp);
}
}
public void PeptideCountElements()
{
Peptide pep = new Peptide("G");
pep.AddModification(new OldSchoolModification(1));
Assert.AreEqual(5, pep.ElementCountWithIsotopes("H"));
pep.AddModification(new OldSchoolChemicalFormulaModification(ChemicalFormula.ParseFormula("H{1}")));
Assert.AreEqual(5, pep.ElementCountWithIsotopes("H")); // NOTHING HAS BEEN ADDED!
pep.AddModification(new OldSchoolChemicalFormulaModification(ChemicalFormula.ParseFormula("H{1}"), ModificationSites.G));
Assert.AreEqual(6, pep.ElementCountWithIsotopes("H"));
Isotope isotope = PeriodicTable.GetElement("H").PrincipalIsotope;
Assert.AreEqual(1, pep.SpecificIsotopeCount(isotope));
}
private void initialize(Isotope isotope)
{
AtomicMassLabel.Text = isotope.AtomicMass + " aem";
IsotopeName.Text = isotope.Name;
var time = " s";
var halfLife = isotope.HalfLife;
if (isotope.HalfLife < 1.0)
{
time = " ms"; halfLife = isotope.HalfLife * 1000.0;
}
if (isotope.HalfLife >= 60)
{
time = " mins"; halfLife = isotope.HalfLife / 60.0;
}
if (isotope.HalfLife >= 3600)
{
time = " hs"; halfLife = isotope.HalfLife / 3600.0;
}
if (isotope.HalfLife >= 86400)
{
time = " days"; halfLife = isotope.HalfLife / 86400.0;
}
if (isotope.HalfLife >= 31536000)
{
time = " yrs"; halfLife = isotope.HalfLife / 31536000;
}
HalfLifeLabel.Text = halfLife + time;
decaysPanel.Controls.Clear();
if (Isotope.Decays.Count == 0)
{
label5.Text = ""; HalfLifeLabel.Text = "stable";
}
foreach (var decay in Isotope.Decays)
{
var decayView = new DecayInfoView(decay.Value);
decaysPanel.Controls.Add(decayView);
decayView.Dock = DockStyle.Top;
}
var csView = new CrossSectionInfoView(Isotope.CrossSections.Select(x => x.Value).ToList());
crossSectionPanel.Controls.Clear();
crossSectionPanel.Controls.Add(csView);
csView.Dock = DockStyle.Top;
}
private void Submit_Click(object sender, EventArgs e)
{
if (txtB_Nuclear.Text == null || txtB_Nuclear.Text == "")
{
MessageBox.Show("Не правльный формат названия изотопа, должно быть U-235", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
return;
}
try
{
var iso = Endf.GetIsotope(txtB_Nuclear.Text);
var str = Isotope.ShowIsotope(iso);
txtB_Info.Text = str;
}
catch (Exception ex)
{
MessageBox.Show(ex.Message, "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
}
}
/// <summary>
/// Parse text field to as non-negative double,
/// assign value to current isotopics instance,
/// format the active text field for user display.
/// </summary>
/// <param name="sender">dialog text field event handler</param>
/// <param name="i">isotopic entry index</param>
private void IsoSigmaNNCheck(TextBox sender, Isotope i)
{
m_iso.modified |= Format.ToNN(sender.Text, ref m_iso[i].sigma);
sender.Text = m_iso[i].sigma.ToString("F6");
}
/// <summary>
/// Parse text field to as percent (double),
/// assign value to current isotopics instance,
/// format the active text field for user display.
/// </summary>
/// <param name="sender">dialog text field event handler</param>
/// <param name="i">isotopic entry index</param>
private void IsoPctCheck(TextBox sender, Isotope i)
{
m_iso.modified |= Format.ToPct(sender.Text, ref m_iso[i].v);
sender.Text = m_iso[i].v.ToString("F6");
}
private static void drawnode(Isotope.Layout.BoxHierarchy.Node<object> node, Isotope.Drawing.Rectangle rect,
object data)
{
}
