private void TranslatePoints(int atmIdx, Vector3[][] points, int pointDensity, IAtom atom, Vector3 cp)
{
var totalRadius = PeriodicTable.GetVdwRadius(atom.Symbol).Value + solventRadius;
var area = 4 * Math.PI * (totalRadius * totalRadius) * points.Length / pointDensity;
double sumx = 0.0;
double sumy = 0.0;
double sumz = 0.0;
foreach (var point in points)
{
var p = point[1];
sumx += p.X;
sumy += p.Y;
sumz += p.Z;
}
var vconst = 4.0 / 3.0 * Math.PI / (double)pointDensity;
var dotp1 = (atom.Point3D.Value.X - cp.X) * sumx
+ (atom.Point3D.Value.Y - cp.Y) * sumy
+ (atom.Point3D.Value.Z - cp.Z) * sumz;
var volume = vconst * (totalRadius * totalRadius) * dotp1 + (totalRadius * totalRadius * totalRadius) * points.Length;
this.areas[atmIdx] = area;
this.volumes[atmIdx] = volume;
var tmp = new List <Vector3>();
foreach (var point in points)
{
tmp.Add(point[0]);
}
this.surfPoints[atmIdx] = tmp;
}
public static void createEarth()
{
List <double> percentageList = new List <double>();
ChemicalElement element;
List <ChemicalElement> chemicalElements = new List <ChemicalElement>();
element = PeriodicTable.findByName("Nitrogen");
chemicalElements.Add(element);
percentageList.Add(78.08);
element = PeriodicTable.findByName("Oxygen");
chemicalElements.Add(element);
percentageList.Add(20.95);
element = PeriodicTable.findByName("Argon");
chemicalElements.Add(element);
percentageList.Add(0.93);
element = PeriodicTable.findByName("Carbon");
chemicalElements.Add(element);
percentageList.Add(0.04);
ChemicalComposition chemicalComposition = new ChemicalComposition(chemicalElements, percentageList);
Planet x = new Planet(chemicalComposition, ParametriUtente.Science.r_t, ParametriUtente.Science.AU);
x.initPlanet();
Console.WriteLine("Earth created check debug values");
}
public static void ValidatePeriodicTable()
{
Assert.IsTrue(PeriodicTable.ValidateAverageMasses(1e-2));
Assert.IsFalse(PeriodicTable.ValidateAverageMasses(1e-3));
Assert.IsTrue(PeriodicTable.ValidateAbundances(1e-15));
Assert.IsFalse(PeriodicTable.ValidateAbundances(0));
}
/// <summary>
/// <pre>
/// -C#N
/// -[N+]#[C-]
/// -C=[N+]=N
/// -N=[N+]=N
/// </pre>
/// </summary>
internal static bool IsColinear(IAtom atom, IEnumerable <IBond> bonds)
{
if (PeriodicTable.IsMetal(atom.AtomicNumber))
{
return(bonds.Count() == 2);
}
int numSgl = atom.ImplicitHydrogenCount ?? 0;
int numDbl = 0;
int numTpl = 0;
int count = 0;
foreach (var bond in bonds)
{
++count;
switch (bond.Order.Numeric())
{
case 1:
numSgl++;
break;
case 2:
numDbl++;
break;
case 3:
numTpl++;
break;
case 4:
return(true);
default:
return(false);
}
}
if (count != 2)
{
return(false);
}
switch (atom.AtomicNumber)
{
case 6:
case 7:
case 14:
case 32:
if (numTpl == 1 && numSgl == 1)
{
return(true);
}
if (numDbl == 2 && numSgl == 0)
{
return(true);
}
break;
}
return(false);
}
public void TestNullArguments()
{
ChemicalFormula formulaA = new ChemicalFormula("CO");
IHasChemicalFormula ok = null;
Assert.AreEqual("item", Assert.Throws <ArgumentNullException>(() => { formulaA.Add(ok); }).ParamName);
ChemicalFormula ok2 = null;
Assert.AreEqual("formula", Assert.Throws <ArgumentNullException>(() => { formulaA.Add(ok2); }).ParamName);
Assert.AreEqual("other", Assert.Throws <ArgumentNullException>(() => { new ChemicalFormula(ok2); }).ParamName);
Element ok3 = null;
Assert.AreEqual("element", Assert.Throws <ArgumentNullException>(() => { formulaA.AddPrincipalIsotopesOf(ok3, 0); }).ParamName);
Assert.AreEqual("item", Assert.Throws <ArgumentNullException>(() => { formulaA.Remove(ok); }).ParamName);
Assert.AreEqual("formula", Assert.Throws <ArgumentNullException>(() => { formulaA.Remove(ok2); }).ParamName);
Assert.AreEqual("formula", Assert.Throws <ArgumentNullException>(() => { formulaA.IsSubsetOf(ok2); }).ParamName);
Assert.AreEqual("formula", Assert.Throws <ArgumentNullException>(() => { formulaA.IsSupersetOf(ok2); }).ParamName);
Assert.AreEqual("element", Assert.Throws <ArgumentNullException>(() => { formulaA.CountWithIsotopes(ok3); }).ParamName);
Assert.AreEqual("element", Assert.Throws <ArgumentNullException>(() => { formulaA.CountSpecificIsotopes(ok3, 0); }).ParamName);
Assert.IsFalse(formulaA.Equals(ok2));
IEnumerable <IHasChemicalFormula> ok4 = null;
Assert.AreEqual("formulas", Assert.Throws <ArgumentNullException>(() => { ChemicalFormula.Combine(ok4); }).ParamName);
Assert.AreEqual("element", Assert.Throws <ArgumentNullException>(() => { PeriodicTable.Add(ok3); }).ParamName);
Assert.AreEqual("formula", Assert.Throws <ArgumentNullException>(() => { new IsotopicDistribution(ok2); }).ParamName);
IHasMass ok5 = null;
Assert.AreEqual("objectWithMass", Assert.Throws <ArgumentNullException>(() => { ok5.ToMZ(0); }).ParamName);
var ok7 = new PhysicalObjectWithChemicalFormula("C");
}
public void TestReplaceIsotopes()
{
ChemicalFormula formulaA = new ChemicalFormula("CC{13}2H3NO");
formulaA.Replace(PeriodicTable.GetElement("C")[13], PeriodicTable.GetElement("C")[12]);
Assert.AreEqual("CC{12}2H3NO", formulaA.Formula);
}
public void TestBug1245()
{
var ins = ResourceLoader.GetAsStream("NCDK.Data.CML.(1R)-1-aminoethan-1-ol.cml");
var reader = new CMLReader(ins);
try
{
IChemFile cfile = reader.Read(ChemObjectBuilder.Instance.NewChemFile());
Assert.IsNotNull(cfile, "ChemFile was Null");
var containers = ChemFileManipulator.GetAllAtomContainers(cfile);
Assert.AreEqual(1, containers.Count(), "Expected a single atom container");
IAtomContainer container = containers.First();
Assert.IsNotNull(container, "Null atom container read");
foreach (var atom in container.Atoms)
{
Assert.AreEqual(
PeriodicTable.GetAtomicNumber(atom.Symbol),
atom.AtomicNumber,
"Incorrect atomic number");
}
}
finally
{
reader.Close();
}
}
/// <summary>
/// Create initial invariant labeling corresponds to step 1
/// </summary>
/// <returns>List containing the</returns>
private static List <InvPair> CreateInvarLabel(IAtomContainer atomContainer)
{
var atoms = atomContainer.Atoms;
StringBuilder inv;
var vect = new List <InvPair>();
foreach (var a in atoms)
{
inv = new StringBuilder();
var connectedAtoms = atomContainer.GetConnectedAtoms(a).ToReadOnlyList();
inv.Append(connectedAtoms.Count + (a.ImplicitHydrogenCount ?? 0)); //Num connections
inv.Append(connectedAtoms.Count); //Num of non H bonds
inv.Append(PeriodicTable.GetAtomicNumber(a.Symbol));
double charge = a.Charge ?? 0;
if (charge < 0) //Sign of charge
{
inv.Append(1);
}
else
{
inv.Append(0); //Absolute charge
}
inv.Append((int)Math.Abs((a.FormalCharge ?? 0))); //Hydrogen count
inv.Append((a.ImplicitHydrogenCount ?? 0));
vect.Add(new InvPair(long.Parse(inv.ToString(), NumberFormatInfo.InvariantInfo), a));
}
return(vect);
}
/// <summary>
/// Mass number for a atom with a given atomic number and exact mass.
/// </summary>
/// <param name="atomicNumber">atomic number</param>
/// <param name="exactMass">exact mass</param>
/// <returns>the mass number (or <see langword="null"/>>) if no mass number was found</returns>
/// <exception cref="IOException">isotope configuration could not be loaded</exception>
private static int?MassNumber(int atomicNumber, double exactMass)
{
var symbol = PeriodicTable.GetSymbol(atomicNumber);
var isotope = CDK.IsotopeFactory.GetIsotope(symbol, exactMass, 0.001);
return(isotope?.MassNumber);
}
private static void BenchmarkTimeGettingElementFromPeriodicTable()
{
Console.WriteLine("Starting benchmark BenchmarkTimeGettingElementFromPeriodicTable");
int numRepetitions = 100000000;
Stopwatch stopWatch = new Stopwatch();
stopWatch.Restart();
for (int i = 0; i < numRepetitions; i++)
{
var a = PeriodicTable.GetElement(1);
var b = a.Protons + a.AverageMass + 4;
}
stopWatch.Stop();
Console.WriteLine("Time for getting by atomic number: " + stopWatch.Elapsed);
stopWatch.Restart();
for (int i = 0; i < numRepetitions; i++)
{
var a = PeriodicTable.GetElement("H");
var b = a.Protons + a.AverageMass + 4;
}
stopWatch.Stop();
Console.WriteLine("Time for getting by atomic symbol: " + stopWatch.Elapsed);
Console.WriteLine("Benchmark BenchmarkTimeGettingElementFromPeriodicTable finished");
}
public override bool Matches(IAtom atom)
{
string symbol = atom.Symbol;
int group = PeriodicTable.GetGroup(symbol);
return(group == this.groupNumber);
}
static void loop(PeriodicTable table)
{
while (true)
{
Console.Write("Enter an element symbol: ");
string input = Console.ReadLine();
Element result = null;
if (table.Elements.ContainsKey(input))
{
result = table[input];
}
else if (int.TryParse(input, out int index))
{
if (index > 0 && index <= 118)
{
result = table[index];
}
}
if (result != null)
{
Console.WriteLine(result.ToString().Replace("; ", "\n> ").Insert(0, "> "));
}
else
{
Console.WriteLine("Element not found.");
}
}
}
private BODRIsotopeFactory()
{
string configFile = "NCDK.Config.Data.isotopes.dat";
var ins = ResourceLoader.GetAsStream(configFile);
var buffer = new byte[8];
ins.Read(buffer, 0, 4);
Array.Reverse(buffer, 0, 4);
int isotopeCount = BitConverter.ToInt32(buffer, 0);
for (int i = 0; i < isotopeCount; i++)
{
var atomicNum = ins.ReadByte();
ins.Read(buffer, 0, 2);
Array.Reverse(buffer, 0, 2);
var massNum = BitConverter.ToInt16(buffer, 0);
ins.Read(buffer, 0, 8);
Array.Reverse(buffer, 0, 8);
var exactMass = BitConverter.ToDouble(buffer, 0);
double natAbund;
if (ins.ReadByte() == 1)
{
ins.Read(buffer, 0, 8);
Array.Reverse(buffer, 0, 8);
natAbund = BitConverter.ToDouble(buffer, 0);
}
else
{
natAbund = 0;
}
var isotope = new BODRIsotope(PeriodicTable.GetSymbol(atomicNum), atomicNum, massNum, exactMass, natAbund);
Add(isotope);
}
}
public void ChemicalForulaMyTest()
{
ChemicalFormula formula = new ChemicalFormula();
formula.Add(new ChemicalFormula("C3H5NO"));
Assert.AreEqual(PeriodicTable.GetElement("C").PrincipalIsotope.AtomicMass * 3 + PeriodicTable.GetElement("H").PrincipalIsotope.AtomicMass * 5 + PeriodicTable.GetElement("N").PrincipalIsotope.AtomicMass + PeriodicTable.GetElement("O").PrincipalIsotope.AtomicMass, formula.MonoisotopicMass);
}
private void CreationKit_Load(object sender, EventArgs e)
{
Partita newGame = new Partita();
newGame = Partita.createPartita_form();
this.sessione = newGame;
PeriodicTable.init();
this.StarSeedElements.DataSource = elementsComboBox_ds.periodicTable_UI;
this.Element.DataSource = elementsComboBox_ds.periodicTable_UI;
this.Element.DisplayMember = "completeName";
this.Element.ValueMember = "Self";
foreach (Object obj in Enum.GetValues(typeof(PlanetClassification)))
{
this.PlanetClassTxt.Items.Add(obj);
}
foreach (Object obj in Enum.GetValues(typeof(NucleusClassification)))
{
this.NucleusClassTxt.Items.Add(obj);
}
}
/// <summary>
/// Populates the page with content passed during navigation. Any saved state is also
/// provided when recreating a page from a prior session.
/// </summary>
/// <param name="navigationParameter">The parameter value passed to
/// <see cref="Frame.Navigate(Type, Object)"/> when this page was initially requested.
/// </param>
/// <param name="pageState">A dictionary of state preserved by this page during an earlier
/// session. This will be null the first time a page is visited.</param>
protected override async void LoadState(Object navigationParameter, Dictionary <String, Object> pageState)
{
// TODO: Create an appropriate data model for your problem domain to replace the sample data
/*var sampleDataGroups = SampleDataSource.GetGroups((String)navigationParameter);
* this.DefaultViewModel["Items"] = sampleDataGroups;*/
theTable = await PeriodicTable.LoadTable();
}
public void RemoveIsotopeCompletelyFromFromula()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
ChemicalFormula formulaB = new ChemicalFormula("C2NO");
formulaA.RemoveIsotopesOf(PeriodicTable.GetElement("H"));
Assert.AreEqual(formulaA, formulaB);
}
public void AddIsotopeWithExistingMassNumber()
{
Element al = PeriodicTable.GetElement("Al");
Assert.Throws <ArgumentException>(() =>
{
al.AddIsotope(27, 28, 1);
}, "Isotope with mass number " + 28 + " already exists");
}
public static void RemoveElementCompletelyFromFromula()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("C2H3NO");
ChemicalFormula formulaB = ChemicalFormula.ParseFormula("C2NO");
formulaA.RemoveIsotopesOf(PeriodicTable.GetElement("H"));
Assert.AreEqual(formulaB, formulaA);
}
public void RemoveNegativeElementFromFromula()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
ChemicalFormula formulaB = new ChemicalFormula("C2H5NO");
formulaA.Remove(PeriodicTable.GetElement("H"), -2);
Assert.AreEqual(formulaA, formulaB);
}
public ItemsPage()
{
theTable = new PeriodicTable();
LoadTable();
this.InitializeComponent();
DataContext = this;
}
public void RemoveZeroIsotopeFromFromula()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
ChemicalFormula formulaB = new ChemicalFormula("C2H3NO");
formulaA.Remove(PeriodicTable.GetElement("H")[1], 0);
Assert.AreEqual(formulaA, formulaB);
}
public void RemoveElementCompletelyFromFromulaWithHeavyIsotope()
{
ChemicalFormula formulaA = new ChemicalFormula("C2C{13}H3NO");
ChemicalFormula formulaB = new ChemicalFormula("H3NO");
formulaA.Remove(PeriodicTable.GetElement("C"));
Assert.AreEqual(formulaA, formulaB);
}
public static void RemoveElementFromFromula()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("C2H3NO");
ChemicalFormula formulaB = ChemicalFormula.ParseFormula("C2HNO");
formulaA.Remove(PeriodicTable.GetElement("H"), 2);
Assert.AreEqual(formulaA, formulaB);
}
public void TestUpdateElements()
{
var elementLocation = Path.Combine(TestContext.CurrentContext.TestDirectory, "lal.dat");
Loaders.UpdateElements(elementLocation);
Loaders.UpdateElements(elementLocation);
Assert.IsTrue(PeriodicTable.ValidateAbundances(1e-15));
Assert.IsTrue(PeriodicTable.ValidateAverageMasses(1e-2));
}
public void ThresholdProbability()
{
ChemicalFormula formulaA = new ChemicalFormula("CO");
// Only the principal isotopes have joint probability of 0.5! So one result when calcuating isotopic distribution
var a = new IsotopicDistribution(formulaA, 0.0001, 0.5);
Assert.AreEqual(1, a.Masses.Count());
Assert.IsTrue((PeriodicTable.GetElement("C").PrincipalIsotope.AtomicMass + PeriodicTable.GetElement("O").PrincipalIsotope.AtomicMass).MassEquals(a.Masses[0]));
}
public HumanPlayer(Color color)
: base(color)
{
healthBar = new ProgressBar(new Zone(0, 0, 10, 2));
healthBar.BorderThickness = 0;
resourceBar = new ResourceBar(new Zone(0, 0, 40, 6));
resourceBar.BorderThickness = 0;
pt = new PeriodicTable(this);
selectionCircle = new Animation("SelectionCircleSmall");
}
private static int GetAtomicNumber(ILigand ligand)
{
var atomNumber = ligand.LigandAtom.AtomicNumber;
if (atomNumber != 0)
{
return(atomNumber);
}
return(PeriodicTable.GetAtomicNumber(ligand.LigandAtom.Symbol));
}
public static void ThresholdProbability()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("CO");
// Only the principal isotopes have joint probability of 0.5! So one result when calcuating isotopic distribution
var a = IsotopicDistribution.GetDistribution(formulaA, 0.0001, 0.5);
Assert.AreEqual(1, a.Masses.Count());
Assert.IsTrue(Math.Abs((PeriodicTable.GetElement("C").PrincipalIsotope.AtomicMass + PeriodicTable.GetElement("O").PrincipalIsotope.AtomicMass - a.Masses.First())) < 1e-9);
}
private void RunCustomGenericCollection()
{
PeriodicTable < Element > elements = new PeriodicTable<Element>();
elements.AddElement( new Element( ElementType.Fluorine ) );
elements.AddElement( new Element( ElementType.Carbon ) );
elements.AddElement( new Element( ElementType.Lithium ) );
foreach( Element element in elements )
element.Display();
}
/// <summary>
/// Initialize the surface, generating the points on the accessible surface
/// area of each atom as well as calculating the surface area of each atom.
/// </summary>
private void Init()
{
// invariants
foreach (var atom in atoms)
{
if (atom.Point3D == null)
{
throw new ArgumentException("One or more atoms had no 3D coordinate set");
}
}
// get r_f and geometric center
var cp = new Vector3(0, 0, 0);
double maxRadius = 0;
foreach (var atom in atoms)
{
var vdwr = PeriodicTable.GetVdwRadius(atom.Symbol).Value;
if (vdwr + solventRadius > maxRadius)
{
maxRadius = PeriodicTable.GetVdwRadius(atom.Symbol).Value + solventRadius;
}
cp.X = cp.X + atom.Point3D.Value.X;
cp.Y = cp.Y + atom.Point3D.Value.Y;
cp.Z = cp.Z + atom.Point3D.Value.Z;
}
cp.X = cp.X / atoms.Length;
cp.Y = cp.Y / atoms.Length;
cp.Z = cp.Z / atoms.Length;
// do the tesselation
var tess = new Tessellate("ico", tesslevel);
tess.DoTessellate();
Trace.TraceInformation($"Got tesselation, number of triangles = {tess.GetNumberOfTriangles()}");
// get neighbor list
var nbrlist = new NeighborList(atoms, maxRadius + solventRadius);
Trace.TraceInformation("Got neighbor list");
// loop over atoms and get surface points
this.surfPoints = new List <Vector3> [atoms.Length];
this.areas = new double[atoms.Length];
this.volumes = new double[atoms.Length];
for (int i = 0; i < atoms.Length; i++)
{
var pointDensity = tess.GetNumberOfTriangles() * 3;
var points = AtomicSurfacePoints(nbrlist, i, atoms[i], tess);
TranslatePoints(i, points, pointDensity, atoms[i], cp);
}
Trace.TraceInformation("Obtained points, areas and volumes");
}
public static void LoadElements()
{
// has the periodic table already been loaded?
if (PeriodicTable.GetElement(1) != null)
{
return;
}
// periodic table has not been loaded yet - load it
PeriodicTableLoader.Load();
}
