/// <summary>
/// In the minimal IMolecularFormula must contain all those IElement found in the
/// minimal IMolecularFormula.
/// </summary>
/// <param name="formulaMax">A IMolecularFormula which contains the maximal representation of the Elements</param>
/// <param name="formulaMin">A IMolecularFormula which contains the minimal representation of the Elements</param>
/// <returns>True, if the correlation is valid</returns>
private static bool ValidCorrelation(IMolecularFormula formulaMin, IMolecularFormula formulaMax)
{
foreach (var element in MolecularFormulaManipulator.Elements(formulaMin))
{
if (!MolecularFormulaManipulator.ContainsElement(formulaMax, element))
{
return(false);
}
}
return(true);
}
/// <summary>
/// Validate the occurrence of this IMolecularFormula.
/// </summary>
/// <param name="formula">Parameter is the IMolecularFormula</param>
/// <returns>An ArrayList containing 9 elements in the order described above</returns>
public double Validate(IMolecularFormula formula)
{
Trace.TraceInformation("Start validation of ", formula);
double isValid = 1.0;
foreach (var element in MolecularFormulaManipulator.Elements(formula))
{
int occur = MolecularFormulaManipulator.GetElementCount(formula, element);
if (occur > hashMap[element.Symbol])
{
isValid = 0.0;
break;
}
}
return(isValid);
}
/// <summary>
/// Validate the occurrence of this <see cref="IMolecularFormula"/>.
/// </summary>
/// <param name="formula">Parameter is the <see cref="IMolecularFormula"/></param>
/// <returns>An ArrayList containing 9 elements in the order described above</returns>
public double Validate(IMolecularFormula formula)
{
Trace.TraceInformation("Start validation of ", formula);
EnsureDefaultOccurElements(formula.Builder);
double isValid = 1.0;
foreach (var element in MolecularFormulaManipulator.Elements(formula))
{
int occur = MolecularFormulaManipulator.GetElementCount(formula, element);
var elemIsotope = formula.Builder.NewIsotope(element.Symbol);
if ((occur < mfRange.GetIsotopeCountMin(elemIsotope)) || (occur > mfRange.GetIsotopeCountMax(elemIsotope)))
{
isValid = 0.0;
break;
}
}
return(isValid);
}
/// <summary>
/// Remove all those IMolecularFormula which are not fit theirs IElement
/// occurrence into a limits. The limits are given from formulaMax and formulaMin.
/// In the minimal IMolecularFormula must contain all those IElement found in the
/// minimal IMolecularFormula.
/// </summary>
/// <param name="formulaSet">IMolecularFormulaSet to look for</param>
/// <param name="formulaMax">A IMolecularFormula which contains the maximal representation of the Elements</param>
/// <param name="formulaMin">A IMolecularFormula which contains the minimal representation of the Elements</param>
/// <returns>A IMolecularFormulaSet with only the IMolecularFormula which the IElements
/// are into the correct occurrence</returns>
public static IMolecularFormulaSet Remove(IMolecularFormulaSet formulaSet, IMolecularFormula formulaMin, IMolecularFormula formulaMax)
{
// prove the correlation between maximum and minimum molecularFormula
if (!ValidCorrelation(formulaMin, formulaMax))
{
return(null);
}
var newFormulaSet = formulaSet.Builder.NewMolecularFormulaSet();
foreach (var formula in formulaSet)
{
bool flagPass = true;
// the formula must contain all element found into the formulaMin
if (!ValidCorrelation(formula, formulaMin))
{
continue;
}
foreach (var element in MolecularFormulaManipulator.Elements(formulaMin))
{
int occur = MolecularFormulaManipulator.GetElementCount(formula, element);
int occurMax = MolecularFormulaManipulator.GetElementCount(formulaMax, element);
int occurMin = MolecularFormulaManipulator.GetElementCount(formulaMin, element);
if (!(occurMin <= occur) || !(occur <= occurMax))
{
flagPass = false;
break;
}
}
if (flagPass) // stored if each IElement occurrence is into the limits
{
newFormulaSet.Add(formula);
}
}
return(newFormulaSet);
}
// Private procedures
private void WriteCrystal(ICrystal crystal)
{
var title = crystal.Title;
if (title != null && title.Trim().Length > 0)
{
Writeln($"TITL {title.Trim()}");
}
else
{
Writeln("TITL Produced with CDK (http://cdk.sf.net/)");
}
Vector3 a = crystal.A;
Vector3 b = crystal.B;
Vector3 c = crystal.C;
double alength = a.Length();
double blength = b.Length();
double clength = c.Length();
double alpha = Vectors.RadianToDegree(Vectors.Angle(b, c));
double beta = Vectors.RadianToDegree(Vectors.Angle(a, c));
double gamma = Vectors.RadianToDegree(Vectors.Angle(a, b));
Write("CELL " + 1.54184.ToString("F5", NumberFormatInfo.InvariantInfo) + " ");
Write(alength.ToString("F5", NumberFormatInfo.InvariantInfo) + " ");
Write(blength.ToString("F5", NumberFormatInfo.InvariantInfo) + " ");
Write(clength.ToString("F5", NumberFormatInfo.InvariantInfo) + " ");
Write(alpha.ToString("F4", NumberFormatInfo.InvariantInfo) + " ");
Write(beta.ToString("F4", NumberFormatInfo.InvariantInfo) + " ");
Write(gamma.ToString("F4", NumberFormatInfo.InvariantInfo) + " ");
Writeln("ZERR " + ((double)crystal.Z).ToString("F5", NumberFormatInfo.InvariantInfo)
+ " 0.01000 0.01000 0.01000 0.0100 0.0100 0.0100");
string spaceGroup = crystal.SpaceGroup;
if (string.Equals("P1", spaceGroup, StringComparison.Ordinal))
{
Writeln("LATT -1");
}
else if (string.Equals("P 2_1 2_1 2_1", spaceGroup, StringComparison.Ordinal))
{
Writeln("LATT -1");
Writeln("SYMM 1/2+X , 1/2-Y , -Z");
Writeln("SYMM -X , 1/2+Y , 1/2-Z");
Writeln("SYMM 1/2-X , -Y , 1/2+Z");
}
string elemNames = "";
string elemCounts = "";
IMolecularFormula formula = MolecularFormulaManipulator.GetMolecularFormula(crystal);
var asortedElements = MolecularFormulaManipulator.Elements(formula).ToReadOnlyList();
foreach (var element in asortedElements)
{
string symbol = element.Symbol;
elemNames += symbol + " ".Substring(symbol.Length);
string countS = MolecularFormulaManipulator.GetElementCount(formula, element).ToString(NumberFormatInfo.InvariantInfo);
elemCounts += countS + " ".Substring(countS.Length);
}
Writeln("SFAC " + elemNames);
Writeln("UNIT " + elemCounts);
/* write atoms */
for (int i = 0; i < crystal.Atoms.Count; i++)
{
IAtom atom = crystal.Atoms[i];
Vector3 cartCoord = atom.Point3D.Value;
Vector3 fracCoord = CrystalGeometryTools.CartesianToFractional(a, b, c, cartCoord);
string symbol = atom.Symbol;
string output = symbol + (i + 1);
Write(output);
for (int j = 1; j < 5 - output.Length; j++)
{
Write(" ");
}
Write(" ");
string elemID = null;
for (int elemidx = 0; elemidx < asortedElements.Count; elemidx++)
{
var elem = asortedElements[elemidx];
if (elem.Symbol.Equals(symbol, StringComparison.Ordinal))
{
elemID = (elemidx + 1).ToString(NumberFormatInfo.InvariantInfo);
break;
}
}
Write(elemID);
Write(" ".Substring(elemID.Length));
Write(fracCoord.X.ToString("F5", NumberFormatInfo.InvariantInfo) + " ");
Write(fracCoord.Y.ToString("F5", NumberFormatInfo.InvariantInfo) + " ");
Writeln(fracCoord.Y.ToString("F5", NumberFormatInfo.InvariantInfo) + " 11.00000 0.05000");
}
Writeln("END");
}