/// <summary>
/// get symmetry matrix for a specific symmetry operation string
/// may need translation
/// linear search
/// </summary>
/// <param name="symOpMatrices"></param>
/// <param name="symOpString"></param>
/// <returns></returns>
public SymOpMatrix GetSymmetryMatrixFromSymmetryString(SymOpMatrix[] symOpMatrices, string symOpString)
{
int index1 = symOpString.IndexOf("_");
int index2 = symOpString.LastIndexOf("_");
string symOpNum = "";
string symString = "";
if (index1 == index2)
{
symOpNum = symOpString.Substring(0, index1);
symString = symOpString.Substring(index1 + 1, symOpString.Length - index1 - 1);
}
else
{
symOpNum = symOpString.Substring(index1 + 1, index2 - index1 - 1);
symString = symOpString.Substring(index2 + 1, symOpString.Length - index2 - 1);
}
SymOpMatrix convertedSymOpMatrix = null;
foreach (SymOpMatrix symOpMatrix in symOpMatrices)
{
if (symOpMatrix.symmetryOpNum == symOpNum)
{
convertedSymOpMatrix = (SymOpMatrix)symOpMatrix.Clone();
break;
}
}
if (convertedSymOpMatrix != null)
{
if (symString.Length == 3)
{
for (int i = 0; i < 3; i++)
{
if (symString[i] == '5')
{
continue;
}
convertedSymOpMatrix.Add(i, 3, convertedSymOpMatrix.Value(i, 3) + (double)(Convert.ToInt32(symString[i].ToString()) - 5));
}
}
/* should deal with a symmetry string with translate vectors > 5
* format of this type of symmetry string: 1_+10-1+6
* translate vector (+5, -6, +1)
*/
else if (symString.Length > 3)
{
string[] vectStrings = SeparateSymmetryString(symString);
convertedSymOpMatrix.Add(0, 3, convertedSymOpMatrix.Value(0, 3) +
(double)(Convert.ToInt32(vectStrings[0]) - 5));
convertedSymOpMatrix.Add(1, 3, convertedSymOpMatrix.Value(1, 3) +
(double)(Convert.ToInt32(vectStrings[1]) - 5));
convertedSymOpMatrix.Add(2, 3, convertedSymOpMatrix.Value(2, 3) +
(double)(Convert.ToInt32(vectStrings[2]) - 5));
}
}
return(convertedSymOpMatrix);
}
/// <summary>
/// get matrix from a symmetry operation string
/// </summary>
/// <param name="symOpStr"></param>
/// <param name="symOpMatrix"></param>
public void SetSymOpMatrix(string fullSymOpStr, /*string symOpString,*/ ref SymOpMatrix symOpMatrix)
{
double[] indexValues = new double [3];
string [] symOpRows = fullSymOpStr.ToUpper().Split(',');
for (int dimNo = 0; dimNo < 3; dimNo++)
{
string symOpRow = symOpRows[dimNo];
symOpMatrix.Add(dimNo, 0, GetDimIndex(symOpRow, "X"));
symOpMatrix.Add(dimNo, 1, GetDimIndex(symOpRow, "Y"));
symOpMatrix.Add(dimNo, 2, GetDimIndex(symOpRow, "Z"));
//int transVector = Convert.ToInt32 (symOpString[dimNo].ToString ()) - 5;
//symOpMatrix.Add (dimNo, 3, GetVectorValue(symOpRow) - transVector);
symOpMatrix.Add(dimNo, 3, GetVectorValue(symOpRow));
}
}
/// <summary>
/// the symmetry operator string
/// </summary>
/// <param name="infoNode"></param>
/// <returns></returns>
public SymOpMatrix GetOrigCoordSymOpMatrix()
{
SymOpMatrix symOpMatrix = new SymOpMatrix();
List<double> itemList = new List<double> ();
itemList.Add(1.0);
itemList.Add(0.0);
itemList.Add(0.0);
itemList.Add(0.0);
symOpMatrix.Add(0, itemList.ToArray ());
itemList.Clear();
itemList.Add(0.0);
itemList.Add(1.0);
itemList.Add(0.0);
itemList.Add(0.0);
symOpMatrix.Add(1, itemList.ToArray ());
itemList.Clear();
itemList.Add(0.0);
itemList.Add(0.0);
itemList.Add(1.0);
itemList.Add(0.0);
symOpMatrix.Add(2, itemList.ToArray ());
return symOpMatrix;
}
/// <summary>
/// the symmetry operator string
/// </summary>
/// <param name="infoNode"></param>
/// <returns></returns>
public SymOpMatrix GetCoordSymOpMatrix(string matrixString)
{
string[] fields = matrixString.Split(',');
SymOpMatrix symOpMatrix = new SymOpMatrix();
List<double> itemList = new List<double> ();
itemList.Add(Convert.ToDouble(fields[0]));
itemList.Add(Convert.ToDouble(fields[1]));
itemList.Add(Convert.ToDouble(fields[2]));
itemList.Add(Convert.ToDouble(fields[3]));
symOpMatrix.Add(0, itemList.ToArray ());
itemList.Clear();
itemList.Add(Convert.ToDouble(fields[4]));
itemList.Add(Convert.ToDouble(fields[5]));
itemList.Add(Convert.ToDouble(fields[6]));
itemList.Add(Convert.ToDouble(fields[7]));
symOpMatrix.Add(1, itemList.ToArray ());
itemList.Clear();
itemList.Add(Convert.ToDouble(fields[8]));
itemList.Add(Convert.ToDouble(fields[9]));
itemList.Add(Convert.ToDouble(fields[10]));
itemList.Add(Convert.ToDouble(fields[11]));
symOpMatrix.Add(2, itemList.ToArray ());
return symOpMatrix;
}
/// <summary>
/// the symmetry matrix from matrix string
/// s00, s01, s02, v0, s10, s11, s12, v1, s20, s21, s22, v2
/// </summary>
/// <param name="matrixString"></param>
/// <returns></returns>
private SymOpMatrix GetSymMatrixFromMatrixString(string matrixString)
{
string[] fields = matrixString.Split(',');
SymOpMatrix symOpMatrix = new SymOpMatrix();
int numOfCol = 4;
int colNum = -1;
int rowNum = -1;
for (int i = 0; i < fields.Length; i++)
{
colNum++;
if (i % numOfCol == 0)
{
rowNum++;
colNum = 0;
}
symOpMatrix.Add(rowNum, colNum, Convert.ToDouble(fields[i]));
}
return(symOpMatrix);
}