/// <summary>
/// Calculates the extended adjacency matrix index.
/// An implementation of the algorithm published in <token>cdk-cite-HU96</token>.
/// </summary>
// @cdk.keyword EAID number
public static double GetEAIDNumber(IAtomContainer atomContainer)
{
GIMatrix matrix = new GIMatrix(GetExtendedAdjacenyMatrix(atomContainer));
GIMatrix tempMatrix = matrix;
GIMatrix fixedMatrix = matrix;
for (int i = 2; i < atomContainer.Atoms.Count; i++)
{
tempMatrix = tempMatrix.Multiply(fixedMatrix);
matrix = matrix.Add(tempMatrix);
}
for (int i = 0; i < atomContainer.Atoms.Count; i++)
{
matrix.SetValueAt(i, i, matrix.GetValueAt(i, i) + 1);
}
double eaid = matrix.Trace();
Debug.WriteLine("final matrix - the sum of the powers of EA matrix: ");
DisplayMatrix(matrix.ArrayValue);
Debug.WriteLine($"eaid number: {eaid}");
return(eaid);
}
} // method Multiply(double)
/// <summary>
/// Returns the result of the matrix multiplication of this matrix by another one. The matrix passed
/// as parameter <i>follows</i> this matrix in the multiplication, so for an example if the dimension of
/// the actual matrix is mxn, the dimension of the second one should be nxp in order for the multiplication
/// to be performed (otherwise an exception will be thrown) and the resulting matrix will have dimension mxp.
/// </summary>
/// <param name="matrix">the matrix following this one in the matrix multiplication</param>
/// <returns>the resulting matrix of the matrix multiplication</returns>
/// <exception cref="BadMatrixFormatException">if the matrix passed in arguments has wrong dimensions</exception>
public GIMatrix Multiply(GIMatrix matrix)
{
if (Width != matrix.Height)
{
throw new BadMatrixFormatException(); // unsuitable dimensions
}
int p = matrix.Width;
double[][] temp = Arrays.CreateJagged <double>(Height, p);
double[][] multiplied = matrix.ArrayValue;
for (int i = 0; i < Height; i++)
{
// line index of the first matrix
for (int k = 0; k < p; k++)
{ // column index of the second matrix
temp[i][k] = array[i][0] * multiplied[0][k]; // first multiplication
for (int j = 1; j < Width; j++)
{
// sum of multiplications
temp[i][k] = temp[i][k] + array[i][j] * multiplied[j][k];
}
}
}
return(new GIMatrix(temp));
} // method Multiply(Matrix)
} // method IsInvertible()
/// <summary>
/// Returns the transpose of this matrix. The transpose of a matrix A = {a(i,j)} is the matrix B = {b(i,j)}
/// such that b(i,j) = a(j,i) for every i,j i.e. it is the symmetrical reflection of the matrix along its
/// diagonal. The matrix must be square to use this method, otherwise an exception will be thrown.
/// </summary>
/// <returns>the matrix's transpose as a Matrix object</returns>
public GIMatrix Inverse()
{
try
{
if (!IsInvertible())
{
throw new MatrixNotInvertibleException();
}
}
catch (BadMatrixFormatException)
{
throw new MatrixNotInvertibleException();
}
GIMatrix I = CreateIdentity(Width); // Creates an identity matrix of same dimensions
GIMatrix table;
try
{
GIMatrix[][] temp = new[] { new[] { this, I } };
table = new GIMatrix(temp);
}
catch (BadMatrixFormatException)
{
return(null);
} // never happens
table = table.GaussJordan(); // linear reduction method applied
double[][] inv = Arrays.CreateJagged <double>(Height, Width);
for (int i = 0; i < Height; i++)
{
// extracts inverse matrix
for (int j = Width; j < 2 * Width; j++)
{
try
{
inv[i][j - Width] = table.GetValueAt(i, j);
}
catch (IndexOutOfRangeException)
{
return(null);
} // never happens
}
}
try
{
return(new GIMatrix(inv));
}
catch (BadMatrixFormatException)
{
return(null);
} // never happens...
} // method Inverse()
} // method SetLine(int,Matrix)
/// <summary>
/// Sets the column of the matrix at the specified index to a new value.
/// </summary>
/// <param name="j">the column number</param>
/// <param name="column">the column to be placed at the specified index</param>
/// <exception cref="ArgumentOutOfRangeException">if the given index is out of the matrix's range</exception>
/// <exception cref="BadMatrixFormatException">in case the given Matrix is unproper to replace a column of this Matrix</exception>
public void SetColumn(int j, GIMatrix column)
{
if ((j < 0) || (j >= Width))
{
throw new ArgumentOutOfRangeException(nameof(j));
}
if ((column.Height != Height) || (column.Width != 1))
{
throw new BadMatrixFormatException();
}
for (int k = 0; k < Height; k++)
{
array[k][j] = column.GetValueAt(k, 0);
}
} // method SetColumn(int,Matrix)
} // method GetColumn(int)
/// <summary>
/// Sets the line of the matrix at the specified index to a new value.
/// </summary>
/// <param name="i">the line number</param>
/// <param name="line">the line to be placed at the specified index</param>
/// <exception cref="ArgumentOutOfRangeException">if the given index is out of the matrix's range</exception>
/// <exception cref="BadMatrixFormatException">in case the given Matrix is unproper to replace a line of this Matrix</exception>
public void SetLine(int i, GIMatrix line)
{
if ((i < 0) || (i >= Height))
{
throw new ArgumentOutOfRangeException(nameof(i));
}
if ((line.Height != 1) || (line.Width != Width))
{
throw new BadMatrixFormatException();
}
for (int k = 0; k < Width; k++)
{
array[i][k] = line.GetValueAt(0, k);
}
} // method SetLine(int,Matrix)
} // method AddLine(int,int,double)
/// <summary>
/// Addition from two matrices.
/// </summary>
public GIMatrix Add(GIMatrix b)
{
if ((b == null) || (Height != b.Height) || (Width != b.Width))
{
return(null);
}
int i, j;
GIMatrix result = new GIMatrix(Height, Width);
for (i = 0; i < Height; i++)
{
for (j = 0; j < Width; j++)
{
result.array[i][j] = array[i][j] + b.array[i][j];
}
}
return(result);
}
} // method Zero(int,int)
/// <summary>
/// Verifies if two given matrix are equal or not. The matrix must be of the same size and dimensions,
/// otherwise an exception will be thrown.
/// </summary>
/// <param name="matrix">the Matrix object to be compared to</param>
/// <returns>true if both matrix are equal element to element</returns>
/// <exception cref="BadMatrixFormatException">if the given matrix doesn't have the same dimensions as this one</exception>
public bool Equals(GIMatrix matrix)
{
if ((Height != matrix.Height) || (Width != matrix.Width))
{
throw new BadMatrixFormatException();
}
double[][] temp = matrix.ArrayValue;
for (int i = 0; i < Height; i++)
{
for (int j = 0; j < Width; j++)
{
if (!(array[i][j] == temp[i][j]))
{
return(false);
}
}
}
return(true);
} // method Equals(Matrix)
} // constructor Matrix(Matrix)
/// <summary>
/// Class constructor. Creates a new Matrix object using a table of matrices (an array of Matrix objects).
/// The given array should be properly instantiated i.e. it must contain a fixed number of lines and columns,
/// otherwise an exception will be thrown.
/// </summary>
/// <param name="table">an array of matrices</param>
/// <exception cref="BadMatrixFormatException">if the table is not properly instantiated</exception>
public GIMatrix(GIMatrix[][] table)
{
VerifyTableFormat(table);
Height = Width = 0;
for (int i = 0; i < table.Length; i++)
{
Height += table[i][0].Height;
}
for (int j = 0; j < table[0].Length; j++)
{
Width += table[0][j].Width;
}
double[][] temp = Arrays.CreateJagged <double>(Height, Width);
int k = 0; // counters for matrices
for (int i = 0; i < Height; i++)
{
temp[i] = new double[Width]; // line by line ...
if (i == table[k][0].Height)
{
k++; // last line of matrix reached
}
int h = 0;
for (int j = 0; j < Width; j++)
{
if (j == table[k][h].Width)
{
h++; // last column of matrix reached
}
try
{
GIMatrix tempMatrix = table[k][h];
temp[i][j] = tempMatrix.GetValueAt(i - k * tempMatrix.Height, j - h * tempMatrix.Width);
}
catch (IndexOutOfRangeException)
{
} // never happens
}
}
this.array = temp;
} // constructor Matrix(Matrix)
} // constructor Matrix(int,int)
/// <summary>
/// Class constructor. Copies an already existing Matrix object in a new Matrix object.
/// </summary>
/// <param name="matrix">a Matrix object</param>
public GIMatrix(GIMatrix matrix)
{
double[][] temp = new double[matrix.Height][];
for (int i = 0; i < matrix.Height; i++)
{
temp[i] = new double[matrix.Width]; // line by line ...
for (int j = 0; j < matrix.Width; j++)
{
try
{
temp[i][j] = matrix.GetValueAt(i, j);
}
catch (IndexOutOfRangeException)
{
} // never happens
}
}
this.array = temp;
Height = array.Length;
Width = array[0].Length;
} // constructor Matrix(Matrix)
} // method Inverse()
/// <summary>
/// Gauss-Jordan algorithm. Returns the reduced-echeloned matrix of this matrix. The
/// algorithm has not yet been optimised but since it is quite simple, it should not be
/// a serious problem.
/// </summary>
/// <returns>the reduced matrix</returns>
public GIMatrix GaussJordan()
{
GIMatrix tempMatrix = new GIMatrix(this);
try
{
int i = 0;
int j = 0;
int k = 0;
bool end = false;
while ((i < Height) && (!end))
{
bool allZero = true; // true if all elements under line i are null (zero)
while (j < Width)
{ // determination of the pivot
for (k = i; k < Height; k++)
{
if (!(tempMatrix.GetValueAt(k, j) == 0.0))
{ // if an element != 0
allZero = false;
break;
}
}
if (allZero)
{
j++;
}
else
{
break;
}
}
if (j == Width)
{
end = true;
}
else
{
if (k != i)
{
tempMatrix = tempMatrix.InvertLine(i, k);
}
if (!(tempMatrix.GetValueAt(i, j) == 1.0)) // if element != 1
{
tempMatrix = // A = L(i)(1/a(i,j))(A)
tempMatrix.MultiplyLine(i, 1 / tempMatrix.GetValueAt(i, j));
}
for (int q = 0; q < Height; q++)
{
if (q != i) // A = L(q,i)(-a(q,j))(A)
{
tempMatrix = tempMatrix.AddLine(q, i, -tempMatrix.GetValueAt(q, j));
}
}
}
i++;
}
// normally here, r = i-1
return(tempMatrix);
}
catch (IndexOutOfRangeException)
{
return(null);
} // never happens... well I hope ;)
// From: LEROUX, P. Algebre lineaire: une approche matricielle. Modulo Editeur, 1983. p. 75. (In French)
} // method GaussJordan()
