/// <summary>
/// Performs ICP Alignment using LIBICP 1.4.7.
/// Checks if the proteins fit the minimum requirements of the alignment.
/// Throws if it does not, or if there are less than two proteins loaded.
/// Extract the alpha carbon matrix from the proteins. Sets up the translation and rotation matrices.
/// Fits the two matrices using ICP. The rotation matrix is applied to a full atom matrix of Protein2.
/// Protein2 is then translated. Calls RMSD() to calculate the RMSD between the two proteins.
/// </summary>
/// <returns>RMSD value between the two proteins.</returns>
public double ICPAlignment()
{
if (Protein1.Count == 0)
{
throw (new Exception("Alignment Error: Protein 1 not found."));
}
if (Protein2.Count == 0)
{
throw (new Exception("Alignment Error: Protein 2 not found."));
}
//LIBICP doesnt work with less than 5 points
if (Protein1.CACount < 5 || Protein2.CACount < 5)
{
throw (new Exception("Alignment Error: Not enough atoms for alignment."));
}
//aligns by CA backbone
double[,] prot1Mat = m_prot1.CAMatrix();
double[,] prot2Mat = m_prot2.CAMatrix();
icp_net.ManagedICP align = new icp_net.ManagedICP(prot1Mat, Protein1.CACount, 3);
//set up return Rotation matrix
double[,] RMat = new double[3, 3];
RMat[0, 0] = 1.0;
RMat[1, 1] = 1.0;
RMat[2, 2] = 1.0;
//set up return Translation matrix
double[] TMat = new double[3];
//last parameter is inlier distance, if <= 0, uses all points
align.fit(prot2Mat, Protein2.CACount, RMat, TMat, -1);
//get full atom matrix to transform
// LIBICP actually takes in a n x 3 matrix, but we need a 3 x n matrix for the math, so ToMatrix() gives a full atom matrix in that orientation
double[,] prot2FullMat = m_prot2.ToMatrix();
//create objects of Matrix type to perfrom matrix multiplication
Matrix <double> prot2MatObj = DenseMatrix.OfArray(prot2FullMat);
Matrix <double> RMatObj = DenseMatrix.OfArray(RMat);
/*To get the Final dataset B, given dataset A
* B = RMat * A + TMat;
* Thus Rotation is applied first
*/
prot2MatObj = RMatObj * prot2MatObj;
//sets the protein coordinates to the matrix
m_prot2.FromMatrix(prot2MatObj);
//translate
m_prot2.Translate(TMat[0], TMat[1], TMat[2]);
return(RMSD());
}
/// <summary>
/// Performs ICP Alignment using LIBICP 1.4.7.
/// Checks if the proteins fit the minimum requirements of the alignment.
/// Throws if it does not, or if there are less than two proteins loaded.
/// Extract the alpha carbon matrix from the proteins. Sets up the translation and rotation matrices.
/// Fits the two matrices using ICP. The rotation matrix is applied to a full atom matrix of Protein2.
/// Protein2 is then translated. Calls RMSD() to calculate the RMSD between the two proteins.
/// </summary>
/// <returns>RMSD value between the two proteins.</returns>
public double ICPAlignment()
{
if (Protein1.Count == 0)
{
throw (new Exception("Alignment Error: Protein 1 not found."));
}
if (Protein2.Count == 0)
{
throw (new Exception("Alignment Error: Protein 2 not found."));
}
//LIBICP doesnt work with less than 5 points
if (Protein1.CACount < 5 || Protein2.CACount < 5)
{
throw (new Exception("Alignment Error: Not enough atoms for alignment."));
}
//aligns by CA backbone
double[,] prot1Mat = m_prot1.CAMatrix();
double[,] prot2Mat = m_prot2.CAMatrix();
icp_net.ManagedICP align = new icp_net.ManagedICP(prot1Mat, Protein1.CACount, 3);
//set up return Rotation matrix
double[,] RMat = new double[3, 3];
RMat[0, 0] = 1.0;
RMat[1, 1] = 1.0;
RMat[2, 2] = 1.0;
//set up return Translation matrix
double[] TMat = new double[3];
//last parameter is inlier distance, if <= 0, uses all points
align.fit(prot2Mat, Protein2.CACount, RMat, TMat, -1);
//get full atom matrix to transform
// LIBICP actually takes in a n x 3 matrix, but we need a 3 x n matrix for the math, so ToMatrix() gives a full atom matrix in that orientation
double[,] prot2FullMat = m_prot2.ToMatrix();
//create objects of Matrix type to perfrom matrix multiplication
Matrix<double> prot2MatObj = DenseMatrix.OfArray(prot2FullMat);
Matrix<double> RMatObj = DenseMatrix.OfArray(RMat);
/*To get the Final dataset B, given dataset A
* B = RMat * A + TMat;
* Thus Rotation is applied first
*/
prot2MatObj = RMatObj * prot2MatObj;
//sets the protein coordinates to the matrix
m_prot2.FromMatrix(prot2MatObj);
//translate
m_prot2.Translate(TMat[0], TMat[1], TMat[2]);
return RMSD();
}