/// <summary>
///
/// </summary>
/// <param name="chain1"></param>
/// <param name="chain2"></param>
/// <param name="modelType">local, or global</param>
/// <returns></returns>
public StructAlignOutput AlignTwoChains(ChainAtoms chain1, ChainAtoms chain2, string modelType)
{
AtomInfo[] calphaAtoms1 = chain1.CalphaAtoms();
AtomInfo[] calphaAtoms2 = chain2.CalphaAtoms();
StructAlignOutput alignOutput = AlignTwoSetsAtoms(calphaAtoms1, calphaAtoms2, modelType);
return(alignOutput);
}
/// <summary>
///
/// </summary>
/// <param name="chain1"></param>
/// <param name="chain2"></param>
public StructAlignOutput AlignTwoSetsAtoms(AtomInfo[] atoms1, AtomInfo[] atoms2, string modelType)
{
Coordinate[] coords1 = GetCoordinates(atoms1);
Coordinate[] coords2 = GetCoordinates(atoms2);
StructAlignOutput alignOutput = AlignTwoSetsCoordinates(coords1, coords2, modelType);
if (alignOutput != null)
{
int startPos = -1;
int endPos = -1;
alignOutput.alignment1 = ChangeOutputAlignmentToResidues(atoms1, alignOutput.alignment1, out startPos, out endPos);
alignOutput.startPos1 = startPos;
alignOutput.endPos1 = endPos;
alignOutput.alignment2 = ChangeOutputAlignmentToResidues(atoms2, alignOutput.alignment2, out startPos, out endPos);
alignOutput.startPos2 = startPos;
alignOutput.endPos2 = endPos;
}
return(alignOutput);
}
/// <summary>
///
/// </summary>
/// <param name="chain1"></param>
/// <param name="chain2"></param>
public StructAlignOutput AlignTwoSetsCoordinates(Coordinate[] coords1, Coordinate[] coords2, string modelType)
{
double bestScore = -1;
int endI = -1;
int endJ = -1;
double[,] distanceMatrix = CreateDistanceMatrix(coords1, coords2);
List <int> indexListI = new List <int>();
List <int> indexListJ = new List <int>();
// the dp matrix is one more than for both lists of the coords
if (modelType == "local")
{
double[,] dpMatrix = CreateLocalMatrix(coords1.Length, coords2.Length, distanceMatrix, out bestScore, out endI, out endJ);
AlignLocal(dpMatrix, endI, endJ, distanceMatrix, ref indexListI, ref indexListJ);
}
else
{
double[,] dpMatrix = CreateGlobalMatrix(coords1.Length, coords2.Length, distanceMatrix, out bestScore, out endI, out endJ);
AlignGlobal(dpMatrix, endI, endJ, distanceMatrix, ref indexListI, ref indexListJ);
}
if (indexListI.Count == 0 || indexListJ.Count == 0) // no local alignment
{
return(null);
}
int[] indexesI = new int[indexListI.Count];
indexListI.CopyTo(indexesI);
int[] indexesJ = new int[indexListJ.Count];
indexListJ.CopyTo(indexesJ);
StructAlignOutput alignOutput = new StructAlignOutput();
alignOutput.startPos1 = indexesI[0];
alignOutput.endPos1 = indexesI[indexesI.Length - 1];
alignOutput.startPos2 = indexesJ[0];
alignOutput.endPos2 = indexesJ[indexesJ.Length - 1];
alignOutput.alignScore = bestScore;
alignOutput.rmsd = 0;
string alignment1 = "";
string alignment2 = "";
int coordI = 0;
int coordJ = 0;
List <Coordinate> rmsdCoordsList1 = new List <Coordinate> ();
List <Coordinate> rmsdCoordsList2 = new List <Coordinate> ();
for (int i = 0; i < indexesI.Length; i++)
{
if (indexesI[i] > -1)
{
coordI = indexesI[i] - 1;
alignment1 += (coordI.ToString() + ",");
}
else
{
alignment1 += "-,";
}
if (indexesJ[i] > -1)
{
coordJ = indexesJ[i] - 1;
alignment2 += (coordJ.ToString() + ",");
}
else
{
alignment2 += "-,";
}
if (indexesI[i] > -1 && indexesJ[i] > -1)
{
rmsdCoordsList1.Add(coords1[coordI]);
rmsdCoordsList2.Add(coords2[coordJ]);
}
}
double rmsd = rmsdCalculator.CalculateRmsd(rmsdCoordsList1.ToArray(), rmsdCoordsList2.ToArray());
alignOutput.rmsd = rmsd;
alignOutput.alignment1 = alignment1.TrimEnd(',');
alignOutput.alignment2 = alignment2.TrimEnd(',');
return(alignOutput);
}