private returnV GetStructAfterRotation(string refStructure, string modelStructure)
{
float[,] transMatrix = null;
float [] cent1 = new float [3];
float [] cent2 = new float [3];
if (!pdbs.molDic.ContainsKey(refStructure) || !pdbs.molDic.ContainsKey(modelStructure))
{
return(null);
}
posMOL locPosMol = Optimization.PrepareData(pdbs.molDic[refStructure], pdbs.molDic[modelStructure], true);
//opt.Rmsd(locPosMol.posmol1, locPosMol.posmol2, cent1, cent2, true);
/* float [,]mm=new float [3,3];
*
* mm[0, 0] = 0; mm[0, 1] = 0; mm[0, 2] = 1;
* mm[1, 0] = 1; mm[1, 1] = 0; mm[1, 2] = 0;
* mm[2, 0] = 0; mm[2, 1] = 1; mm[2, 2] = 0;
*
* float [,]test=Optimization.MultMatrixTrans(locPosMol.posmol1, mm);*/
transMatrix = Optimization.TransMatrix(locPosMol.posmol2, locPosMol.posmol1);
//transMatrix = opt.TransMatrix(locPosMol.posmol1, test);
if (transMatrix == null)
{
return(null);
}
// float[,] akk = Optimization.MultMatrixTrans(test, transMatrix);
transMatrix = Optimization.MultMatrixTrans(locPosMol.posmol2, transMatrix);
returnV r = new returnV();
r.x = transMatrix;
r.y = locPosMol.atoms;
return(r);
//return Optimization.MultMatrixTrans(test, transMatrix);
//return akk;
//return opt.posMolRot;
//return opt.TransMatrix(opt.posMol1, opt.posMol2);
}
private returnV GetStructAfterRotation(string refStructure, string modelStructure)
{
float[,] transMatrix=null;
float []cent1=new float [3];
float []cent2=new float [3];
if (!pdbs.molDic.ContainsKey(refStructure) || !pdbs.molDic.ContainsKey(modelStructure))
return null;
posMOL locPosMol=Optimization.PrepareData(pdbs.molDic[refStructure], pdbs.molDic[modelStructure],true);
//opt.Rmsd(locPosMol.posmol1, locPosMol.posmol2, cent1, cent2, true);
/* float [,]mm=new float [3,3];
mm[0, 0] = 0; mm[0, 1] = 0; mm[0, 2] = 1;
mm[1, 0] = 1; mm[1, 1] = 0; mm[1, 2] = 0;
mm[2, 0] = 0; mm[2, 1] = 1; mm[2, 2] = 0;
float [,]test=Optimization.MultMatrixTrans(locPosMol.posmol1, mm);*/
transMatrix = Optimization.TransMatrix(locPosMol.posmol2, locPosMol.posmol1);
//transMatrix = opt.TransMatrix(locPosMol.posmol1, test);
if (transMatrix == null)
return null;
// float[,] akk = Optimization.MultMatrixTrans(test, transMatrix);
transMatrix = Optimization.MultMatrixTrans(locPosMol.posmol2, transMatrix);
returnV r=new returnV();
r.x = transMatrix;
r.y = locPosMol.atoms;
return r;
//return Optimization.MultMatrixTrans(test, transMatrix);
//return akk;
//return opt.posMolRot;
//return opt.TransMatrix(opt.posMol1, opt.posMol2);
}
private float[,,] CalcRefPosition(List <string> structures, Dictionary <string, float[, , ]> aRotMol)
{
//float[,] refPosition = null;
int[] counts;
aRotMol.Clear();
if (pdbs.molDic.Keys.Count == 1)
{
pdbs.EmptyAlignment(structures[0]);
}
float[, ,] refPosition = new float[pdbs.molDic[structures[0]].indexMol.Length, atomDic.Keys.Count, 3];
//refPosition = new float[maxV, 3];
counts = new int[pdbs.molDic[structures[0]].indexMol.Length];
//Find longest structure (based on Atoms)
string refLength = "";
int maxLength = 0;
foreach (var item in structures)
{
int localMax = 0;
foreach (var it in pdbs.molDic[item].mol.Chains[0].Residues)
{
localMax += it.Atoms.Count;
}
if (localMax > maxLength)
{
maxLength = localMax;
refLength = item;
}
}
foreach (var item in structures)
{
returnV aux = GetStructAfterRotation(refLength, item);
if (aux == null)
{
continue;
}
float[, ,] auxK = new float[pdbs.molDic[refLength].indexMol.Length, atomDic.Keys.Count, 3];
for (int i = 0, m = 0; i < aux.y.Length; i++)
{
for (int j = 0; j < aux.y[i].Count; j++, m++)
{
for (int n = 0; n < 3; n++)
{
refPosition[i, atomDic[aux.y[i][j]], n] += aux.x[m, n];
auxK[i, atomDic[aux.y[i][j]], n] = aux.x[m, n];
}
counts[i]++;
}
}
aRotMol.Add(item, auxK);
}
for (int i = 0; i < refPosition.GetLength(0); i++)
{
if (counts[i] > 0)
{
for (int j = 0; j < refPosition.GetLength(1); j++)
{
for (int n = 0; n < refPosition.GetLength(2); n++)
{
refPosition[i, j, n] /= counts[i];
}
}
}
}
return(refPosition);
}