public override int GetDistance(string refStructure, string modelStructure)
{
if (!pdbs.molDic.ContainsKey(refStructure) || !pdbs.molDic.ContainsKey(modelStructure))
{
return(errorValue);
}
if (pdbPos == null)
{
posMOL locPosMol = Optimization.PrepareData(pdbs.molDic[refStructure], pdbs.molDic[modelStructure]);
return((int)(Optimization.Rmsd(locPosMol.posmol1, locPosMol.posmol2, false) * 100));
}
else
{
return((int)(Optimization.Rmsd(pdbPos[hashIndex[refStructure]], pdbPos[hashIndex[modelStructure]], false) * 100));
}
}
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);
}
public override int GetDistance(string refStructure, string modelStructure)
{
KeyValuePair <List <int>, float[, ]> bestpair = default(KeyValuePair <List <int>, float[, ]>);
if (!pdbs.molDic.ContainsKey(refStructure) || !pdbs.molDic.ContainsKey(modelStructure))
{
return(errorValue);
}
posMOL locPosMol = Optimization.PrepareData(pdbs.molDic[refStructure], pdbs.molDic[modelStructure]);
foreach (var item in segments)
{
if (locPosMol.posmol1.GetLength(0) < item)
{
continue;
}
KeyValuePair <List <int>, float[, ]> seg = FindLongestSegment(item, Threshold, locPosMol.posmol1, locPosMol.posmol2);
if (seg.Key != null && (bestpair.Equals(default(KeyValuePair <List <int>, float[, ]>)) || bestpair.Key.Count < seg.Key.Count))
{
bestpair = seg;
}
}
if (!bestpair.Equals(default(KeyValuePair <List <int>, float[, ]>)))
{
if (bestpair.Key == null)
{
return(0);
}
else
{
return(bestpair.Key.Count * 100 / pdbs.molDic[refStructure].molLength);
}
}
return(0);
}
public override int GetDistance(string refStructure, string modelStructure)
{
int seedL = 4;
//float maxDist = 3.5f;
float maxDist = 5.0f;
if (!pdbs.molDic.ContainsKey(refStructure) || !pdbs.molDic.ContainsKey(modelStructure))
{
return(errorValue);
}
posMOL locPosMol = Optimization.PrepareData(pdbs.molDic[refStructure], pdbs.molDic[modelStructure]);
KeyValuePair <List <int>, float[, ]> seg = FindLongestSegment(seedL, maxDist, locPosMol.posmol1, locPosMol.posmol2);
if (seg.Key == null)
{
return(0);
}
float sum = 0;
float mDist = maxDist * maxDist;
float rmsd = 0;
foreach (var item in seg.Key)
{
float dist = 0;
dist = calcDist(locPosMol.posmol1, seg.Value, item);
rmsd += dist;
dist *= dist;
sum += 100 / (1 + dist / mDist);
}
rmsd /= seg.Key.Count;
return(100 - (int)((sum / pdbs.molDic[refStructure].molLength)));//locPosMol.posmol1.GetLength(0)));
}
/* public static posMOL PrepareData(MolData mol1, MolData mol2, bool atomList = false)
* {
* posMOL globPosMol = new posMOL();
*
* globPosMol.posmol1 = new float[mol1.mol.Residues.Count, 3];
* globPosMol.posmol2 = new float[mol2.mol.Residues.Count, 3];
*
* for (int i = 0; i < mol1.mol.Residues.Count; i++)
* {
* globPosMol.posmol1[i, 0] = mol1.mol.Residues[i].Atoms[0].Position.X;
* globPosMol.posmol1[i, 1] = mol1.mol.Residues[i].Atoms[0].Position.Y;
* globPosMol.posmol1[i, 2] = mol1.mol.Residues[i].Atoms[0].Position.Z;
* }
* for (int i = 0; i < mol2.mol.Residues.Count; i++)
* {
* globPosMol.posmol2[i, 0] = mol2.mol.Residues[i].Atoms[0].Position.X;
* globPosMol.posmol2[i, 1] = mol2.mol.Residues[i].Atoms[0].Position.Y;
* globPosMol.posmol2[i, 2] = mol2.mol.Residues[i].Atoms[0].Position.Z;
* }
*
* float[] center = new float[3];
*
* CenterMol(globPosMol.posmol1, center);
* CenterMol(globPosMol.posmol2, center);
*
* return globPosMol;
*
* }*/
public static posMOL PrepareData(MolData mol1, MolData mol2, bool atomList = false)
{
int count = 0;
posMOL globPosMol = new posMOL();
Dictionary <string, int> atomNameMol1 = null;
for (int i = 0; i < mol1.mol.Residues.Count; i++)
{
if (mol1.mol.Residues[i].Atoms.Count > count)
{
count = mol1.mol.Residues[i].Atoms.Count;
}
}
atomNameMol1 = new Dictionary <string, int>(count);
count = 0;
for (int i = 0; i < mol1.indexMol.Length; i++)
{
if (mol1.indexMol[i] != -1 && mol2.indexMol[i] != -1)// && mol1.mol.Residues[mol1.indexMol[i]].ResidueName != 'X' && mol2.mol.Residues[mol2.indexMol[i]].ResidueName != 'X')
{
atomNameMol1.Clear();
List <Atom> atoms = mol1.mol.Residues[mol1.indexMol[i]].Atoms;
for (int j = 0; j < atoms.Count; j++)
{
atomNameMol1.Add(atoms[j].AtomName, j);
}
foreach (var item in mol2.mol.Residues[mol2.indexMol[i]].Atoms)
{
if (atomNameMol1.ContainsKey(item.AtomName))
{
count++;
}
}
}
}
// index1 = mol1.indexMol;
//index2 = mol2.indexMol;
if (globPosMol.posmol1 == null || count != globPosMol.posmol1.GetLength(0))
{
globPosMol.posmol1 = new float[count, 3];
globPosMol.posmol2 = new float[count, 3];
}
if (atomList)
{
globPosMol.atoms = new List <string> [mol1.indexMol.Length];
for (int i = 0; i < mol1.indexMol.Length; i++)
{
globPosMol.atoms[i] = new List <string>();
}
}
count = 0;
for (int i = 0; i < mol1.indexMol.Length; i++)
{
if (mol1.indexMol[i] != -1 && mol2.indexMol[i] != -1)// && mol1.mol.Residues[mol1.indexMol[i]].ResidueName != 'X' && mol2.mol.Residues[mol2.indexMol[i]].ResidueName != 'X')
{
atomNameMol1.Clear();
List <Atom> atoms = mol1.mol.Residues[mol1.indexMol[i]].Atoms;
for (int j = 0; j < atoms.Count; j++)
{
atomNameMol1.Add(atoms[j].AtomName, j);
}
foreach (var item in mol2.mol.Residues[mol2.indexMol[i]].Atoms)
{
if (atomNameMol1.ContainsKey(item.AtomName))
{
Atom aux = mol1.mol.Residues[mol1.indexMol[i]].Atoms[atomNameMol1[item.AtomName]];
globPosMol.posmol1[count, 0] = aux.Position.X;
globPosMol.posmol1[count, 1] = aux.Position.Y;
globPosMol.posmol1[count, 2] = aux.Position.Z;
globPosMol.posmol2[count, 0] = item.Position.X;
globPosMol.posmol2[count, 1] = item.Position.Y;
globPosMol.posmol2[count, 2] = item.Position.Z;
if (atomList)
{
globPosMol.atoms[i].Add(item.AtomName);
}
count++;
}
}
}
}
float[] center = new float[3];
CenterMol(globPosMol.posmol1, center);
CenterMol(globPosMol.posmol2, center);
return(globPosMol);
}
public static posMOL PrepareData(MolData mol1,MolData mol2,bool atomList=false)
{
int count=0;
posMOL globPosMol = new posMOL();
Dictionary<string, int> atomNameMol1 = null;
for (int i = 0; i < mol1.mol.Residues.Count; i++)
if (mol1.mol.Residues[i].Atoms.Count > count)
count = mol1.mol.Residues[i].Atoms.Count;
atomNameMol1 = new Dictionary<string, int>(count);
count = 0;
for (int i = 0; i < mol1.indexMol.Length; i++)
if (mol1.indexMol[i] != -1 && mol2.indexMol[i] != -1)// && mol1.mol.Residues[mol1.indexMol[i]].ResidueName != 'X' && mol2.mol.Residues[mol2.indexMol[i]].ResidueName != 'X')
{
atomNameMol1.Clear();
List<Atom> atoms = mol1.mol.Residues[mol1.indexMol[i]].Atoms;
for (int j = 0; j < atoms.Count;j++ )
atomNameMol1.Add(atoms[j].AtomName, j);
foreach (var item in mol2.mol.Residues[mol2.indexMol[i]].Atoms)
if (atomNameMol1.ContainsKey(item.AtomName))
count++;
}
// index1 = mol1.indexMol;
//index2 = mol2.indexMol;
if (globPosMol.posmol1==null || count != globPosMol.posmol1.GetLength(0))
{
globPosMol.posmol1 = new float[count, 3];
globPosMol.posmol2 = new float[count, 3];
}
if (atomList)
{
globPosMol.atoms = new List<string>[mol1.indexMol.Length];
for(int i=0;i<mol1.indexMol.Length;i++)
{
globPosMol.atoms[i] = new List<string>();
}
}
count = 0;
for (int i = 0; i < mol1.indexMol.Length; i++)
if (mol1.indexMol[i] != -1 && mol2.indexMol[i] != -1)// && mol1.mol.Residues[mol1.indexMol[i]].ResidueName != 'X' && mol2.mol.Residues[mol2.indexMol[i]].ResidueName != 'X')
{
atomNameMol1.Clear();
List<Atom> atoms = mol1.mol.Residues[mol1.indexMol[i]].Atoms;
for (int j = 0; j < atoms.Count; j++)
atomNameMol1.Add(atoms[j].AtomName, j);
foreach (var item in mol2.mol.Residues[mol2.indexMol[i]].Atoms)
if (atomNameMol1.ContainsKey(item.AtomName))
{
Atom aux = mol1.mol.Residues[mol1.indexMol[i]].Atoms[atomNameMol1[item.AtomName]];
globPosMol.posmol1[count, 0] = aux.Position.X;
globPosMol.posmol1[count, 1] = aux.Position.Y;
globPosMol.posmol1[count, 2] = aux.Position.Z;
globPosMol.posmol2[count, 0] = item.Position.X;
globPosMol.posmol2[count, 1] = item.Position.Y;
globPosMol.posmol2[count, 2] = item.Position.Z;
if(atomList)
globPosMol.atoms[i].Add(item.AtomName);
count++;
}
}
float[] center = new float[3];
CenterMol(globPosMol.posmol1, center);
CenterMol(globPosMol.posmol2, center);
return globPosMol;
}
