private void ThreadLibrary(object o)
{
int[] inx = (int [])o;
if (fragBagLibrary[0].GetLength(0) + inx[2] > res.Count)
{
resetEvents[inx[3]].Set();
return;
}
for (int n = 0; n < fragBagLibrary[0].GetLength(0); n++)
{
chunk[inx[3]][n, 0] = res[inx[2] + n].Atoms[0].Position.X;
chunk[inx[3]][n, 1] = res[inx[2] + n].Atoms[0].Position.Y;
chunk[inx[3]][n, 2] = res[inx[2] + n].Atoms[0].Position.Z;
}
Optimization.CenterMol(chunk[inx[3]], center[inx[3]]);
for (int j = inx[0]; j < inx[1]; j++)
{
distData[j] = Optimization.Rmsd(fragBagLibrary[j], chunk[inx[3]], false);
}
resetEvents[inx[3]].Set();
}
private void PreparePDBPos()
{
//Check if all alignm have the same length
foreach (var item in pdbs.molDic)
{
foreach (var itemIndex in item.Value.indexMol)
{
if (itemIndex == -1)
{
return;
}
}
}
pdbPos = new float[structures.Count][, ];
for (int i = 0; i < structures.Count; i++)
{
pdbPos[i] = new float[pdbs.molDic[structures[0]].indexMol.Length, 3];
}
float [] center = new float [3];
for (int i = 0; i < structures.Count; i++)
{
int count = 0;
for (int j = 0; j < pdbs.molDic[structures[i]].mol.Residues.Count; j++)
{
for (int n = 0; n < pdbs.molDic[structures[i]].mol.Residues[j].Atoms.Count; n++)
{
pdbPos[i][count, 0] = pdbs.molDic[structures[i]].mol.Residues[j].Atoms[n].Position.X;
pdbPos[i][count, 1] = pdbs.molDic[structures[i]].mol.Residues[j].Atoms[n].Position.Y;
pdbPos[i][count++, 2] = pdbs.molDic[structures[i]].mol.Residues[j].Atoms[n].Position.Z;
}
}
Optimization.CenterMol(pdbPos[i], center);
}
}
public void ReadLibrary()
{
string[] files;
string location = Path.GetDirectoryName(Assembly.GetExecutingAssembly().Location) +
Path.DirectorySeparatorChar + "fragLib";
if (Directory.Exists(location))
{
files = Directory.GetFiles(location);
}
else
{
throw new Exception("Directory fragLib not exists. Profile fragBag cannot be used!");
}
fragBagLibrary.Clear();
string libraryName;
if (dirSettings.mode == INPUTMODE.PROTEIN)
{
libraryName = "fragBagProtein.txt";
}
else
{
libraryName = "fragBagRNAv2.txt";
}
libraryName = location + Path.DirectorySeparatorChar + libraryName;
if (!File.Exists(libraryName))
{
throw new Exception("Cannot find: " + libraryName + " Profile fragBag cannot be used!");
}
using (StreamReader s = new StreamReader(libraryName))
{
string line = s.ReadLine();
float[] cent = new float[3];
while (line != null)
{
if (line.Contains("----"))
{
line = s.ReadLine();
List <float[]> str = new List <float[]>();
while (line != null && !line.Contains("***"))
{
try
{
line = line.Trim();
line = Regex.Replace(line, @"\s+", " ");
string[] aux = line.Split(' ');
float[] p = new float[3];
for (int i = 0; i < 3; i++)
{
p[i] = (float)Convert.ToDouble(aux[i], System.Globalization.CultureInfo.InvariantCulture);
}
str.Add(p);
}
catch (Exception ex)
{
throw new Exception("Error in frag bag library: " + line);
}
line = s.ReadLine();
}
// if (str.Count > 5)
// Console.WriteLine("UPS");
float[,] auxTab = new float[str.Count, 3];
for (int i = 0; i < str.Count; i++)
{
for (int j = 0; j < str[i].Length; j++)
{
auxTab[i, j] = str[i][j];
}
}
Optimization.CenterMol(auxTab, cent);
fragBagLibrary.Add(auxTab);
}
line = s.ReadLine();
}
}
if (fragBagLibrary.Count == 0)
{
throw new Exception("Frag Bag Library is empty!");
}
distData = new float[fragBagLibrary.Count];
index = new int[fragBagLibrary.Count];
zeroCount = new int[fragBagLibrary.Count];
profile = new int[fragBagLibrary.Count];
}
