public static SuperCell ReadMol2_complex(string fileName, int atomsPerCell)
{
SuperCell superCell = new SuperCell();
superCell.isError = false;
superCell.isParent = true;
superCell.errorType = SuperCellError.NoError;
superCell.filePath = fileName;
#region RawDataReader
Queue<string> atomLines = new Queue<string>();
List<string> bondLines = new List<string>();
StreamReader reader = File.OpenText(fileName);
string line;
bool startReading = false;
bool bondsPresent = false;
bool latticePresent = false;
while (true)
{
if (startReading)
{
while ((line = reader.ReadLine()) != null)
{
if (line == "@<TRIPOS>BOND")
{
bondsPresent = true;
break;
}
else
{
atomLines.Enqueue(line);
}
}
break;
}
else
{
line = reader.ReadLine();
if (line == "@<TRIPOS>ATOM") startReading = true;
}
}
if (bondsPresent)
{
while ((line = reader.ReadLine()) != null)
{
if (line == "@<TRIPOS>CRYSIN")
{
latticePresent = true;
break;
}
else
{
bondLines.Add(line);
}
}
}
else
{
superCell.isError = true;
superCell.errorType = SuperCellError.Base_NoBonds;
return superCell;
}
string latticeLine;
if (!latticePresent)
{
superCell.isError = true;
superCell.errorType = SuperCellError.Base_NoLattice;
return superCell;
}
else
{
latticeLine = reader.ReadLine();
}
#endregion
#region OrderFinder
Queue<int[]> bondsQueue = new Queue<int[]>();
Queue<int> bondTypesQueue = new Queue<int>();
int[] tempBond;
int numBonds = 0;
while (true)
{
string[] items = bondLines[bondsQueue.Count].Split(' ');
tempBond = new int[2] { int.Parse(items[1]), int.Parse(items[2]) };
if (tempBond[0] > atomsPerCell || tempBond[1] > atomsPerCell)
{
break;
}
else
{
bondsQueue.Enqueue(tempBond);
bondTypesQueue.Enqueue(int.Parse(items[3]));
numBonds++;
}
}
Node headNode = new Node();
Node thisAtom;
superCell.bonds = new int[bondsQueue.Count, 2];
superCell.bondTypes = new int[bondsQueue.Count];
int count = 0;
while (bondsQueue.Count > 0)
{
tempBond = bondsQueue.Dequeue();
superCell.bonds[count, 0] = tempBond[0];
superCell.bonds[count, 1] = tempBond[1];
superCell.bondTypes[count] = bondTypesQueue.Dequeue();
thisAtom = headNode.SearchChildren(tempBond[0]);
if (thisAtom != null)
{
Node otherAtom = headNode.SearchChildren(tempBond[1]);
if (otherAtom != null)
{
otherAtom.ChangeParent(thisAtom);
}
else
{
thisAtom.AddChild(new Node(tempBond[1]));
}
}
else
{
Node otherAtom = headNode.SearchChildren(tempBond[1]);
if (otherAtom != null)
{
otherAtom.AddChild(new Node(tempBond[0]));
}
else
{
Node tempNode = new Node(tempBond[0]);
headNode.AddChild(tempNode);
tempNode.AddChild(new Node(tempBond[1]));
}
}
count++;
}
if (headNode.Children.Count > 0)
{
superCell.order = headNode.FindOrder();
}
else
{
superCell.isError = true;
superCell.errorType = SuperCellError.Base_CouldntFindOrder;
return superCell;
}
#endregion
#region RawDataProcessor
int numAtoms = atomLines.Count;
int molsPerCell = superCell.order.GetLength(0);
int atomsPerMol = superCell.order.GetLength(1);
int numCells = numAtoms / atomsPerCell;
int numMols = molsPerCell*numCells;
superCell.types = new string[atomsPerCell];
superCell.mols = new List<Molecule>();
for (int cell = 0; cell < numCells; cell++)
{
double[,] atomsBuffer = new double[atomsPerCell, 3];
for (int atom = 0; atom < atomsPerCell; atom++)
{
string[] items = atomLines.Dequeue().Split(' ');
if (cell == 0)
{
if (items[5].Length > 2)
{
superCell.types[atom] = items[5].Remove(items[5].Length - 2);
}
else
{
superCell.types[atom] = items[5];
}
}
atomsBuffer[atom, 0] = double.Parse(items[2]);
atomsBuffer[atom, 1] = double.Parse(items[3]);
atomsBuffer[atom, 2] = double.Parse(items[4]);
}
for (int mol = 0; mol < molsPerCell; mol++)
{
double[,] thisMol = new double[atomsPerMol, 3];
for (int atom = 0; atom < atomsPerMol; atom++)
{
thisMol[atom, 0] = atomsBuffer[superCell.order[mol, atom], 0];
thisMol[atom, 1] = atomsBuffer[superCell.order[mol, atom], 1];
thisMol[atom, 2] = atomsBuffer[superCell.order[mol, atom], 2];
}
superCell.mols.Add(new Molecule(thisMol, true));
}
}
superCell.centroids = DenseMatrix.Create(numMols, 3, 0);
superCell.directions = DenseMatrix.Create(numMols, 3, 0);
count = 0;
foreach (Molecule mol in superCell.mols)
{
superCell.centroids.SetRow(count, mol.centroid);
superCell.directions.SetRow(count, mol.direction);
count++;
}
#endregion
#region LatticeFinder
string[] latticeItems = latticeLine.Split(' ');
double[,] incompleteLattice = new double[2, 3] { { double.Parse(latticeItems[0]), double.Parse(latticeItems[1]), double.Parse(latticeItems[2]) },
{ double.Parse(latticeItems[3]), double.Parse(latticeItems[4]), double.Parse(latticeItems[5]) } };
superCell.latticeParams = new double[2, 3] { { 0.0, 0.0, 0.0 }, { incompleteLattice[1, 0], incompleteLattice[1, 1], incompleteLattice[1, 2] } };
superCell.superCellSize = new int[3] { 0, 0, 0 };
superCell.latticeVectors = DenseMatrix.OfArray(new double[,] { { 0, 0, 0 }, { 0, 0, 0 }, { 0, 0, 0 } });
bool[] cellDone = new bool[3] { false, false, false };
double tempA;
double tempB;
double tempC;
int cellA=0;
int cellB=0;
int cellC=0;
if (numMols > 1)
{
for (int i = 0; i < 3; i++)
{
tempA = (superCell.mols[molsPerCell].centroid - superCell.mols[0].centroid).L2Norm();
double tempLatticeRatio = incompleteLattice[0, i] / tempA;
if (Math.Abs(tempLatticeRatio - Math.Round(tempLatticeRatio)) < 0.001)
{
cellA = (int)Math.Round(tempLatticeRatio);
superCell.superCellSize[i] = cellA;
superCell.latticeParams[0, i] = tempA;
cellDone[i] = true;
superCell.latticeVectors.SetColumn(i, superCell.mols[molsPerCell].centroid - superCell.mols[0].centroid);
break;
}
}
}
else
{
superCell.isError = true;
superCell.errorType = SuperCellError.Base_SingleMol;
return superCell;
}
if (numMols > cellA)
{
for (int i = 0; i < 3; i++)
{
if (cellDone[i] == true) continue;
tempB = (superCell.mols[cellA*molsPerCell].centroid - superCell.mols[0].centroid).L2Norm();
double tempLatticeRatio = incompleteLattice[0, i] / tempB;
if (Math.Abs(tempLatticeRatio - Math.Round(tempLatticeRatio)) < 0.001)
{
cellB = (int)Math.Round(tempLatticeRatio);
superCell.superCellSize[i] = cellB;
superCell.latticeParams[0, i] = tempB;
cellDone[i] = true;
superCell.latticeVectors.SetColumn(i, superCell.mols[cellA*molsPerCell].centroid - superCell.mols[0].centroid);
break;
}
}
}
else
{
superCell.isError = true;
superCell.errorType = SuperCellError.Base_LineCell;
return superCell;
}
if (numMols > cellA * cellB)
{
for (int i = 0; i < 3; i++)
{
if (cellDone[i] == true) continue;
tempC = (superCell.mols[cellA * cellB * molsPerCell].centroid - superCell.mols[0].centroid).L2Norm();
double tempLatticeRatio = incompleteLattice[0, i] / tempC;
if (Math.Abs(tempLatticeRatio - Math.Round(tempLatticeRatio)) < 0.001)
{
cellC = (int)Math.Round(tempLatticeRatio);
superCell.superCellSize[i] = cellC;
superCell.latticeParams[0, i] = tempC;
cellDone[i] = true;
superCell.latticeVectors.SetColumn(i, superCell.mols[cellA*cellB*molsPerCell].centroid - superCell.mols[0].centroid);
break;
}
}
}
else
{
int cIndex = 3;
for (int i = 0; i < 3; i++)
{
if (cellDone[i] == false) cIndex = i;
}
superCell.superCellSize[cIndex] = 1;
superCell.latticeParams[0,cIndex] = incompleteLattice[0, cIndex];
superCell.latticeVectors.SetColumn(cIndex, FindCVect(superCell.latticeVectors.Column((cIndex + 1) % 3), superCell.latticeVectors.Column((cIndex + 2) % 3), superCell.latticeParams[1, (cIndex + 1) % 3], superCell.latticeParams[1, (cIndex + 2) % 3], superCell.latticeParams[0, cIndex]));
}
#endregion
superCell.CalculateDirectionDerivatives();
return superCell;
}
public void ChangeParent(Node parent)
{
if (Parent.Parent != null)
{
Parent.ChangeParent(this);
}
Parent.Children.Remove(this);
parent.AddChild(this);
}
public Node(int mol, Node parent)
{
AtomNumber = mol;
parent.AddChild(this);
Children = new List<Node>();
}
public void AddChild(Node child)
{
Children.Add(child);
child.Parent = this;
}
public Node(int mol)
{
this.AtomNumber = mol;
Parent = null;
Children = new List<Node>();
}
