public static void Run()
{
Console.WriteLine("Parsing PBD File");
Stopwatch stopWatch = new Stopwatch();
stopWatch.Start();
PrimaryStructure model = PDBStructureParser.GetPrimaryStructure(inputFilePath + inputFileName);
stopWatch.Stop();
Console.WriteLine("Structure Parsing Complete [" + stopWatch.ElapsedMilliseconds + " ms]");
Console.WriteLine("Atom Count: " + model.Atoms().Count);
Console.WriteLine("Running Stride Analysis");
stopWatch = new Stopwatch();
stopWatch.Start();
StrideAnalysis stride = new StrideAnalysis(exePath);
SecondaryStructure structure = stride.GetSecondaryStructure(inputFilePath + inputFileName);
// Console.WriteLine("Secondary structure:\n\n" + structure);
stopWatch.Stop();
Console.WriteLine("Processing complete [" + stopWatch.ElapsedMilliseconds + " ms]");
Console.WriteLine("End Testing Stride");
foreach (Chain chain in model.Chains())
{
Console.WriteLine("Chain ID: " + chain.ID);
if (chain.ResidueType != StandardResidue.AminoAcid)
{
Console.WriteLine("Not a protein chain");
continue;
}
foreach (Residue residue in chain.MainChainResidues)
{
if (residue.CarbonylOxygen == null)
{
Console.WriteLine("Residue ID: " + residue.ID + " has no oxygen");
}
SecondaryStructureInfomation structureInfo = structure.GetStructureInformation(residue.Index);
if (structureInfo == null)
{
Console.WriteLine("Couldn't find structure info for residue index: " + residue.Index);
}
else
{
Console.WriteLine("Residue [" + residue.ID + "][" + residue.Name + "] has structure [" + structureInfo.ToString() + "] and Alpha Carbon: " + residue.AlphaCarbon);
}
}
}
}
// private static string inputFileFileName = @"lipoprotein_DS.pdb";
//private static string inputFileFileName = @"lipoprotein.pdb";
//private static string inputFilePath = @"D:\Molecule Examples\PDB Example Files\";
//private static string inputFileFileName = @"Zika_Virus_5ire.pdb";
public static void Run()
{
Console.WriteLine("Parsing PBD File");
Stopwatch stopWatch = new Stopwatch();
stopWatch.Start();
// PrimaryStructure model = PDBStructureParser.GetStructure(inputFilePath + inputFileFileName);
PrimaryStructure model = GROStructureParser.GetStructure(inputFilePath + inputFileFileName);
stopWatch.Stop();
Console.WriteLine("Structure Parsing Complete [" + stopWatch.ElapsedMilliseconds + " ms]");
Console.WriteLine("Atom Count: " + model.Atoms().Count);
// Console.WriteLine(model.ToString());
foreach (Chain chain in model.Chains())
{
Console.WriteLine("Chain " + chain.ID + ": ");// + residue.ToString());
if (chain.ResidueType == StandardResidue.AminoAcid)
{
foreach (Residue residue in chain.MainChainResidues)
{
Console.WriteLine(residue);
}
//foreach (Atom mainChainAtom in chain.Value.MainChainAtoms) {
// Console.WriteLine(mainChainAtom);
//}
}
else
{
Console.WriteLine("Chain " + chain.ID + " is not a protein chain");
//foreach (KeyValuePair<int, Residue> residue in chain.Value.Residues) {
// Console.WriteLine(residue.Value.ResidueType.ToString());
//}
}
}
}
public static void ParseGromacs()
{
Console.WriteLine("Parsing GRO File");
Stopwatch stopWatch = new Stopwatch();
stopWatch.Start();
PrimaryStructure model = GROStructureParser.GetStructure(filepath + structureFile);
stopWatch.Stop();
Console.WriteLine("Structure Parsing Complete [" + stopWatch.ElapsedMilliseconds + " ms]");
Console.WriteLine("Atom Count: " + model.Atoms().Count);
foreach (Atom atom in model.Atoms())
{
Console.WriteLine("Atom " + atom.Index + ": " + atom.ToString());
}
Console.WriteLine("\n---------------------\n");
Dictionary <Element, Dictionary <int, Atom> > atomSet = model.GetAtomsByElement();
foreach (KeyValuePair <Element, Dictionary <int, Atom> > set in atomSet)
{
Element element = set.Key;
Console.WriteLine("Element: " + element.ToString());
Dictionary <int, Atom> atoms = set.Value;
foreach (KeyValuePair <int, Atom> atom in atoms)
{
Console.WriteLine("Atom: " + atom.Value.ToString());
}
}
foreach (Chain chain in model.Chains())
{
Console.WriteLine("\n---------------------\n");
Console.WriteLine("Chain ID: " + chain.ID);
Console.WriteLine("Chain Residue Count: " + chain.Residues.Count);
foreach (Residue residue in chain.Residues)
{
Console.WriteLine("ResidueID: " + residue.ID + ", Residue Name: " + residue.Name);
}
}
stopWatch.Reset();
stopWatch.Start();
int NumberOfProcessorCores = 6;
Dictionary <int, Bond> bonds = model.GenerateBonds(NumberOfProcessorCores);
Console.WriteLine("Bond generation complete [" + stopWatch.ElapsedMilliseconds + " ms]");
int count = 0;
foreach (KeyValuePair <int, Bond> bond in bonds)
{
Atom atom1 = model.Atoms()[bond.Value.Atom1Index];
Atom atom2 = model.Atoms()[bond.Value.Atom2Index];
if ((atom1.Element == Element.O && atom2.Element == Element.H) ||
(atom2.Element == Element.O && atom1.Element == Element.H))
{
Console.WriteLine("O-H bond found. Distance: " + Vector3.Distance(atom1.Position, atom2.Position));
count++;
if (count > 5)
{
break;
}
}
}
Console.WriteLine("Getting frame count from trajectory file");
stopWatch.Reset();
stopWatch.Start();
count = XTCTrajectoryParser.GetFrameCount(filepath + trajectoryFile);
stopWatch.Stop();
Console.WriteLine("Frame count complete [" + stopWatch.ElapsedMilliseconds + " ms]");
Console.WriteLine("Frames counted: " + count);
}
/// <summary>
/// generate a box from a provided Primary Structure
/// </summary>
/// <returns></returns>
public BoundingBox(PrimaryStructure structure, bool flipZ = false)
{
float minx = 0;
float maxx = 0;
float miny = 0;
float maxy = 0;
float minz = 0;
float maxz = 0;
bool firstAtom = true;
foreach (Atom atom in structure.Atoms())
{
if (firstAtom)
{
minx = atom.Position.x;
maxx = atom.Position.x;
miny = atom.Position.y;
maxy = atom.Position.y;
minz = atom.Position.z;
maxz = atom.Position.z;
firstAtom = false;
}
else
{
if (atom.Position.x < minx)
{
minx = atom.Position.x;
}
if (atom.Position.x > maxx)
{
maxx = atom.Position.x;
}
if (atom.Position.y < miny)
{
miny = atom.Position.y;
}
if (atom.Position.y > maxy)
{
maxy = atom.Position.y;
}
if (atom.Position.z < minz)
{
minz = atom.Position.z;
}
if (atom.Position.z > maxz)
{
maxz = atom.Position.z;
}
}
}
float edgeBuffer = 0.1f;
minx -= edgeBuffer;
maxx += edgeBuffer;
miny -= edgeBuffer;
maxy += edgeBuffer;
minz -= edgeBuffer;
maxz += edgeBuffer;
if (flipZ)
{
minz *= -1;
maxz *= -1;
}
setVectors(minx, maxx, miny, maxy, minz, maxz);
}
private static PrimaryStructure GetFrame(StreamReader sr)
{
PrimaryStructure model;
// todo: improve file format error handling for misformatted files
try {
model = new PrimaryStructure();
string titleLine = sr.ReadLine();
// remove any blank lines before title line
while (titleLine != null && titleLine.Trim().Equals(""))
{
titleLine = sr.ReadLine();
}
if (titleLine == null)
{
return(null);
}
model.Title = titleLine;
model.Time = 0;
Regex g = new Regex(@"\st=\s*(\d+\.?\d*)");
Match m = g.Match(titleLine);
if (m.Success)
{
string frameTimeString = m.Groups[1].Value;
model.Time = float.Parse(frameTimeString);
// Console.WriteLine("Success parsing[" + titleLine + "] for frame time");
}
else
{
// no frame time in header. Assume structure file, leave frame time at 0;
// return false;
}
int residueIndex = 0;
int chainIndex = 0;
Chain chain = null;
Residue residue = null;
int currentResidueID = -1;
Residue lastResidue = null;
int atomCount = Int32.Parse(sr.ReadLine().Trim());
for (int i = 0; i < atomCount; i++)
{
string atomLine = sr.ReadLine();
if (atomLine == null) // if something is wrong with the file, i.e. ends before total atom count
{
break;
}
// if atom residue number not the existing residue number store the existing residue and instantiate new residue
int atomResidueID = int.Parse(atomLine.Substring(0, 5).Trim());
if (atomResidueID != currentResidueID)
{
// store residue - first time here will be null
if (residue != null)
{
model.AddResidue(residueIndex, residue);
if (chain != null)
{
chain.AddResidue(residueIndex, residue);
}
}
residueIndex++;
currentResidueID = atomResidueID;
string residueName = atomLine.Substring(5, 5).Trim();
lastResidue = residue;
residue = new Residue(residueIndex, currentResidueID, residueName);
// Residue type changes used to capture chain information. May not be 100% accurate but not parsing topology files so options are limited.
// Also checking to see if last two atoms before end of amino acid were Oxygen, signifying a chain terminator
if ((lastResidue == null || residue.ResidueType != lastResidue.ResidueType) ||
(lastResidue.ResidueType == StandardResidue.AminoAcid && model.Atoms()[i - 1].Element == Element.O && model.Atoms()[i - 2].Element == Element.O))
{
if (chain != null)
{
model.AddChain(chain);
}
chainIndex++;
chain = new Chain(chainIndex, chainIndex.ToString());
}
}
int atomIndex = i;
int atomID = int.Parse((atomLine.Substring(15, 5)).Trim());
string atomName = atomLine.Substring(10, 5).Trim();
Element element = ElementHelper.Parse(atomName);
Vector3 position = new Vector3();
position.x = float.Parse(atomLine.Substring(20, 8));
position.y = float.Parse(atomLine.Substring(28, 8));
position.z = float.Parse(atomLine.Substring(36, 8));
Atom atom = new Atom(atomIndex, atomID, atomName, element, position);
// check for and store main chain elements.
if (residue.ResidueType != StandardResidue.None)
{
switch (atom.Name)
{
case "N":
residue.AmineNitrogen = atom;
break;
case "CA":
residue.AlphaCarbon = atom;
break;
case "C":
residue.CarbonylCarbon = atom;
break;
case "O":
case "O1":
case "OT1":
residue.CarbonylOxygen = atom;
break;
}
}
atom.ResidueIndex = residueIndex;
atom.ResidueID = currentResidueID;
atom.ResidueName = residue.Name;
atom.ResidueType = residue.ResidueType;
atom.ChainID = chainIndex.ToString();
residue.Atoms.Add(atomIndex, atom);
model.AddAtom(atomIndex, atom);
}
if (residue != null)
{
model.AddResidue(residueIndex, residue);
if (chain != null)
{
chain.AddResidue(residueIndex, residue);
}
}
if (chain != null)
{
model.AddChain(chain);
}
// Parse box vectors.
// todo: test and make this more robust for various string lengths
float[] vertices = parseBoxLine(sr.ReadLine());
model.OriginalBoundingBox = new BoundingBox(vertices[0], vertices[1], vertices[2], vertices[3], vertices[4], vertices[5], vertices[6], vertices[7], vertices[8]);
}
catch (Exception e) {
throw new FileParseException(e.Message);
}
return(model);
}
