public static void Run()
{
// get the primary structure
Console.WriteLine("Parsing GRO File");
Stopwatch stopWatch = new Stopwatch();
stopWatch.Start();
PrimaryStructure primaryStructure = GROStructureParser.GetStructure(inputFilePath + inputFileName);
stopWatch.Stop();
Console.WriteLine("Structure Parsing Complete [" + stopWatch.ElapsedMilliseconds + " ms]");
// get the structure trajectory
int atomCount = XTCTrajectoryParser.GetAtomCount(inputFilePath + trajectoryFileName);
if (atomCount == primaryStructure.AtomCount())
{
Console.WriteLine("Atom Count matches.");
}
else
{
Console.WriteLine("Atom count doesnt match between primary structure and trajectory");
}
Stopwatch stopWatch2 = new Stopwatch();
stopWatch2.Start();
PrimaryStructureTrajectory trajectory = XTCTrajectoryParser.GetTrajectory(inputFilePath + trajectoryFileName, 0, 100, 1);
stopWatch2.Stop();
Console.WriteLine("Trajectory Parsing Complete [" + stopWatch2.ElapsedMilliseconds + " ms]");
// get the secondary structure for the base primary structure
Stopwatch stopWatch3 = new Stopwatch();
stopWatch3.Start();
SecondaryStructure secondaryStructure = SecondaryStructure.CreateFromPrimaryStructure(primaryStructure, strideExePath, tmpFilePath);
Console.WriteLine("Main Secondary Structure Parsing Complete [" + stopWatch3.ElapsedMilliseconds + " ms]");
Console.WriteLine(secondaryStructure);
// get the secondary structure for a frame of the trajectory
Stopwatch stopWatch4 = new Stopwatch();
stopWatch4.Start();
SecondaryStructureTrajectory secondaryStructureTrajectory = new SecondaryStructureTrajectory(primaryStructure, trajectory, strideExePath, tmpFilePath);
SecondaryStructure secondaryStructure2 = secondaryStructureTrajectory.GetStructure(50);
Console.WriteLine("Secondary Structure Parsing for frame 50 Complete [" + stopWatch3.ElapsedMilliseconds + " ms]");
Console.WriteLine(secondaryStructure2);
}
// 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 Run()
{
Console.WriteLine("Parsing GRO File");
Stopwatch stopWatch = new Stopwatch();
stopWatch.Start();
PrimaryStructure primaryStructure = GROStructureParser.GetStructure(filepath + structureFile);
stopWatch.Stop();
Console.WriteLine("Structure Parsing Complete [" + stopWatch.ElapsedMilliseconds + " ms]");
stopWatch.Reset();
stopWatch.Start();
SecondaryStructure secondaryStructure = SecondaryStructure.CreateFromPrimaryStructure(primaryStructure, strideExePath, tmpFilePath);
Console.WriteLine("Main Secondary Structure Parsing Complete [" + stopWatch.ElapsedMilliseconds + " ms]");
foreach (Chain chain in primaryStructure.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("Residue index: " + residue.Index + ", ResidueID: " + residue.ID + ", Residue Name: " + residue.Name);
SecondaryStructureInfomation information = secondaryStructure.GetStructureInformation(residue.Index);
if (information == null)
{
Console.WriteLine("information null: " + residue.Index);
}
}
}
}
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);
}
