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);
}
public static void Run()
{
Console.WriteLine("Parsing PDB File");
Stopwatch stopWatch = new Stopwatch();
stopWatch.Start();
PrimaryStructure primaryStructure = PDBStructureParser.GetPrimaryStructure(filepath + structureFile);
stopWatch.Stop();
Console.WriteLine("Structure Parsing Complete [" + stopWatch.ElapsedMilliseconds + " ms]");
stopWatch.Reset();
stopWatch.Start();
SecondaryStructure.CreateFromPrimaryStructure(primaryStructure, strideExePath, tmpFilePath);
Console.WriteLine("Main Secondary Structure Parsing Complete [" + stopWatch.ElapsedMilliseconds + " ms]");
foreach (Chain chain in primaryStructure.Chains())
{
foreach (Atom atom in chain.MainChainAtoms)
{
// if no frame number use the base structure coordinates.
if (atom == null)
{
Console.WriteLine("Main chain atom is null");
}
else
{
Console.WriteLine("Atom found: " + atom.ToString());
}
}
//Console.WriteLine("\n---------------------\n");
//Console.WriteLine("Chain ID: " + chain.ID);
//Console.WriteLine("Chain Residue Count: " + chain.Residues.Count);
//if (chain.ResidueType == MolecularDynamics.Definitions.StandardResidue.AminoAcid) {
// 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);
// }
// }
//}
//else {
// Console.WriteLine("Not an amino acid residue");
//}
}
}
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);
}
}
}
}
