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);
}
}
}
}
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");
//}
}
}
// 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);
}
public void CreatePDBFile(string filePath, bool mainChainOnly = false, bool omitHetatoms = false, bool omitHydrogen = false)
{
using (StreamWriter writer = new StreamWriter(filePath)) {
//string testRecord = TestLine(); // for debugging output records
//writer.WriteLine(testRecord);
string crystRecord = CrystRecord();
writer.WriteLine(crystRecord);
int atomIndex = 1;
foreach (Chain chain in structure.Chains())
{
if (omitHetatoms && chain.ResidueType == StandardResidue.None)
{
continue;
}
Atom lastAtom = null;
IEnumerable <Residue> residues = null;
if (mainChainOnly)
{
residues = chain.MainChainResidues;
}
else
{
residues = chain.Residues;
}
foreach (Residue residue in residues)
{
foreach (Atom atom in residue.Atoms.Values)
{
if (omitHydrogen && atom.Element == Element.H)
{
continue;
}
bool hetAtom = atom.ResidueType != StandardResidue.None ? false : true;
Vector3 position;
// if no frame number use the primary structure coordinates.
if (frame == null)
{
position = new Vector3(atom.Position.x, atom.Position.y, atom.Position.z);
}
else
{
position = new Vector3(frame.Coords[atom.Index * 3], frame.Coords[(atom.Index * 3) + 1], frame.Coords[(atom.Index * 3) + 2]);
}
string atomRecord = AtomRecord(
hetAtom,
atomIndex,
atom.Name,
atom.ResidueName,
chain.ID.ToString()[0],
atom.ResidueIndex.ToString(),
position.x * 10,
position.y * 10,
position.z * 10,
atom.Element.ToString()
);
writer.WriteLine(atomRecord);
atomIndex++;
lastAtom = atom;
}
}
if (lastAtom != null)
{
string terRecord = TerRecord(
atomIndex,
lastAtom.ResidueName,
chain.ID.ToString()[0],
lastAtom.ResidueIndex.ToString()
);
writer.WriteLine(terRecord);
atomIndex++;
}
lastAtom = null;
}
string endRecord = EndRecord();
writer.WriteLine(endRecord);
}
}