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 PrimaryStructureTrajectory GetTrajectory(string filename, int startFrame, int numFrames, int frameFrequency)
{
StreamReader sr = null;
PrimaryStructureTrajectory trajectory = new PrimaryStructureTrajectory();
try {
sr = new StreamReader(filename);
// discard first frame, which should be the structure
getFrame(sr); // discard frame
for (int i = 0; i < startFrame; i++)
{
getFrame(sr); // discard frame
}
int framesAdded = 0;
int currentFrame = 0;
while (framesAdded < numFrames)
{
currentFrame++;
if (currentFrame % frameFrequency == 0)
{
PrimaryStructureFrame frame = getFrame(sr);
if (frame == null) // end of file, no more frames in file
{
break;
}
trajectory.AddFrame(frame);
framesAdded++;
}
else
{
PrimaryStructureFrame frame = getFrame(sr); // discard frame
if (frame == null) // end of file, no more frames in file
{
break;
}
}
}
}
catch (Exception e) {
throw new FileParseException(e.Message);
}
finally {
if (sr != null)
{
sr.Close();
}
}
return(trajectory);
}
public SecondaryStructureTrajectory(PrimaryStructure primaryStructure, PrimaryStructureTrajectory primaryTrajectory, string strideExePath, string tmpFilePath)
{
this.primaryStructure = primaryStructure;
this.primaryTrajectory = primaryTrajectory;
this.strideExePath = strideExePath;
this.tmpFilePath = tmpFilePath;
secondaryStructuresFrames = new Dictionary <int, SecondaryStructure>();
badFrames = new HashSet <int>();
}
public static PrimaryStructureTrajectory GetTrajectory(string filename, int startFrame, int numFrames, int frameFrequency)
{
PrimaryStructureTrajectory trajectory = new PrimaryStructureTrajectory();
BinaryReader reader = null;
try {
int frameCount;
int atomCount;
bool cellInfo;
string title;
reader = new BinaryReader(new FileStream(filename, FileMode.Open));
parseDCDHeader(reader, out frameCount, out atomCount, out cellInfo, out title);
for (int i = 0; i < startFrame; i++)
{
discardFrame(reader, cellInfo, atomCount);
}
int frameIndex = 0;
int currentFrame = 0;
while (reader.BaseStream.Position != reader.BaseStream.Length && frameIndex < numFrames)
{
currentFrame++;
if (currentFrame % frameFrequency == 0)
{
PrimaryStructureFrame frame = new PrimaryStructureFrame();
frame.AtomCount = atomCount;
//frame.Step = ;
//frame.Time = ;
parseFrame(reader, cellInfo, frame);
trajectory.AddFrame(frame);
frameIndex++;
}
else
{
discardFrame(reader, cellInfo, atomCount);
}
}
}
catch (Exception e) {
throw new FileParseException(e.Message);
}
finally {
if (reader != null)
{
reader.Close();
}
}
return(trajectory);
}
public static PrimaryStructureTrajectory GetTrajectory(string filename, int startFrame, int numFrames, int frameFrequency)
{
PrimaryStructureTrajectory trajectory = new PrimaryStructureTrajectory();
BinaryReader reader = null;
try {
reader = new BinaryReader(new FileStream(filename, FileMode.Open));
for (int i = 0; i < startFrame; i++)
{
discardFrame(reader);
}
int framesAdded = 0;
int currentFrame = 0;
while (reader.BaseStream.Position != reader.BaseStream.Length && framesAdded < numFrames)
{
currentFrame++;
if (currentFrame % frameFrequency == 0)
{
trajectory.AddFrame(getFrame(reader));
framesAdded++;
}
else
{
discardFrame(reader);
}
}
}
catch (Exception e) {
// handle end of file corruption gracefully.
if (trajectory.FrameCount() > 0)
{
return(trajectory);
}
else
{
throw new FileParseException(e.Message);
}
}
finally {
if (reader != null)
{
reader.Close();
}
}
return(trajectory);
}
public static void GetTrajectoryColours(string filename, PrimaryStructure model, PrimaryStructureTrajectory trajectory, int startFrame, int numFrames, int frameFrequency)
{
Stopwatch watch = new Stopwatch();
watch.Start();
StreamReader reader = null;
Regex g = new Regex(@"\s*(\d+)\s*(\d+\.?\d*)");
try {
reader = new StreamReader(filename);
discardFrames(reader, startFrame);
List <float[]> colourFrames = new List <float[]>();
int colourFrameNumber = -1;
int atomIndex = 0;
float colour = 0;
float[] colourFrame = null;
string line;
while ((line = readLine(reader)) != null && colourFrames.Count < numFrames)
{
if (line.Trim().Length == 0) // is empty string?
{
continue;
}
// discard everything but matches
Match m = g.Match(line);
if (m.Success)
{
atomIndex = int.Parse(m.Groups[1].Value);
colour = float.Parse(m.Groups[2].Value);
if (atomIndex == 1)
{
colourFrameNumber++;
// save colours
if (colourFrame != null)
{
colourFrames.Add(colourFrame);
colourFrame = null;
}
if (colourFrameNumber % frameFrequency == 0)
{
// initialise new colour arrary
colourFrame = new float[model.AtomCount()];
for (int i = 0; i < colourFrame.Length; i++)
{
colourFrame[i] = DEFAULT_COLOUR_VALUE;
}
}
}
if (colourFrame != null)
{
if (atomIndex > 0 && atomIndex <= colourFrame.Length)
{
colourFrame[atomIndex - 1] = colour;
}
}
}
}
PrimaryStructureFrame currentFrame = null;
int frameNumber = 0;
// copy all colour frames to trajectory frames
foreach (float[] frame in colourFrames)
{
currentFrame = trajectory.GetFrame(frameNumber);
currentFrame.Colours = frame;
frameNumber++;
// if we've run out of trajectory frames then stop copying
if (frameNumber >= trajectory.FrameCount())
{
break;
}
}
// if more trajectory frames than colour frames fill in rest of trajectory frames with default colours
float[] colours = new float[model.AtomCount()];
for (int i = 0; i < colours.Length; i++)
{
colours[i] = 0f;
}
foreach (PrimaryStructureFrame frame in trajectory.GetFrames())
{
if (frame.Colours == null)
{
frame.Colours = colours;
}
}
}
catch (Exception e) {
throw new FileParseException(e.Message);
}
finally {
if (reader != null)
{
reader.Close();
}
}
}
public static void GetTrajectoryColours(string filename, PrimaryStructure model, PrimaryStructureTrajectory trajectory)
{
GetTrajectoryColours(filename, model, trajectory, 0, DEFAULT_FRAME_READ, 1);
}