/// <summary>
/// Reads a timestep from an .xtc file.
/// </summary>
private static PrimaryStructureFrame getFrame(BinaryReader reader)
{
PrimaryStructureFrame frame = new PrimaryStructureFrame();
// Check magic number
if (getInt32(reader) != magicNumber)
{
throw new FileParseException("XTC file not well formed, no magic number in frame header");
}
// get timestep header info
frame.AtomCount = getInt32(reader);
frame.Step = getInt32(reader);
frame.Time = getFloat32(reader);
// read and discard the box
for (int i = 0; i < 9; i++)
{
getFloat32(reader);
}
// get the coordinates
float[] coords = new float[3 * frame.AtomCount];
xtc_3dfcoord(reader, coords);
frame.Coords = coords;
return(frame);
}
/// <summary>
/// Returns the number of atoms in the first frame of the trajectory.
/// </summary>
/// <param name="filename"></param>
/// <returns></returns>
public static int GetAtomCount(string filename)
{
StreamReader sr = null;
int atomCount = 0;
try {
sr = new StreamReader(filename);
// discard first frame, which should be the structure
getFrame(sr); // discard frame
PrimaryStructureFrame frame = getFrame(sr); // get first trajectory frame
if (frame != null)
{
atomCount = frame.AtomCount;
}
}
catch (Exception e) {
throw new FileParseException(e.Message);
}
finally {
if (sr != null)
{
sr.Close();
}
}
return(atomCount);
}
private static PrimaryStructureFrame getFrame(StreamReader sr)
{
PrimaryStructureFrame frame;
try {
frame = new PrimaryStructureFrame();
string titleLine = sr.ReadLine();
// remove any blank lines before title line
while (titleLine != null && titleLine.Trim().Equals(""))
{
titleLine = sr.ReadLine();
}
if (titleLine == null) // if we have reached the end of the file
{
return(null);
}
frame.Time = 0;
Regex g = new Regex(@"\st=\s*(\d+\.?\d*)");
Match m = g.Match(titleLine);
if (m.Success)
{
string frameTimeString = m.Groups[1].Value;
frame.Time = float.Parse(frameTimeString);
// Console.WriteLine("Success parsing [" + titleLine + "] for frame time");
}
frame.AtomCount = Int32.Parse(sr.ReadLine().Trim());
float[] coords = new float[3 * frame.AtomCount];
for (int i = 0; i < frame.AtomCount; i++)
{
string atomLine = sr.ReadLine();
if (atomLine == null) // if something is wrong with the file, i.e. ends before total atom count
{
throw new FileParseException("Error reading atoms. Frame atom count doesn't equal frame atom total");
}
coords[3 * i] = float.Parse(atomLine.Substring(20, 8));
coords[3 * i] = float.Parse(atomLine.Substring(28, 8));
coords[3 * i] = float.Parse(atomLine.Substring(36, 8));
frame.Coords = coords;
}
// read box vectors.
string boxLine = sr.ReadLine();
}
catch (Exception e) {
throw new FileParseException(e.Message);
}
return(frame);
}
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 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);
}
private static void parseFrame(BinaryReader reader, bool cellInfo, PrimaryStructureFrame frame)
{
// discard cell information if present
if (cellInfo)
{
int cellInfoLength = reader.ReadInt32();
reader.ReadBytes(cellInfoLength);
reader.ReadInt32(); // discard end of index array length
}
float[] coords = new float[3 * frame.AtomCount];
reader.ReadInt32(); // discard block size
for (int i = 0; i < frame.AtomCount; i++)
{
coords[3 * i] = (float)Math.Round((decimal)(reader.ReadSingle() / 10f), 3);
}
reader.ReadInt32(); // discard block size
reader.ReadInt32(); // discard block size
for (int i = 0; i < frame.AtomCount; i++)
{
coords[3 * i + 1] = (float)Math.Round((decimal)(reader.ReadSingle() / 10f), 3);
}
reader.ReadInt32(); // discard block size
reader.ReadInt32(); // discard block size
for (int i = 0; i < frame.AtomCount; i++)
{
byte[] input = reader.ReadBytes(4);
float num = System.BitConverter.ToSingle(input, 0);
if (num < 0)
{
// Console.WriteLine("Negative number: " + num);
}
coords[3 * i + 2] = (float)Math.Round((decimal)(num / 10f), 3);
}
reader.ReadInt32(); // discard block size
frame.Coords = coords;
}
private static void discardFrame(BinaryReader reader)
{
PrimaryStructureFrame frame = new PrimaryStructureFrame();
// Check magic number
if (getInt32(reader) != magicNumber)
{
throw new FileParseException("XTC file not well formed, no magic number in frame header");
}
// discard 12 frame metadata fields
reader.BaseStream.Seek(12 * 4, SeekOrigin.Current);
// discard the coordinates metadata & data
int lsize = getInt32(reader);
if (lsize <= 9)
{
reader.BaseStream.Seek(lsize * 3 * 4, SeekOrigin.Current);
return;
}
else
{
// discard 7 coord metadata fields
reader.BaseStream.Seek(8 * 4, SeekOrigin.Current);
// get length of coord data
int len = getInt32(reader);
if (len < 1)
{
throw new FileParseException("Error reading coordinates");
}
// discard coordinate data
reader.BaseStream.Seek(len, SeekOrigin.Current);
// round out byte read to nearest 4 bytes
if (len % 4 != 0)
{
reader.BaseStream.Seek(4 - (len % 4), SeekOrigin.Current);
}
}
}
public override string ToString()
{
string output = "";
if (frames != null)
{
for (int i = 0; i < frames.Count; i++)
{
if (i > 10)
{
break;
}
output += "Frame[" + (i + 1) + "]\n";
PrimaryStructureFrame frame = frames[i];
int totalCoords = 0;
for (int j = 0; j < frame.AtomCount; j++)
{
if (j > 10)
{
break;
}
float x = frame.Coords[j * 3];
float y = frame.Coords[j * 3 + 1];
float z = frame.Coords[j * 3 + 2];
output += "Time [" + frame.Time + "] Coords[" + j + "]: [" + x + ", " + y + ", " + z + "]\n";
totalCoords++;
}
output += "\n";
}
}
else
{
output = "No frames in trajectory";
}
return(output);
}
/// <summary>
/// Returns the number of atoms in the first frame of the trajectory file.
/// </summary>
/// <param name="filename"></param>
/// <returns></returns>
public static int GetAtomCount(string filename)
{
BinaryReader reader = null;
int count = 0;
try {
reader = new BinaryReader(new FileStream(filename, FileMode.Open));
PrimaryStructureFrame frame = getFrame(reader);
count = frame.Coords.Length / 3;
}
catch (Exception e) {
throw new FileParseException(e.Message);
}
finally {
if (reader != null)
{
reader.Close();
}
}
return(count);
}
public PDBStructureCreator(PrimaryStructure structure, PrimaryStructureFrame frame)
{
this.structure = structure;
this.frame = frame;
}
/// <summary>
/// generate a box from a provided Primary Structure
/// </summary>
/// <returns></returns>
public BoundingBox(PrimaryStructureFrame frame, bool flipZ = false)
{
float minx = 0;
float maxx = 0;
float miny = 0;
float maxy = 0;
float minz = 0;
float maxz = 0;
if (frame.Coords.Length <= 0)
{
return;
}
// foreach (KeyValuePair<int, Atom> atom in structure.Atoms()) {
for (int i = 0; i < frame.AtomCount; i++)
{
float[] coords = frame.GetAtomCoords(i);
if (i == 0)
{
minx = coords[0];
maxx = coords[0];
miny = coords[1];
maxy = coords[1];
minz = coords[2];
maxz = coords[2];
}
else
{
if (coords[0] < minx)
{
minx = coords[0];
}
if (coords[0] > maxx)
{
maxx = coords[0];
}
if (coords[1] < miny)
{
miny = coords[1];
}
if (coords[1] > maxy)
{
maxy = coords[1];
}
if (coords[2] < minz)
{
minz = coords[2];
}
if (coords[2] > maxz)
{
maxz = coords[2];
}
}
}
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);
}
public void AddFrame(PrimaryStructureFrame frame)
{
frames.Add(frame);
}
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();
}
}
}
