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);
}
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);
}