public void SetTrajectory(PrimaryStructureTrajectory trajectory)
{
this.PrimaryStructureTrajectory = trajectory;
this.secondaryStructureTrajectory = new SecondaryStructureTrajectory(PrimaryStructure, trajectory, Settings.StrideExecutablePath, Settings.TmpFilePath);
}
public IEnumerator Render(int meshQuality)
{
// if currently rendering, then store render request
if (rendering)
{
awaitingMeshQuality = meshQuality;
awaitingRender = true;
yield break;
}
rendering = true;
System.Diagnostics.Stopwatch watch = new System.Diagnostics.Stopwatch();
watch.Start();
// primary structure render
PrimaryStructureFrame frame = null;
if (PrimaryStructureTrajectory != null && frameNumber != null)
{
frame = PrimaryStructureTrajectory.GetFrame((int)frameNumber);
}
// We use a clone of the render settings so any settings updates dont interfere with the builds
MoleculeRenderSettings renderSettingsClone = renderSettings.Clone();
yield return(StartCoroutine(primaryStructureRenderer.RenderStructure(renderSettingsClone, frame, meshQuality)));
// secondary structure render
SecondaryStructure secondaryStructureToBuild = null;
if (secondaryStructureTrajectory != null && frameNumber != null && buildSecondaryStructureTrajectory)
{
string loadException = null;
Thread thread = new Thread(() => {
try {
secondaryStructureToBuild = secondaryStructureTrajectory.GetStructure((int)frameNumber);
}
catch (FileParseException ex) {
loadException = ex.Message;
}
});
thread.Start();
while (thread.IsAlive)
{
yield return(null);
}
if (loadException != null)
{
MoleculeEvents.RaiseShowMessage(loadException + " - Aborting trajectory secondary structure builds.", true);
buildSecondaryStructureTrajectory = false;
}
}
else
{
secondaryStructureToBuild = secondaryStructure;
}
yield return(StartCoroutine(secondaryStructureRenderer.RenderStructure(renderSettingsClone, frame, secondaryStructureToBuild)));
primaryStructureRenderer.ShowStructure();
secondaryStructureRenderer.ShowStructure();
// simulation box render
if (renderSettingsClone.ShowSimulationBox)
{
moleculeBox.gameObject.SetActive(true);
BoundingBox box = boundingBox;
if (renderSettingsClone.CalculateBoxEveryFrame && frame != null)
{
box = new BoundingBox(frame, true);
}
moleculeBox.Build(box);
}
else
{
moleculeBox.gameObject.SetActive(false);
}
//Cleanup.ForeceGC();
rendering = false;
watch.Stop();
if (Settings.DebugMessages)
{
//console.BannerBuildTime = watch.ElapsedMilliseconds.ToString();
}
//UnityEngine.Debug.Log("Ending model build. Elapsed time [" + watch.ElapsedMilliseconds.ToString() + "]");
yield break;
}
// Loads a molecule trajectory. Will only work if molecule is already loaded
public IEnumerator LoadMoleculeTrajectory(int moleculeID, string filePath)
{
if (!molecules.ContainsKey(moleculeID))
{
MoleculeEvents.RaiseShowMessage("Can't load molecule trajectory. No molecule found.", true);
yield break;
}
if (loadingTrajectory)
{
MoleculeEvents.RaiseShowMessage("Can't Load Trajectory: another trajectory currently loading", true);
yield break;
}
PrimaryStructure primaryStructure = molecules[moleculeID].PrimaryStructure;
int atomCount = loadTrajectoryAtomCount(filePath);
if (atomCount != primaryStructure.AtomCount())
{
MoleculeEvents.RaiseShowMessage("Trajectory atom count [" + atomCount + " doesn't match loaded structure atom count [" + primaryStructure.AtomCount() + "]", true);
yield break;
}
MoleculeEvents.RaiseShowMessage("Loading trajectory. Please wait", false);
loadingTrajectory = true;
PrimaryStructureTrajectory trajectory = null;
string loadException = null;
Thread thread = new Thread(() => {
try {
int startFrame = 0;
int frameFrequency = 1;
int frameCount = Settings.MaxTrajectoryFrames;
if (filePath.EndsWith(".xtc"))
{
trajectory = XTCTrajectoryParser.GetTrajectory(filePath, startFrame, frameCount, frameFrequency);
}
else if (filePath.EndsWith(".dcd"))
{
trajectory = DCDTrajectoryParser.GetTrajectory(filePath, startFrame, frameCount, frameFrequency);
}
else if (filePath.EndsWith(".gro"))
{
trajectory = GROTrajectoryParser.GetTrajectory(filePath, startFrame, frameCount, frameFrequency);
}
}
catch (FileParseException ex) {
loadException = ex.Message;
}
});
thread.Start();
while (thread.IsAlive)
{
yield return(null);
}
if (loadException != null)
{
MoleculeEvents.RaiseShowMessage("Error Loading Trajectory File: " + loadException, true);
loadingTrajectory = false;
yield break;
}
if (trajectory != null)
{
molecules[moleculeID].SetTrajectory(trajectory);
MoleculeEvents.RaiseTrajectoryLoaded(moleculeID, filePath, trajectory.FrameCount());
}
loadingTrajectory = false;
}
