private void initialiseResidueRenderSettings(PrimaryStructure primaryStructure)
{
if (primaryStructure.ResidueNames == null || primaryStructure.ResidueNames.Count == 0 ||
primaryStructure.ResidueIDs == null || primaryStructure.ResidueIDs.Count == 0)
{
return;
}
// initialise the residue render settings for the molecule
if (selectedMolecule.RenderSettings.EnabledResidueNames == null)
{
selectedMolecule.RenderSettings.EnabledResidueNames = new HashSet <string>(primaryStructure.ResidueNames);
}
if (selectedMolecule.RenderSettings.CustomResidueNames == null)
{
selectedMolecule.RenderSettings.CustomResidueNames = new HashSet <string>();
}
if (selectedMolecule.RenderSettings.EnabledResidueIDs == null)
{
selectedMolecule.RenderSettings.EnabledResidueIDs = new HashSet <int>(primaryStructure.ResidueIDs);
}
if (selectedMolecule.RenderSettings.CustomResidueRenderSettings == null)
{
selectedMolecule.RenderSettings.CustomResidueRenderSettings = new Dictionary <int, ResidueRenderSettings>();
}
}
public void Initialise(string residueName, MoleculeRenderSettings settings, PrimaryStructure primaryStructure, SaveCustomResidueSettingsDelegate saveCustomResidueSettings, ResidueRenderSettingsUpdated settingsUpdatedCallback, ClosedResidueSettingsPanel onClose)
{
this.residueName = residueName;
this.moleculeRenderSettings = settings;
this.primaryStructure = primaryStructure;
this.saveCustomResidueSettings = saveCustomResidueSettings;
this.settingsUpdatedCallback = settingsUpdatedCallback;
this.onClose = onClose;
ResidueNameInformationText.text = "Showing residue IDs for " + residueName;
residueIDs = primaryStructure.GetResidueIDs(new List <String>()
{
residueName
}).ToList();
residueIDs.Sort();
renderResidueIDButtons();
allResiduesEnabled = true;
foreach (int residueID in residueIDs)
{
if (!moleculeRenderSettings.EnabledResidueIDs.Contains(residueID))
{
allResiduesEnabled = false;
break;
}
}
updateToggleResidueButtonText();
residueIDsPanel.SetActive(true);
}
public static void RaiseMoleculeLoaded(int moleculeID, string name, PrimaryStructure primaryStructure)
{
if (OnMoleculeLoaded != null)
{
OnMoleculeLoaded(moleculeID, name, primaryStructure);
}
}
private void showResidueNamesPanel(MoleculeRenderSettings renderSettings, PrimaryStructure primaryStructure)
{
residueNamesPanel.Initialise(renderSettings, primaryStructure, updateMoleculeRender);
if (primaryStructure.ResidueNames == null || primaryStructure.ResidueNames.Count == 0 ||
primaryStructure.ResidueIDs == null || primaryStructure.ResidueIDs.Count == 0)
{
residueNamesPanelGO.gameObject.SetActive(false);
}
else
{
residueNamesPanelGO.gameObject.SetActive(true);
}
}
public void SetPrimaryStructure(int moleculeID, PrimaryStructure primaryStructure)
{
if (primaryStructures == null)
{
primaryStructures = new Dictionary <int, PrimaryStructure>();
}
if (!primaryStructures.ContainsKey(moleculeID))
{
primaryStructures.Add(moleculeID, primaryStructure);
}
else
{
primaryStructures[moleculeID] = primaryStructure;
}
}
public void Initialise(MoleculeRenderSettings moleculeRenderSettings, PrimaryStructure primaryStructure, ResidueRenderSettingsUpdated settingsUpdatedCallback)
{
this.moleculeRenderSettings = moleculeRenderSettings;
this.primaryStructure = primaryStructure;
this.settingsUpdatedCallback = settingsUpdatedCallback;
residueNames = primaryStructure.ResidueNames.ToList();
residueNames.Sort();
renderResidueNameButtons();
allResiduesEnabled = false;
if (this.moleculeRenderSettings.EnabledResidueNames != null && residueNameButtons.Count == this.moleculeRenderSettings.EnabledResidueNames.Count)
{
allResiduesEnabled = true;
}
updateToggleResidueButtonText();
residueNamesPanel.SetActive(true);
}
public void Initialise(int id, PrimaryStructure primaryStructure, MoleculeRenderSettings renderSettings)
{
if (primaryStructure == null)
{
return;
}
this.ID = id;
this.PrimaryStructure = primaryStructure;
this.renderSettings = renderSettings;
this.frameNumber = null;
try {
secondaryStructure = SecondaryStructure.CreateFromPrimaryStructure(primaryStructure, Settings.StrideExecutablePath, Settings.TmpFilePath);
}
catch (Exception ex) {
Debug.Log("Error Parsing Secondary Structure from Structure File: " + ex.Message);
buildSecondaryStructureTrajectory = false;
}
moleculeBox.gameObject.SetActive(renderSettings.ShowSimulationBox);
boundingBox = new BoundingBox(primaryStructure, true);
moleculeRender.transform.position = new Vector3(-1 * boundingBox.Centre.x, -1 * boundingBox.Centre.y, -1 * boundingBox.Centre.z);
this.transform.position = new Vector3(boundingBox.Centre.x, boundingBox.Centre.y, boundingBox.Centre.z);
if (renderSettings.ShowSimulationBox)
{
moleculeBox.Build(boundingBox);
}
primaryStructureRenderer.Initialise(primaryStructure);
secondaryStructureRenderer.Initialise(primaryStructure);
moleculeInput.enabled = false;
autoRotateEnabled = false;
AutoRotateSpeed = 0f;
}
public void UpdateSelectedMolecule()
{
if (isActiveAndEnabled)
{
selectedMolecule = molecules.GetSelected();
if (selectedMolecule != null)
{
selectedMoleculeText.text = "Modifying settings for molecule - " + selectedMolecule.FileName;
if (primaryStructures.ContainsKey(selectedMolecule.ID))
{
PrimaryStructure primaryStructure = primaryStructures[selectedMolecule.ID];
initialiseResidueRenderSettings(primaryStructure);
showResidueNamesPanel(selectedMolecule.RenderSettings, primaryStructure);
}
}
else
{
selectedMoleculeText.text = "< no molecule selected >";
}
}
}
public void Initialise(PrimaryStructure structure)
{
primaryStructure = structure;
}
public void MoleculeLoaded(int id, string name, PrimaryStructure primaryStructure)
{
moleculeSettingsPanel.MoleculeLoaded(id, name, primaryStructure.Title, primaryStructure.AtomCount(), primaryStructure.ResidueCount());
elementsSettingsPanel.SetModelElements(id, primaryStructure.ElementNames);
residuesSettingsPanel.SetPrimaryStructure(id, primaryStructure);
}
public void Initialise(PrimaryStructure primaryStructure)
{
this.primaryStructure = primaryStructure;
//structureCache = new Dictionary<string, Mesh>();
initialised = true;
}
// Loads and renders a molecule using a structure file path and render settings
public IEnumerator LoadMoleculeStructure(int moleculeID, string filePath, MoleculeRenderSettings settings)
{
if (molecules.ContainsKey(moleculeID))
{
MoleculeEvents.RaiseShowMessage("Error Loading Molecule: already loaded", true);
MoleculeEvents.RaiseOnMoleculeLoadFailed(moleculeID);
yield break;
}
if (loadingStructure)
{
MoleculeEvents.RaiseShowMessage("Can't Load Molecule: another molecule currently loading", true);
MoleculeEvents.RaiseOnMoleculeLoadFailed(moleculeID);
yield break;
}
var watch = System.Diagnostics.Stopwatch.StartNew();
MoleculeEvents.RaiseShowMessage("Loading Structure File: " + filePath, false);
loadingStructure = true;
int oldAtomMeshQuality = generalSettings.MeshQuality;
Debug.Log("Loading structure");
PrimaryStructure primaryStructure = null;
string loadException = null;
Thread thread = new Thread(() => {
try {
if (filePath.EndsWith(".gro"))
{
primaryStructure = GROStructureParser.GetStructure(filePath);
}
else if (filePath.EndsWith(".xyz"))
{
primaryStructure = XYZStructureParser.GetStructure(filePath);
}
else if (filePath.EndsWith(".pdb"))
{
primaryStructure = PDBStructureParser.GetPrimaryStructure(filePath);
}
}
catch (FileParseException ex) {
loadException = ex.Message;
}
});
thread.Start();
while (thread.IsAlive)
{
yield return(null);
}
Debug.Log("Finished Loading structure");
if (loadException != null)
{
Debug.Log("Error Loading Structure File: " + loadException);
MoleculeEvents.RaiseShowMessage("Error Loading Structure File: " + loadException, true);
MoleculeEvents.RaiseOnMoleculeLoadFailed(moleculeID);
loadingStructure = false;
yield break;
}
watch.Stop();
MoleculeEvents.RaiseShowMessage("Structure File Load Complete [" + watch.ElapsedMilliseconds + "ms]", false);
yield return(null);
if (primaryStructure != null)
{
GameObject moleculeGO = GameObject.Instantiate(MoleculePrefab);
moleculeGO.transform.parent = this.transform;
moleculeGO.SetActive(true);
Molecule molecule = moleculeGO.GetComponent <Molecule>();
molecule.Initialise(moleculeID, primaryStructure, settings);
molecule.AutoRotateSpeed = generalSettings.AutoRotateSpeed;
molecule.SetInputSensitivity(generalSettings.MoleculeInputSensitivity);
molecule.SetSpaceNavigatorControlEnabled(generalSettings.SpaceNavigatorMoleculeControlEnabled);
molecules.Add(moleculeID, molecule);
// check to see if the meshQuality needs to change given the new primary structure
updateMeshQuality();
molecule.SetRenderSettings(settings);
yield return(StartCoroutine(molecule.Render(generalSettings.MeshQuality)));
MoleculeEvents.RaiseMoleculeLoaded(moleculeID, Path.GetFileName(filePath), primaryStructure);
}
if (oldAtomMeshQuality != generalSettings.MeshQuality)
{
reRenderMolecules();
}
SaveCurrentMoleculeTransformAsDefault(moleculeID);
loadingStructure = false;
}
// 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;
}
