public void Initialise(AtomRenderSettings settings, ResidueCustomColourSelect colourSelectPanel, AtomButtonClickDelegate onClick)
{
this.AtomSettings = settings;
this.colourSelectPanel = colourSelectPanel;
this.onClick = onClick;
updateAtomSettingsDisplay();
}
public AtomRenderSettings Clone()
{
AtomRenderSettings clone = new AtomRenderSettings(AtomName, defaultColour);
clone.Representation = Representation;
clone.CustomColour = CustomColour;
clone.AtomColour = AtomColour;
return(clone);
}
public bool Equals(AtomRenderSettings other)
{
if (other.AtomName == AtomName &&
other.Representation == Representation &&
other.CustomColour == CustomColour &&
other.AtomColour.Equals(AtomColour))
{
return(true);
}
return(false);
}
private float getAtomRadius(Atom atom)
{
MolecularRepresentation?customRepresentation = null;
if (renderSettings.CustomResidueRenderSettings != null && renderSettings.CustomResidueRenderSettings.ContainsKey(atom.ResidueID))
{
ResidueRenderSettings residueSettings = renderSettings.CustomResidueRenderSettings[atom.ResidueID];
if (residueSettings != null)
{
// use the atom specific settings if available.
if (residueSettings.AtomSettings.ContainsKey(atom.Name))
{
AtomRenderSettings atomSettings = residueSettings.AtomSettings[atom.Name];
if (atomSettings.Representation != MolecularRepresentation.None)
{
customRepresentation = atomSettings.Representation;
}
}
// if we didn't get from atom specific settings then try residue settings
if (customRepresentation == null)
{
if (residueSettings.AtomRepresentation != MolecularRepresentation.None)
{
customRepresentation = residueSettings.AtomRepresentation;
}
}
}
}
float atomRadius;
if (!renderSettings.ShowAtoms)
{
atomRadius = 0.001f;
}
else if (customRepresentation != null && customRepresentation != MolecularRepresentation.None)
{
atomRadius = (MolecularRepresentation)customRepresentation == MolecularRepresentation.VDW ? atom.VDWRadius : atom.AtomicRadius / 2f;
atomRadius *= renderSettings.AtomScale;
}
else
{
atomRadius = renderSettings.Representation == MolecularRepresentation.VDW ? atom.VDWRadius : atom.AtomicRadius / 2f;
atomRadius *= renderSettings.AtomScale;
}
return(atomRadius);
}
private IEnumerator createModelAtomsByElement(MoleculeRenderSettings renderSettings, PrimaryStructureFrame frame, int meshQuality)
{
Quaternion atomOrientation = Quaternion.Euler(45, 45, 45);
// generate combined meshes (i.e single GameObject) for atoms with same element/colour
Dictionary <Color, List <Matrix4x4> > mergeTransforms = new Dictionary <Color, List <Matrix4x4> >();
Dictionary <int, Atom> atoms = primaryStructure.GetAtoms(renderSettings.ShowStandardResidues, renderSettings.ShowNonStandardResidues, renderSettings.EnabledElements, renderSettings.EnabledResidueNames, renderSettings.EnabledResidueIDs);
foreach (KeyValuePair <int, Atom> item in atoms)
{
Atom atom = item.Value;
Vector3 position;
// if no frame use the base structure coordinates.
if (frame == null)
{
position = new Vector3(atom.Position.x, atom.Position.y, atom.Position.z);
}
else
{
if (atom.Index >= frame.AtomCount)
{
MoleculeEvents.RaiseShowMessage("Atoms not found in frame record. Aborting frame render.", true);
yield break;
}
position = new Vector3(frame.Coords[atom.Index * 3], frame.Coords[(atom.Index * 3) + 1], frame.Coords[(atom.Index * 3) + 2]);
}
// flip coord system for Unity
position.z *= -1;
Color32?customColour = null;
MolecularRepresentation?customRepresentation = null;
if (renderSettings.CustomResidueRenderSettings != null && renderSettings.CustomResidueRenderSettings.ContainsKey(atom.ResidueID))
{
ResidueRenderSettings residueSettings = renderSettings.CustomResidueRenderSettings[atom.ResidueID];
if (residueSettings != null)
{
// use the atom specific settings if available.
if (residueSettings.AtomSettings.ContainsKey(atom.Name))
{
AtomRenderSettings atomSettings = residueSettings.AtomSettings[atom.Name];
if (atomSettings.CustomColour)
{
customColour = atomSettings.AtomColour;
}
if (atomSettings.Representation != MolecularRepresentation.None)
{
customRepresentation = atomSettings.Representation;
}
}
// if we didn't get from atom specific settings then get from residue settings
if (customColour == null && residueSettings.ColourAtoms)
{
customColour = residueSettings.ResidueColour;
}
if (customRepresentation == null)
{
if (residueSettings.AtomRepresentation != MolecularRepresentation.None)
{
customRepresentation = residueSettings.AtomRepresentation;
}
}
}
}
Color32 atomColour = Color.white;
if (customColour != null)
{
atomColour = (Color)customColour;
}
else
{
if (!MolecularConstants.CPKColors.TryGetValue(atom.Element.ToString(), out atomColour))
{
MolecularConstants.CPKColors.TryGetValue("Other", out atomColour);
}
}
float atomDiameter = getAtomRadius(atom, renderSettings, customRepresentation) * 2;
Vector3 scale = new Vector3(atomDiameter, atomDiameter, atomDiameter);
Matrix4x4 atomTransform = Matrix4x4.TRS(position, atomOrientation, scale);
if (!mergeTransforms.ContainsKey(atomColour))
{
mergeTransforms.Add(atomColour, new List <Matrix4x4>());
}
mergeTransforms[atomColour].Add(atomTransform);
}
// create the meshes by colour
GameObject prefab = AtomPrefabs[meshQuality];
GameObject parent = new GameObject("CombinedMeshParent");
parent.SetActive(false);
foreach (KeyValuePair <Color, List <Matrix4x4> > item in mergeTransforms)
{
yield return(StartCoroutine(meshBuilder.CombinedMesh(prefab, item.Value.ToArray(), item.Key, parent)));
}
parent.transform.SetParent(AtomParent.transform, false);
yield break;
}
public void loadSettings()
{
if (residueUpdateType == ResidueUpdateType.ID)
{
if (residueIDs != null && residueIDs.Count > 0)
{
panelTitle.text = "Residue " + residueIDs[0] + " - Custom Settings";
}
else
{
panelTitle.text = "Residue - Custom Settings";
}
}
else if (residueUpdateType == ResidueUpdateType.Name)
{
panelTitle.text = "Residue " + residueName + " - Custom Settings";
}
else
{
panelTitle.text = "Custom Residue Settings";
}
colourAtomsToggle.isOn = renderSettings.ColourAtoms;
cpkToggle.isOn = false;
vdwToggle.isOn = false;
if (renderSettings.AtomRepresentation == MolecularRepresentation.CPK)
{
cpkToggle.isOn = true;
}
else if (renderSettings.AtomRepresentation == MolecularRepresentation.VDW)
{
vdwToggle.isOn = true;
}
colourBondsToggle.isOn = renderSettings.ColourBonds;
largeBondsToggle.isOn = renderSettings.LargeBonds;
colourSecondaryStructureToggle.isOn = renderSettings.ColourSecondaryStructure;
setResidueColourButtonColour(renderSettings.ResidueColour);
// create atom option buttons
atomButtons = new Dictionary <string, ResidueAtomNameButton>();
UnityCleanup.DestroyGameObjects(atomListContentPanel);
if (atomNames != null)
{
foreach (string atomName in atomNames)
{
GameObject atomOptionsButton = GameObject.Instantiate(atomNameButtonPrefab);
atomOptionsButton.transform.SetParent(atomListContentPanel.transform, false);
ResidueAtomNameButton buttonScript = atomOptionsButton.GetComponent <ResidueAtomNameButton>();
AtomRenderSettings atomSettingsCopy = new AtomRenderSettings(atomName, Settings.ResidueColourDefault);
if (renderSettings.AtomSettings.ContainsKey(atomName))
{
atomSettingsCopy = renderSettings.AtomSettings[atomName].Clone();
}
buttonScript.Initialise(atomSettingsCopy, colourSelectPanel, AutoSaveSettings);
if (!atomButtons.ContainsKey(atomName))
{
atomButtons.Add(atomName, buttonScript);
}
else
{
Debug.Log("Duplicate atom name in custom residue settings");
}
}
}
}
