private void openCustomResidueRenderSettings(int residueID)
{
List <Residue> residues = primaryStructure.GetResiduesByID(residueID);
if (residues.Count == 0)
{
return;
}
List <int> residueIDs = new List <int>()
{
residueID
};
List <string> atomNames = new List <string>();
foreach (Atom atom in residues[0].Atoms.Values)
{
atomNames.Add(atom.Name);
}
ResidueRenderSettings residueSettings = new ResidueRenderSettings();
if (moleculeRenderSettings.CustomResidueRenderSettings.ContainsKey(residueID))
{
residueSettings = moleculeRenderSettings.CustomResidueRenderSettings[residueID].Clone();
}
customSettingsPanel.Initialise(residueIDs, residueName, atomNames, ResidueUpdateType.ID, residueSettings, saveCustomResidueIDSettings, onCloseCustomResidueSettings);
//residueIDsPanel.gameObject.SetActive(false);
}
public bool Equals(ResidueRenderSettings other)
{
if (AtomSettings.Count != other.AtomSettings.Count)
{
return(false);
}
foreach (KeyValuePair <string, AtomRenderSettings> atom in AtomSettings)
{
if (other.AtomSettings.ContainsKey(atom.Key) && other.AtomSettings[atom.Key].Equals(atom.Value))
{
continue;
}
return(false);
}
if (other.ColourAtoms != ColourAtoms ||
other.AtomRepresentation != AtomRepresentation ||
!other.ColourBonds.Equals(ColourBonds) ||
other.LargeBonds != LargeBonds ||
other.ColourSecondaryStructure != ColourSecondaryStructure ||
other.ResidueColour != ResidueColour)
{
return(false);
}
return(true);
}
private void saveCustomResidueIDSettings(List <int> residueIDs, ResidueRenderSettings customResidueSettings, ResidueUpdateType updateType)
{
saveCustomResidueSettings(residueIDs, customResidueSettings, updateType);
residueIDsPanel.SetActive(false); // removes partial button updates on screen
renderResidueIDButtons();
residueIDsPanel.SetActive(true);
}
public void SaveRenderSettings()
{
savePanelToRenderSettings();
if (!renderSettings.Equals(savedRenderSettings) || residueUpdateType != ResidueUpdateType.ID)
{
savedRenderSettings = renderSettings.Clone();
saveSettingsCallback(residueIDs, renderSettings, residueUpdateType);
}
}
public void OnUpdateAllResiduesButton()
{
List <string> atomNames = new List <string>();
// atom names for each residue should be the same, but terminating residues can have a few extra atoms.
// the residue ID with the most amount of atoms will be the terminating residue
List <Residue> residues = primaryStructure.GetResiduesByName(residueName);
if (residues == null || residues.Count == 0)
{
return;
}
Residue residueMostAtoms = residues[0];
int firstResidueID = residues[0].ID;
bool residueSettingsAllTheSame = true;
foreach (Residue residue in residues)
{
if (residue.Atoms.Count > residueMostAtoms.Atoms.Count)
{
residueMostAtoms = residue;
break;
}
if (!moleculeRenderSettings.CustomResidueRenderSettings.ContainsKey(residue.ID) ||
!moleculeRenderSettings.CustomResidueRenderSettings[residue.ID].Equals(moleculeRenderSettings.CustomResidueRenderSettings[firstResidueID]))
{
residueSettingsAllTheSame = false;
break;
}
}
foreach (Atom atom in residueMostAtoms.Atoms.Values)
{
atomNames.Add(atom.Name);
}
ResidueRenderSettings panelResidueSettings = new ResidueRenderSettings();
if (residueSettingsAllTheSame)
{
if (moleculeRenderSettings.CustomResidueRenderSettings.ContainsKey(residueMostAtoms.ID))
{
panelResidueSettings = moleculeRenderSettings.CustomResidueRenderSettings[residueMostAtoms.ID].Clone();
}
}
customSettingsPanel.Initialise(residueIDs, residueName, atomNames, ResidueUpdateType.Name, panelResidueSettings, saveCustomResidueIDSettings, onCloseCustomResidueSettings);
}
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);
}
public void Initialise(List <int> residueIDs, string residueName, List <string> atomNames, ResidueUpdateType residueUpdateType, ResidueRenderSettings renderSettings, SaveCustomResidueSettingsDelegate saveSettings, CloseCustomResidueSettingsDelegate onClose)
{
this.residueIDs = residueIDs;
this.residueName = residueName;
this.atomNames = atomNames;
this.renderSettings = renderSettings;
this.residueUpdateType = residueUpdateType;
this.saveSettingsCallback = saveSettings;
this.onCloseCallback = onClose;
this.savedRenderSettings = renderSettings.Clone();
loadSettings();
customSettingsPanel.SetActive(true);
autoSaveSettingUpdates = true;
}
public ResidueRenderSettings Clone()
{
ResidueRenderSettings clone = new ResidueRenderSettings();
clone.ColourAtoms = ColourAtoms;
clone.AtomRepresentation = AtomRepresentation;
clone.ColourBonds = ColourBonds;
clone.LargeBonds = LargeBonds;
clone.ColourSecondaryStructure = ColourSecondaryStructure;
clone.ResidueColour = ResidueColour;
clone.AtomSettings = new Dictionary <string, AtomRenderSettings>();
foreach (KeyValuePair <string, AtomRenderSettings> atom in AtomSettings)
{
clone.AtomSettings.Add(atom.Key, atom.Value.Clone());
}
return(clone);
}
private void saveCustomResidueSettings(List <int> residueIDs, ResidueRenderSettings customResidueSettings, ResidueUpdateType updateType)
{
if (!customResidueSettings.IsDefault())
{
//Debug.Log("Saving residue settings - not default ");
foreach (int residueID in residueIDs)
{
if (moleculeRenderSettings.CustomResidueRenderSettings.ContainsKey(residueID))
{
moleculeRenderSettings.CustomResidueRenderSettings[residueID] = customResidueSettings;
}
else
{
moleculeRenderSettings.CustomResidueRenderSettings.Add(residueID, customResidueSettings);
}
}
}
else
{
//Debug.Log("Removing residue settings - are default");
foreach (int residueID in residueIDs)
{
if (moleculeRenderSettings.CustomResidueRenderSettings.ContainsKey(residueID))
{
moleculeRenderSettings.CustomResidueRenderSettings.Remove(residueID);
}
}
}
updateCustomResidueNameStatus(residueIDs);
//if (updateType == ResidueUpdateType.All) {
// renderResidueNameButtons();
//}
settingsUpdatedCallback();
}
private IEnumerator createModelBonds(MoleculeRenderSettings renderSettings, PrimaryStructureFrame frame, int meshQuality)
{
// set colour for bonds
Color32 bondColour;
if (!MolecularConstants.CPKColors.TryGetValue("Bond", out bondColour))
{
MolecularConstants.CPKColors.TryGetValue("Other", out bondColour);
}
List <Matrix4x4> standardTransforms = new List <Matrix4x4>();
Dictionary <Color, List <Matrix4x4> > highlightedTransforms = new Dictionary <Color, List <Matrix4x4> >();
float standardCylinderWidth = 0.015f * renderSettings.BondScale;
float enlargedCylinderWidth = 0.040f * renderSettings.BondScale;
// get atoms for bonds
Dictionary <int, Atom> atoms;
Dictionary <int, Atom> highLightedAtoms = new Dictionary <int, Atom>();
atoms = primaryStructure.GetAtoms(renderSettings.ShowStandardResidues, renderSettings.ShowNonStandardResidues, renderSettings.EnabledElements, renderSettings.EnabledResidueNames, renderSettings.EnabledResidueIDs);
if (renderSettings.CustomResidueRenderSettings != null)
{
HashSet <int> customResidueIDs = new HashSet <int>(renderSettings.CustomResidueRenderSettings.Keys.ToList());
highLightedAtoms = primaryStructure.GetAtoms(renderSettings.ShowStandardResidues, renderSettings.ShowNonStandardResidues, renderSettings.EnabledElements, renderSettings.EnabledResidueNames, customResidueIDs);
}
foreach (KeyValuePair <int, Bond> bond in bonds)
{
Vector3 atom1pos, atom2pos;
Atom atom1 = null;
Atom atom2 = null;
if (!atoms.TryGetValue(bond.Value.Atom1Index, out atom1) || !atoms.TryGetValue(bond.Value.Atom2Index, out atom2))
{
continue;
}
if (frame == null)
{
atom1pos = new Vector3(atom1.Position.x, atom1.Position.y, atom1.Position.z);
atom2pos = new Vector3(atom2.Position.x, atom2.Position.y, atom2.Position.z);
}
else
{
if (bond.Value.Atom1Index >= frame.AtomCount || bond.Value.Atom2Index >= frame.AtomCount)
{
// no need to send error message as this will have already been done in the atom render
yield break;
}
atom1pos = new Vector3(frame.Coords[bond.Value.Atom1Index * 3], frame.Coords[(bond.Value.Atom1Index * 3) + 1], frame.Coords[(bond.Value.Atom1Index * 3) + 2]);
atom2pos = new Vector3(frame.Coords[bond.Value.Atom2Index * 3], frame.Coords[(bond.Value.Atom2Index * 3) + 1], frame.Coords[(bond.Value.Atom2Index * 3) + 2]);
}
// flip coord system for Unity
atom1pos.z *= -1;
atom2pos.z *= -1;
// bonds aren't recalculated on each frame. In some frames atoms jump from one side of the simulation box to another. When this happens need to disable bond view
float bondLength = (atom2pos - atom1pos).magnitude / 2;
if (bondLength > BondLengths.MaximumLengthAllElements)
{
continue;
}
Vector3 position = ((atom1pos - atom2pos) / 2.0f) + atom2pos;
float length = (atom2pos - atom1pos).magnitude;
Quaternion rotation = Quaternion.FromToRotation(Vector3.up, atom1pos - atom2pos);
if (highLightedAtoms != null && highLightedAtoms.Count > 0 && highLightedAtoms.ContainsKey(atom1.Index) && highLightedAtoms.ContainsKey(atom2.Index))
{
int atom1residue = atom1.ResidueID;
int atom2residue = atom2.ResidueID;
// only colour or highlight bonds between atoms of the same residue
if (atom1residue == atom2residue && renderSettings.CustomResidueRenderSettings.ContainsKey(atom1residue) && renderSettings.CustomResidueRenderSettings[atom1residue].ColourBonds)
{
ResidueRenderSettings options = renderSettings.CustomResidueRenderSettings[atom1residue];
float cylinderWidth = standardCylinderWidth;
if (options.LargeBonds)
{
cylinderWidth = enlargedCylinderWidth;
}
Vector3 localScale = new Vector3(cylinderWidth, length, cylinderWidth);
Matrix4x4 bondTransform = Matrix4x4.TRS(position, rotation, localScale);
if (!highlightedTransforms.ContainsKey(options.ResidueColour))
{
highlightedTransforms.Add(options.ResidueColour, new List <Matrix4x4>());
}
highlightedTransforms[options.ResidueColour].Add(bondTransform);
}
else
{
float cylinderWidth = standardCylinderWidth;
if (atom1residue == atom2residue && renderSettings.CustomResidueRenderSettings.ContainsKey(atom1residue) && renderSettings.CustomResidueRenderSettings[atom1residue].LargeBonds)
{
cylinderWidth = enlargedCylinderWidth;
}
Vector3 localScale = new Vector3(cylinderWidth, length, cylinderWidth);
standardTransforms.Add(Matrix4x4.TRS(position, rotation, localScale));
}
}
else
{
Vector3 localScale = new Vector3(standardCylinderWidth, length, standardCylinderWidth);
standardTransforms.Add(Matrix4x4.TRS(position, rotation, localScale));
}
}
GameObject prefab = BondPrefabs[meshQuality];
GameObject parent = new GameObject("StandardCombinedMeshParent");
parent.SetActive(false);
yield return(StartCoroutine(meshBuilder.CombinedMesh(prefab, standardTransforms.ToArray(), bondColour, parent)));
parent.transform.SetParent(BondParent.transform, false);
parent = new GameObject("HighligtedCombinedMeshParent");
parent.SetActive(false);
foreach (KeyValuePair <Color, List <Matrix4x4> > item in highlightedTransforms)
{
yield return(StartCoroutine(meshBuilder.CombinedMesh(prefab, item.Value.ToArray(), item.Key, parent)));
}
parent.transform.SetParent(BondParent.transform, false);
}
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;
}
private Mesh BuildStructureMesh(MoleculeRenderSettings renderSettings, Chain chain, PrimaryStructureFrame frame, SecondaryStructure secondaryStructure)
{
Mesh structureMesh = null;
int interpolation = 20;
int resolution = 6; // should be in config
float radius = 0.015f;
List <DynamicMeshNode> nodes = new List <DynamicMeshNode>();
Vector3 lastPosition = Vector3.zero;
Vector3 lastNormal = Vector3.zero;
Vector3 averagedNormal = Vector3.zero;
SecondaryStructureType lastType = SecondaryStructureType.Coil;
for (int i = 0; i < chain.MainChainResidues.Count; i++)
{
DynamicMeshNode node = new DynamicMeshNode();
Residue residue = chain.MainChainResidues[i];
// check if residue mainchain information is complete. Ignore if not
if (residue.AlphaCarbon == null || residue.CarbonylCarbon == null || residue.CarbonylOxygen == null)
{
continue;
}
// set position
Atom atom = residue.AlphaCarbon;
// if no frame number use the base structure coordinates.
Vector3 position;
if (frame == null)
{
position = new Vector3(atom.Position.x, atom.Position.y, atom.Position.z);
}
else
{
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;
node.Position = position;
SecondaryStructureInfomation structureInformation = secondaryStructure.GetStructureInformation(residue.Index);
Residue nextResidue = null;
if (i + 1 < chain.MainChainResidues.Count)
{
nextResidue = chain.MainChainResidues[i + 1];
}
SecondaryStructureInfomation nextResidueStructureInfo = null;
if (nextResidue != null)
{
nextResidueStructureInfo = secondaryStructure.GetStructureInformation(nextResidue.Index);
}
// store the node type
if (structureInformation != null)
{
if (renderSettings.ShowHelices &&
(structureInformation.type == SecondaryStructureType.ThreeHelix ||
structureInformation.type == SecondaryStructureType.AlphaHelix ||
structureInformation.type == SecondaryStructureType.FiveHelix))
{
node.Type = DynamicMeshNodeType.SpiralRibbon;
}
else if (renderSettings.ShowSheets &&
structureInformation.type == SecondaryStructureType.BetaSheet)
{
if (nextResidue == null || (nextResidueStructureInfo != null && nextResidueStructureInfo.type != SecondaryStructureType.BetaSheet))
{
node.Type = DynamicMeshNodeType.RibbonHead;
}
else
{
node.Type = DynamicMeshNodeType.Ribbon;
}
}
else if (renderSettings.ShowTurns &&
structureInformation.type == SecondaryStructureType.Turn)
{
node.Type = DynamicMeshNodeType.LargeTube;
}
else
{
node.Type = DynamicMeshNodeType.Tube;
}
// calculate and store the node color
bool foundColour = false;
if (renderSettings.CustomResidueRenderSettings != null && renderSettings.CustomResidueRenderSettings.ContainsKey(residue.ID))
{
ResidueRenderSettings residueRenderSettings = renderSettings.CustomResidueRenderSettings[residue.ID];
if (residueRenderSettings != null && residueRenderSettings.ColourSecondaryStructure)
{
node.VertexColor = residueRenderSettings.ResidueColour;
foundColour = true;
}
}
if (foundColour == false)
{
switch (structureInformation.type)
{
case SecondaryStructureType.ThreeHelix:
node.VertexColor = Settings.ThreeHelixColour;
break;
case SecondaryStructureType.AlphaHelix:
node.VertexColor = Settings.AlphaHelixColour;
break;
case SecondaryStructureType.FiveHelix:
node.VertexColor = Settings.FiveHelixColour;
break;
case SecondaryStructureType.Turn:
node.VertexColor = Settings.TurnColour;
break;
case SecondaryStructureType.BetaSheet:
node.VertexColor = Settings.BetaSheetColour;
break;
case SecondaryStructureType.BetaBridge:
node.VertexColor = Settings.BetaBridgeColour;
break;
case SecondaryStructureType.Bend:
node.VertexColor = Settings.BendColour;
break;
case SecondaryStructureType.Coil:
node.VertexColor = Settings.CoilColour;
break;
default:
node.VertexColor = ErrorColor;
break;
}
}
}
else
{
Debug.Log("*** Structure info null: assigning defaults");
node.Type = DynamicMeshNodeType.Tube;
node.VertexColor = ErrorColor;
}
// determine the node rotation
// calculate the normal from the peptide plane and store as the node rotation
Vector3 vertexA = residue.AlphaCarbon.Position;
Vector3 vertexB = residue.CarbonylCarbon.Position;
Vector3 vertexC = residue.CarbonylOxygen.Position;
// flip coord system for Unity
vertexA.z *= -1;
vertexB.z *= -1;
vertexC.z *= -1;
//// create a triangle to show the peptide plane on the model for debugging purposes
//GameObject residuePlane = createTriangle(vertexA, vertexB, vertexC);
//residuePlane.name = "ResiduePlane";
//AddMeshToModel(residuePlane, StructureParent);
Vector3 direction = Vector3.Cross(vertexB - vertexA, vertexC - vertexA);
Vector3 normal = Vector3.Normalize(direction);
if (structureInformation != null && structureInformation.type == SecondaryStructureType.BetaSheet || lastType == SecondaryStructureType.BetaSheet)
{
if (Vector3.Dot(normal, lastNormal) < 0)
{
normal *= -1;
}
if (lastType != SecondaryStructureType.BetaSheet)
{
averagedNormal = normal;
}
else
{
averagedNormal += normal;
averagedNormal.Normalize();
normal = averagedNormal;
}
}
node.Rotation = normal;
lastNormal = normal;
if (structureInformation != null)
{
lastType = structureInformation.type;
}
else
{
lastType = SecondaryStructureType.Coil;
}
nodes.Add(node);
}
if (renderSettings.SmoothNodes)
{
nodes = smoothMeshNodes(nodes);
}
//// draw debug line from node points along rotation vector
//for (int q = 0; q < nodePositions.Count; q++) {
// Vector3 fromPosition = nodePositions[q];
// Vector3 toPosition = fromPosition + nodeRotations[q] * 0.3f;
// GameObject line = createLine(fromPosition, toPosition, Color.white, Color.red);
// AddMeshToModel(line, StructureParent);
//}
List <Vector3> nodePositions = new List <Vector3>();
foreach (DynamicMeshNode node in nodes)
{
nodePositions.Add(node.Position);
}
List <DynamicMeshNode> splineNodes = new List <DynamicMeshNode>();
IEnumerable splinePoints = Interpolate.NewCatmullRom(nodePositions.ToArray(), interpolation, false);
int j = 0;
foreach (Vector3 position in splinePoints)
{
int nodeIndex = j / (interpolation + 1);
int splinePointsSinceLastNode = j % (interpolation + 1);
DynamicMeshNode node = new DynamicMeshNode();
node.Position = position;
//int colorIndex = nodeIndex % DebugColors.Count;
//node.VertexColor = DebugColors[colorIndex];
node.VertexColor = nodes[nodeIndex].VertexColor;
node.Type = nodes[nodeIndex].Type;
// set the mesh rotations for the node
// dont do rotations on tube structures
switch (node.Type)
{
case DynamicMeshNodeType.Ribbon:
case DynamicMeshNodeType.RibbonHead:
case DynamicMeshNodeType.SpiralRibbon:
if (nodeIndex < nodes.Count - 1)
{
float percentThroughNode = (float)splinePointsSinceLastNode / ((float)interpolation + 1f);
node.Rotation = Vector3.Lerp((Vector3)nodes[nodeIndex].Rotation, (Vector3)nodes[nodeIndex + 1].Rotation, percentThroughNode);
}
else // last node
{
node.Rotation = (Vector3)nodes[nodeIndex].Rotation;
}
break;
}
splineNodes.Add(node);
j++;
}
DynamicMesh dynamicMesh = new DynamicMesh(splineNodes, radius, resolution, interpolation + 1);
structureMesh = dynamicMesh.Build(Settings.DebugFlag);
return(structureMesh);
}
private void openUpdateAllResiduesPanel(List <int> residueIDs)
{
if (residueIDs == null || residueIDs.Count == 0)
{
return;
}
List <Residue> residues = primaryStructure.GetResiduesByID(residueIDs);
if (residues == null || residues.Count == 0)
{
return;
}
Residue selectedResidue = residues[0];
bool atomNamesAllTheSame = true;
HashSet <string> selectedResidueAtomNames = new HashSet <string>();
foreach (Atom atom in selectedResidue.Atoms.Values)
{
selectedResidueAtomNames.Add(atom.Name);
}
foreach (Residue residue in residues)
{
HashSet <string> residueAtomNames = new HashSet <string>();
foreach (Atom atom in residue.Atoms.Values)
{
residueAtomNames.Add(atom.Name);
}
if (!residueAtomNames.SetEquals(selectedResidueAtomNames))
{
atomNamesAllTheSame = false;
}
}
List <string> atomNames = null;
if (atomNamesAllTheSame)
{
atomNames = new List <string>();
foreach (Atom atom in selectedResidue.Atoms.Values)
{
atomNames.Add(atom.Name);
}
}
bool residueSettingsAllTheSame = true;
foreach (Residue residue in residues)
{
if (!moleculeRenderSettings.CustomResidueRenderSettings.ContainsKey(residue.ID) ||
!moleculeRenderSettings.CustomResidueRenderSettings[residue.ID].Equals(moleculeRenderSettings.CustomResidueRenderSettings[selectedResidue.ID]))
{
residueSettingsAllTheSame = false;
break;
}
}
ResidueRenderSettings panelResidueSettings = new ResidueRenderSettings();
if (residueSettingsAllTheSame)
{
if (moleculeRenderSettings.CustomResidueRenderSettings.ContainsKey(selectedResidue.ID))
{
panelResidueSettings = moleculeRenderSettings.CustomResidueRenderSettings[selectedResidue.ID].Clone();
}
}
customSettingsPanel.Initialise(residueIDs, null, atomNames, ResidueUpdateType.All, panelResidueSettings, saveCustomResidueSettings, onCloseCustomResidueSettings);
}