private IEnumerator createMainChains(PrimaryStructureFrame frame)
{
int interpolation = 5;
int resolution = 5; // should be in config
float radius = 0.015f;
int currentIndex = 0;
foreach (Chain chain in primaryStructure.Chains())
{
if (chain.ResidueType != StandardResidue.AminoAcid)
{
// UnityEngine.Debug.Log("Skipping main chain build. Non protein main chain not currently supported.");
continue;
}
List <Vector3> nodePositions = new List <Vector3>();
foreach (Atom atom in chain.MainChainAtoms)
{
// if no frame number use the base structure coordinates.
Vector3 position;
if (frame == null)
{
if (atom == null)
{
UnityEngine.Debug.Log("Main chain atom is 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;
nodePositions.Add(position);
}
List <DynamicMeshNode> nodes = new List <DynamicMeshNode>();
IEnumerable splinePoints = Interpolate.NewCatmullRom(nodePositions.ToArray(), interpolation, false);
Color32 chainColour = ChainColors[currentIndex % ChainColors.Length];
foreach (Vector3 position in splinePoints)
{
DynamicMeshNode node = new DynamicMeshNode();
node.Position = position;
node.VertexColor = chainColour;
nodes.Add(node);
}
DynamicMesh mesh = new DynamicMesh(nodes, radius, resolution, interpolation + 1);
Mesh chainMesh = mesh.Build(Settings.DebugFlag);
GameObject chainStructure = (GameObject)Instantiate(ChainPrefab);
chainStructure.GetComponent <MeshFilter>().sharedMesh = chainMesh;
chainStructure.SetActive(false);
chainStructure.transform.SetParent(ChainParent.transform, false);
currentIndex++;
yield return(null);
}
}
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);
}