public override IEnumerable <Selection> Select(IStructure structure)
{
List <Selection> results = new List <Selection>();
for (int chainIndex = 0; chainIndex < structure.Count; chainIndex++)
{
if (chainIndex == ChainIndex)
{
continue;
}
IChain chain = structure[chainIndex];
List <SSBlock> chainSelections = SecondaryStructure.GetPhiPsiSSBlocks(chain, MinLength);
if (IncludeAdjacentLoops)
{
// Extend the SSBlock ranges to include everything up to the neighboring blocks
List <SSBlock> extendedChainSelections = new List <SSBlock>();
for (int selectionIndex = 0; selectionIndex < chainSelections.Count; selectionIndex++)
{
int start = selectionIndex == 0 ? 0 : chainSelections[selectionIndex - 1].End + 1;
int end = selectionIndex == chainSelections.Count - 1 ? chain.Count - 1 : chainSelections[selectionIndex + 1].Start - 1;
extendedChainSelections.Add(new SSBlock(chainSelections[selectionIndex].SS, start, end));
}
chainSelections = extendedChainSelections;
}
if (SkipCountC != null && SkipCountC > 0)
{
int firstSkipIndex = Math.Max(0, chainSelections.Count - (int)SkipCountC);
chainSelections.RemoveRange(firstSkipIndex, chainSelections.Count - firstSkipIndex);
}
if (SkipCountN != null && SkipCountN > 0)
{
int skipCount = Math.Min((int)SkipCountN, chainSelections.Count);
chainSelections.RemoveRange(0, skipCount);
}
// Convert the computed SS block ranges to an AA selection and add that to list
results.AddRange(chainSelections.Select(block => new Selection(chain[block.Start, block.End])));
}
return(results);
}
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 ParseFile()
{
topY = -99999; bottomY = 99999; leftX = 99999; rightX = -99999; frontZ = 99999; backZ = -99999;
startTime = Time.realtimeSinceStartup;
ConsoleText.text += string.Format(" Reading in DSSP file...");
DSSPfile = GetComponent <HttpTest>().outputfile;
string pattern = @"([0-9]+)\s+(\S+)\s+([A-Z]+)\s+([A-Z]+)..(.)...........(....)(...)(...)(............)(...........)(...........)(...........)(........)(......)(......)(......)(......)\s+(\S+)\s+(\S+)\s+(\S+..)";
string getnumAA = @"([0-9]+)\s+[0-9]+\s+[0-9]+\s+[0-9]+\s+[0-9]+\s+TOTAL NUMBER OF RESIDUES";
string newmolpattern = @"!* 0 0 0 0, 0.0 0, 0.0 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 360.0 0.0 0.0 0.0";
string header = @"# RESIDUE AA STRUCTURE BP1 BP2 ACC N-H-->O O-->H-N N-H-->O O-->H-N TCO KAPPA ALPHA PHI PSI X-CA Y-CA Z-CA CHAIN AUTHCHAIN";
// get total num of amino acids in the protein complex
Regex getnumAAr = new Regex(getnumAA);
int numaa = Convert.ToInt32(getnumAAr.Match(DSSPfile).Groups[1].ToString());
ConsoleText.text += string.Format("\n Total number of amino acids: {0}", numaa);
if (Regex.Split(Regex.Split(DSSPfile, header)[1], newmolpattern) == null)
{
ConsoleText.text += string.Format("\n string[] molecules is null.");
}
string[] molecules = Regex.Split(Regex.Split(DSSPfile, header)[1], newmolpattern);
int totmolnum = molecules.Length; // index of molecule. total num of molecules in a protein complex
List <SecondaryStructure[]> MoleculesSecondaryAssignments = new List <SecondaryStructure[]>(); // We want to make lists of the above vectors per molecule
List <Vector3[]> MoleculesCAPoints = new List <Vector3[]>();
foreach (string molecule in molecules)
{
int te = 0; // temp
SecondaryStructure[] structure = new SecondaryStructure[Regex.Matches(molecule, pattern).Count];
Vector3[] points = new Vector3[Regex.Matches(molecule, pattern).Count];
if (Regex.Matches(molecule, pattern) == null)
{
ConsoleText.text += string.Format("\n Error reading DSSP file. Regex pattern returned no matches. Matches is null.");
}
foreach (Match matches in Regex.Matches(molecule, pattern))
{
structure[te].structure = matches.Groups[5].ToString();
points[te] = new Vector3(float.Parse(matches.Groups[18].ToString()),
float.Parse(matches.Groups[19].ToString()),
float.Parse(matches.Groups[20].ToString()));
te++;
}
MoleculesSecondaryAssignments.Add(structure);
MoleculesCAPoints.Add(points);
}
GameObject ThisFile = new GameObject();
ThisFile.name = string.Format("File {0}", GetComponent <Load>().FileNumber);
ThisFile.transform.parent = GameObject.Find("MoleculeCollection").transform;
ThisFile.transform.localPosition = Vector3.zero;
ThisFile.transform.localScale = Vector3.one;
GameObject RibbonCollection = new GameObject();
RibbonCollection.name = "RibbonCollection";
RibbonCollection.transform.parent = ThisFile.transform;
RibbonCollection.transform.localPosition = Vector3.zero;
RibbonCollection.transform.localScale = Vector3.one;
// TODO : Put this in script Ribbon.cs as "DrawRibbon(Vector3 points)"
GameObject ThisPDB = new GameObject();
ThisPDB.name = string.Format("PDB{0}", GetComponent <Load>().FileNumber);
ThisPDB.transform.parent = RibbonCollection.transform;
ThisPDB.transform.localScale = new Vector3(0.3f, 0.3f, 0.3f);
//ThisPDB.transform.localPosition = new Vector3(0.75f, 0, 0) * (numPDB - 1);
GameObject MoleculeHolder = new GameObject();
MoleculeHolder.transform.parent = ThisPDB.transform;
MeshFilter[] meshFilters = new MeshFilter[totmolnum];
ConsoleText.text += string.Format("\n Total number of molecules: {0}.", totmolnum);
Vector3 offset = new Vector3(0, 0f, 0f);
GameObject parent = GameObject.Find("Hologram Collection"); // TODO: Remove find
for (int tem = 0; tem < totmolnum; tem++)
{
// Make a new vector that has more points in it so it is smoother
// The higher the second number, the more points and thus smoother lines. Changes smoothness exponentially relative to number of amino acids.
Vector3[] newPoints = LineSmoother.SmoothLine(MoleculesCAPoints[tem], 0.8f * (float)Math.Exp(-10f / (float)numaa));
if (newPoints == null)
{
ConsoleText.text += string.Format("\n Error initializing smoothing array. NewPoints is null.");
}
// Second argument adjusts the smoothness. Smaller = smoother
// TODO: Second argument can be adjusted for changing quality using slider
// TODO: These three parameters can be adjustable with sliders
float lineWidth = 0.006f;
float rescale = 100f;
int numofsides = 12;
int[] triangles = new int[6 * numofsides * newPoints.Length];
Vector3[] quad = new Vector3[newPoints.Length * numofsides];
Color[] colors = new Color[quad.Length];
float a = lineWidth;
float b = lineWidth / 2.5f;
ConsoleText.text += string.Format("\n Initialized arrays and variables for molecule {0}...", tem);
//foreach (Vector3 point in newPoints)
foreach (Vector3 point in newPoints)
{
tiltFactor = 30;
int i = Array.IndexOf(newPoints, point);
int totnumofsides = i * numofsides;
int totnumofvertices = totnumofsides * 6;
int div = Convert.ToInt32(Math.Floor(i / ((float)newPoints.Length / (float)MoleculesCAPoints[tem].Length)));
// Adds color based on secondary structure assignment
for (int z = 0; z < numofsides; z++)
{
colors[totnumofsides + z] = Colors(MoleculesSecondaryAssignments[tem][div].structure);
}
}
Parallel.ForEach(newPoints, point =>
{
tiltFactor = 30;
int i = Array.IndexOf(newPoints, point);
int totnumofsides = i * numofsides;
int totnumofvertices = totnumofsides * 6;
int div = Convert.ToInt32(Math.Floor(i / ((float)newPoints.Length / (float)MoleculesCAPoints[tem].Length)));
// for padding on the z axis:
if (totnumofsides < (newPoints.Length - 2) * 6 && Mathf.Abs(point.z - newPoints[i + 1].z) > Mathf.Abs(point.x - newPoints[i + 1].x) && Mathf.Abs(point.z - newPoints[i + 1].z) > Mathf.Abs(point.y - newPoints[i + 1].y))
{
tiltFactor = 45;
}
// Makes an oval
// TODO: Find a way to fix thinness of certain axes (the padding on z axis method right above doesn't entirely work)
for (int side = 0; side < numofsides; side++)
{
float angle = (side * (360f / numofsides)) * Mathf.Deg2Rad;
float x = ((float)a * b) / (float)Mathf.Sqrt(((float)Math.Pow(b, 2) + ((float)Math.Pow(a, 2) * (float)Math.Pow(Mathf.Tan(angle), 2))));
float y = ((float)a * b) / (float)Mathf.Sqrt((float)Mathf.Pow(a, 2) + ((float)Mathf.Pow(b, 2) / (float)Mathf.Pow(Mathf.Tan(angle), 2)));
if (side * (360f / numofsides) > 90 && side * (360f / numofsides) < 270)
{
x = -1 * x;
}
if (side * (360f / numofsides) > 180 && side * (360f / numofsides) < 360)
{
y = -1 * y;
}
// Determine the max/min vertices for resizing and positioning later
if ((point / rescale).y + y > topY)
{
topY = (point / rescale).y + y;
}
if ((point / rescale).y + y < bottomY)
{
bottomY = (point / rescale).y + y;
}
if ((point / rescale).x + x > rightX)
{
rightX = (point / rescale).x + x;
}
if ((point / rescale).x + x < leftX)
{
leftX = (point / rescale).x + x;
}
if ((point / rescale).z > backZ)
{
backZ = (point / rescale).z;
}
if ((point / rescale).z < frontZ)
{
frontZ = (point / rescale).z;
}
quad[totnumofsides + side] = (point / rescale) + offset + new Vector3(x, y, 0);
}
// Creates an array for the triangles
if (i < (newPoints.Length - 1))
{
for (int p = 0; p < totnumofsides; p++)
{
triangles[(p * 6) + 0] = p + 0;
triangles[(p * 6) + 1] = p + numofsides;
triangles[(p * 6) + 2] = p + 1;
triangles[(p * 6) + 3] = p + 1;
triangles[(p * 6) + 4] = p + numofsides;
triangles[(p * 6) + 5] = p + numofsides + 1;
}
}
}
);
// Draw the molecule
GameObject Protein = new GameObject();
Protein.transform.parent = MoleculeHolder.transform; // remove find
Protein.name = string.Format("PDB.{0}.molecule.{1}", GetComponent <Load>().FileNumber, tem);
// some sanity checks
if (GameObject.Find(string.Format("PDB.{0}.molecule.{1}", GetComponent <Load>().FileNumber, tem)) == null)
{
ConsoleText.text += string.Format("\n Molecule {0} GameObject does not exist.", tem);
}
if (quad == null)
{
ConsoleText.text += string.Format("\nQuad is null");
}
if (triangles == null)
{
ConsoleText.text += string.Format("\n Triangles is null.");
}
Protein.AddComponent <MeshFilter>();
Protein.AddComponent <MeshRenderer>();
//Protein.GetComponent<MeshRenderer>().material = new Material(Shader.Find("VertexColorLightmaps"));
Protein.GetComponent <MeshFilter>().mesh.vertices = quad;
Protein.GetComponent <MeshFilter>().mesh.triangles = triangles;
Protein.GetComponent <MeshFilter>().mesh.colors = colors;
Protein.GetComponent <MeshRenderer>().material = new Material(Shader.Find("Custom/SpecularHighlight"));
Protein.GetComponent <MeshFilter>().mesh.RecalculateNormals();
//meshFilters[tem] = Protein.GetComponent<MeshFilter>();
}
/*
* ThisPDB.AddComponent<MeshCollider>();
* ThisPDB.AddComponent<MeshFilter>();
* CombineInstance[] combine = new CombineInstance[meshFilters.Length];
* int inde = 0;
* while (inde < meshFilters.Length)
* {
* combine[inde].mesh = meshFilters[inde].sharedMesh;
* combine[inde].transform = meshFilters[inde].transform.localToWorldMatrix;
* //meshFilters[inde].gameObject.SetActive(false);
* inde++;
* }
* ThisPDB.transform.GetComponent<MeshFilter>().mesh = new Mesh();
* ThisPDB.transform.GetComponent<MeshFilter>().mesh.CombineMeshes(combine);
* ThisPDB.transform.gameObject.SetActive(true);
* ThisPDB.transform.GetComponent<MeshCollider>().sharedMesh = ThisPDB.transform.GetComponent<MeshFilter>().mesh;
* ThisPDB.AddComponent<MeshRenderer>().material = new Material(Shader.Find("Custom/SpecularHighlight"));
*/
MoleculeHolder.transform.localPosition -= new Vector3((rightX + leftX) / 2f, (topY + bottomY) / 2f, (backZ + frontZ) / 2f);
ThisPDB.transform.localPosition = Vector3.zero;
//ThisPDB.AddComponent<BoxCollider>().size = new Vector3(0.5f, 0.5f, 0.5f);
//ThisPDB.AddComponent<MeshRenderer>().material = GameObject.Find("MoleculeCollection").GetComponent<MeshRenderer>().material;
if (Math.Abs(topY - bottomY) >= Math.Abs(rightX - leftX))
{
if (Math.Abs(backZ - frontZ) >= Math.Abs(topY - bottomY))
{
MoleculeHolder.transform.localScale /= Math.Abs(backZ - frontZ) / .3f; // instead of .48f make this localscale of moelculecolelctin
}
else
{
MoleculeHolder.transform.localScale /= Math.Abs(topY - bottomY) / .3f;
}
}
else
{
MoleculeHolder.transform.localScale /= Math.Abs(rightX - leftX) / .3f;
}
// change back to interpolated strings
ConsoleText.text += string.Format("\n Cartoon structure drawn for PDB #{0}.", GetComponent <Load>().FileNumber);
finishTime = Time.realtimeSinceStartup;
ConsoleText.text += string.Format("\n Time taken to draw: {0} seconds.\n", (finishTime - startTime));
Debug.Log($"Time to draw protein: {finishTime - startTime}");
//ThisPDB.AddComponent<BoxCollider>().size = new Vector3(0.48f / ThisPDB.transform.localScale.x, 0.48f / ThisPDB.transform.localScale.x, 0.48f / ThisPDB.transform.localScale.x);
//GameObject.Find("RibbonCollection").GetComponent<BoxCollider>().enabled = true;
//MoleculeHolder.transform.localScale = new Vector3(3, 3, 3);
RibbonCollection.AddComponent <BoundingBoxRig>().ScaleHandleMaterial = BoundingBoxHandle;
RibbonCollection.GetComponent <BoundingBoxRig>().RotateHandleMaterial = BoundingBoxHandle;
RibbonCollection.GetComponent <BoundingBoxRig>().InteractingMaterial = BoundingBoxHandleGrabbed;
RibbonCollection.GetComponent <BoundingBoxRig>().BoundingBoxPrefab = BoundingBoxBasic;
RibbonCollection.GetComponent <BoundingBoxRig>().appBarPrefab = AppBar;
RibbonCollection.AddComponent <MixedRealityToolkit.InputModule.Utilities.Interations.TwoHandManipulatable>().BoundingBoxPrefab = BoundingBoxBasic;
RibbonCollection.GetComponent <MixedRealityToolkit.InputModule.Utilities.Interations.TwoHandManipulatable>().SetManipulationMode(MixedRealityToolkit.InputModule.Utilities.Interations.TwoHandManipulatable.TwoHandedManipulation.MoveRotateScale);
ThisPDB.AddComponent <MeshFilter>().mesh = GameObject.Find("MoleculeCollection").GetComponent <MeshFilter>().mesh;
ThisPDB.AddComponent <MeshCollider>().sharedMesh = ThisPDB.GetComponent <MeshFilter>().mesh;
ThisPDB.AddComponent <MeshRenderer>().material = GameObject.Find("MoleculeCollection").GetComponent <MeshRenderer>().material;
ThisPDB.GetComponent <MeshRenderer>().enabled = false;
GetComponent <Load>().FileNumber++;
}
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;
}
private IEnumerator createSecondaryStructure(MoleculeRenderSettings settings, PrimaryStructureFrame frame, SecondaryStructure secondaryStructure)
{
for (int i = 0; i < primaryStructure.Chains().Count; i++)
{
Chain chain = primaryStructure.Chains()[i];
if (chain.ResidueType != StandardResidue.AminoAcid)
{
// UnityEngine.Debug.Log("Skipping secondary strucure. Non protein structures not currently supported.");
continue;
}
if (chain.MainChainResidues.Count < 2)
{
// UnityEngine.Debug.Log("Skipping secondary strucure. Protein structure doesn't have enough residues for mesh.");
continue;
}
Mesh structureMesh = BuildStructureMesh(settings, chain, frame, secondaryStructure);
GameObject structure = (GameObject)Instantiate(SecondaryStructurePrefab);
structure.GetComponent <MeshFilter>().sharedMesh = structureMesh;
structure.SetActive(false);
structure.transform.SetParent(StructureParent.transform, false);
yield return(null);
}
}
// RenderStructure and ShowStructure are separate to allow the primary and secondary structures to be prerendered and then
// both turned on at the same time. Without this, the show of the structures is staggered and shows some level of flickering
public IEnumerator RenderStructure(MoleculeRenderSettings settings, PrimaryStructureFrame frame, SecondaryStructure secondaryStructure)
{
if (!initialised)
{
yield break;
}
System.Diagnostics.Stopwatch watch = new System.Diagnostics.Stopwatch();
watch.Start();
yield return(null);
storeExistingStructure();
// create mesh
if (secondaryStructure != null && settings.ShowSecondaryStructure)
{
yield return(StartCoroutine(createSecondaryStructure(settings, frame, secondaryStructure)));
}
watch.Stop();
}
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);
}
// Parses sheet secondary structure object specified by the pdb-file line
void ParseSheet(string pdbLine)
{
Chain chain;
char chainId = pdbLine[21];
if (!chains.TryGetValue(chainId, out chain)) chains[chainId] = chain = new Chain() { Name = chainId.ToString() };
SecondaryStructure sheet = new SecondaryStructure();
sheet.StructureType = SecondaryStructureType.Sheet;
sheet.FirstResidueSequenceNumber = int.Parse(pdbLine.Substring(22, 4), CultureInfo.InvariantCulture);
sheet.LastResidueSequenceNumber = int.Parse(pdbLine.Substring(33, 4), CultureInfo.InvariantCulture);
chain.SecondaryStructures.Add(sheet);
}
// Parses helix secondary structure object specified by the pdb-file line
void ParseHelix(string pdbLine)
{
Chain chain;
char chainId = pdbLine[19];
if (!chains.TryGetValue(chainId, out chain)) chains[chainId] = chain = new Chain() { Name = chainId.ToString() };
SecondaryStructure helix = new SecondaryStructure();
helix.StructureType = SecondaryStructureType.Helix;
helix.FirstResidueSequenceNumber = int.Parse(pdbLine.Substring(21, 4), CultureInfo.InvariantCulture);
helix.LastResidueSequenceNumber = int.Parse(pdbLine.Substring(33, 4), CultureInfo.InvariantCulture);
chain.SecondaryStructures.Add(helix);
}
