public static List <Atom> GetAtoms(Ingredient ingredient)
{
Debug.Log("CellPackLoader: GetAtoms");
var name = ingredient.name;
var pdbName = ingredient.source.pdb.Replace(".pdb", "");
var atoms = new List <Atom>();
if ((pdbName == "") || (pdbName == "null") || (pdbName == "None") || pdbName.StartsWith("EMDB"))
{
var filePath = PdbLoader.GetFile(PdbLoader.DefaultPdbDirectory, name, "bin");
if (File.Exists(filePath))
{
var points = MyUtility.ReadBytesAsFloats(filePath);
for (var i = 0; i < points.Length; i += 4)
{
var currentAtom = new Atom
{
position = new Vector3(points[i], points[i + 1], points[i + 2]),
radius = points[i + 3],
symbolId = -1,
chainId = 0
};
atoms.Add(currentAtom);
}
}
}
else
{
// Load atom set from pdb file
atoms = PdbLoader.LoadAtomDataFull(pdbName);
}
// If the set is empty return
if (atoms.Count == 0)
{
throw new Exception("Atom list empty: " + name);
}
return(atoms);
}
//public void AddProteinInstance(string path, Vector3 position, Quaternion rotation)
//{
// if (!ProteinIngredientNames.Contains(path))
// {
// throw new Exception("Ingredient path do not exists");
// }
// var ingredientId = ProteinIngredientNames.IndexOf(path);
// CPUBuffers.Get.ProteinInstanceInfos.Add(new Vector4(ingredientId, (int) InstanceState.Normal, 0));
// CPUBuffers.Get.ProteinInstancePositions.Add(position);
// CPUBuffers.Get.ProteinInstanceRotations.Add(MyUtility.QuanternionToVector4(rotation));
// TotalNumProteinAtoms += CPUBuffers.Get.ProteinAtomCount[ingredientId];
//}
//*** Curve Ingredients ****//
public void AddCurveIngredient(string path, string pdbName)
{
if (SceneHierarchy.Contains(path))
{
throw new Exception("Invalid curve ingredient path: " + path);
}
if (CurveIngredientNames.Contains(path))
{
throw new Exception("Invalid curve ingredient path: " + path);
}
AddIngredientToHierarchy(path);
CurveIngredientNames.Add(path);
var numSteps = 1;
var twistAngle = 0.0f;
var segmentLength = 34.0f;
var color = new Color(1, 1, 1, 1);
if (path.Contains("DNA"))
{
numSteps = 12;
twistAngle = 34.3f;
segmentLength = 34.0f;
color = Color.yellow;
var atomSpheres = PdbLoader.LoadAtomSpheres(pdbName);
CPUBuffers.Get.CurveIngredientsAtomStart.Add(CPUBuffers.Get.CurveIngredientsAtoms.Count);
CPUBuffers.Get.CurveIngredientsAtomCount.Add(atomSpheres.Count);
CPUBuffers.Get.CurveIngredientsAtoms.AddRange(atomSpheres);
}
//else if (path.Contains("mRNA"))
else if (path.Contains("RNA"))
{
numSteps = 12;
twistAngle = 34.3f;
segmentLength = 34.0f;
color = Color.red;
var atomSpheres = PdbLoader.LoadAtomSpheres(pdbName);
CPUBuffers.Get.CurveIngredientsAtomStart.Add(CPUBuffers.Get.CurveIngredientsAtoms.Count);
CPUBuffers.Get.CurveIngredientsAtomCount.Add(atomSpheres.Count);
CPUBuffers.Get.CurveIngredientsAtoms.AddRange(atomSpheres);
}
else if (path.Contains("peptide"))
{
numSteps = 10;
twistAngle = 0;
segmentLength = 20.0f;
color = Color.magenta;
var atomSphere = new Vector4(0, 0, 0, 3);
CPUBuffers.Get.CurveIngredientsAtomStart.Add(CPUBuffers.Get.CurveIngredientsAtoms.Count);
CPUBuffers.Get.CurveIngredientsAtomCount.Add(1);
CPUBuffers.Get.CurveIngredientsAtoms.Add(atomSphere);
}
else if (path.Contains("lypoglycane"))
{
numSteps = 10;
twistAngle = 0;
segmentLength = 20;
color = Color.green;
var atomSphere = new Vector4(0, 0, 0, 8);
CPUBuffers.Get.CurveIngredientsAtomStart.Add(CPUBuffers.Get.CurveIngredientsAtoms.Count);
CPUBuffers.Get.CurveIngredientsAtomCount.Add(1);
CPUBuffers.Get.CurveIngredientsAtoms.Add(atomSphere);
}
else
{
throw new Exception("Curve ingredient unknown");
}
CPUBuffers.Get.CurveIngredientsColors.Add(color);
CPUBuffers.Get.CurveIngredientToggleFlags.Add(1);
CPUBuffers.Get.CurveIngredientsInfos.Add(new Vector4(numSteps, twistAngle, segmentLength, 0));
}
public static void AddProteinIngredient(ref Ingredient ingredient)
{
Debug.Log("CellPackLoader: AddProteinIngredient");
var path = ingredient.path;
var biomt = ingredient.source.biomt;
var pdbName = ingredient.source.pdb.Replace(".pdb", "");
Debug.Log("*****");
Debug.Log("Ingredient: " + ingredient.ingredient_id);
Debug.Log("Name: " + ingredient.path);
Debug.Log("Pdb id: " + ingredient.source.pdb);
// ***** Load atoms *****//
var atoms = GetAtoms(ingredient);
var numChains = AtomHelper.GetNumChains(atoms);
Debug.Log("Num chains: " + numChains);
ingredient.nbChains = numChains;
var isFromCustomStructureFile = AtomHelper.IsFromCustomStructureFile(atoms);
if (isFromCustomStructureFile)
{
Debug.Log("From custom structure file");
}
var alphaCarbonsOnly = AtomHelper.ContainsCarbonAlphaOnly(atoms);
if (alphaCarbonsOnly)
{
AtomHelper.OverwriteRadii(ref atoms, 3);
}
if (alphaCarbonsOnly)
{
Debug.Log("Alpha carbons only");
}
// ***** Compute lod proxies *****//
var lodProxies = new List <List <Vector4> >();
// Define cluster decimation levels
var clusterLevelFactors = new List <float>()
{
0.15f, 0.10f, 0.05f
};
if (alphaCarbonsOnly || isFromCustomStructureFile)
{
clusterLevelFactors = new List <float>()
{
1, 1, 1
}
}
;
if (!biomt)
{
// Center atoms before computing the lod proxies
AtomHelper.CenterAtoms(ref atoms);
var atomSpheres = AtomHelper.GetAtomSpheres(atoms);
lodProxies = AtomHelper.ComputeLodProxies(atomSpheres, clusterLevelFactors);
}
else
{
var atomSpheres = AtomHelper.GetAtomSpheres(atoms);
var biomtTransforms = PdbLoader.LoadBiomtTransforms(pdbName);
// Compute centered lod proxies
lodProxies = AtomHelper.ComputeLodProxiesBiomt(atomSpheres, biomtTransforms, clusterLevelFactors);
// Assemble the atom set from biomt transforms and center
atoms = AtomHelper.BuildBiomt(atoms, biomtTransforms);
var centerPosition = AtomHelper.ComputeBounds(atoms).center;
// Center atoms
AtomHelper.OffsetAtoms(ref atoms, centerPosition);
// Center proxies
for (int i = 0; i < lodProxies.Count; i++)
{
var t = lodProxies[i];
AtomHelper.OffsetSpheres(ref t, centerPosition);
}
}
SceneManager.Get.AddProteinIngredientToCPUBuffer(ingredient, atoms, lodProxies);
Debug.Log("Ingredient added succesfully");
}
public void AddCurveIngredient(string name, string pdbName)
{
if (ProteinNames.Contains(name))
{
return;
}
int numSteps = 1;
float twistAngle = 0;
float segmentLength = 34.0f;
var color = Helper.GetRandomColor();
if (name.Contains("DNA"))
{
numSteps = 12;
twistAngle = 34.3f;
segmentLength = 34.0f;
color = Color.yellow;
var atomSpheres = PdbLoader.LoadAtomSpheres(pdbName);
CurveIngredientsAtomCount.Add(atomSpheres.Count);
CurveIngredientsAtomStart.Add(CurveIngredientsAtoms.Count);
CurveIngredientsAtoms.AddRange(atomSpheres);
}
else if (name.Contains("mRNA"))
{
numSteps = 12;
twistAngle = 34.3f;
segmentLength = 34.0f;
color = Color.red;
var atomSpheres = PdbLoader.LoadAtomSpheres(pdbName);
CurveIngredientsAtomCount.Add(atomSpheres.Count);
CurveIngredientsAtomStart.Add(CurveIngredientsAtoms.Count);
CurveIngredientsAtoms.AddRange(atomSpheres);
}
else if (name.Contains("peptide"))
{
numSteps = 10;
twistAngle = 0;
segmentLength = 20.0f;
color = Color.magenta;
var atomSphere = new Vector4(0, 0, 0, 3);
CurveIngredientsAtomCount.Add(1);
CurveIngredientsAtomStart.Add(CurveIngredientsAtoms.Count);
CurveIngredientsAtoms.Add(atomSphere);
}
else if (name.Contains("lypoglycane"))
{
numSteps = 10;
twistAngle = 0;
segmentLength = 20;
color = Color.green;
var atomSphere = new Vector4(0, 0, 0, 8);
CurveIngredientsAtomCount.Add(1);
CurveIngredientsAtomStart.Add(CurveIngredientsAtoms.Count);
CurveIngredientsAtoms.Add(atomSphere);
}
else
{
throw new Exception("Curve ingredient unknown");
}
CurveIngredientsNames.Add(name);
CurveIngredientsColors.Add(color);
CurveIngredientToggleFlags.Add(1);
CurveIngredientsInfos.Add(new Vector4(numSteps, twistAngle, segmentLength));
}
public static void AddProteinIngredient(JSONNode ingredientDictionary, string prefix)
{
var name = prefix + "_" + ingredientDictionary["name"];
var biomt = (bool)ingredientDictionary["source"]["biomt"].AsBool;
var center = (bool)ingredientDictionary["source"]["transform"]["center"].AsBool;
var pdbName = ingredientDictionary["source"]["pdb"].Value.Replace(".pdb", "");
if (pdbName == "")
{
return;
}
if (pdbName == "null")
{
return;
}
if (pdbName == "None")
{
return;
}
if (pdbName.StartsWith("EMDB"))
{
return;
}
if (pdbName.Contains("1PI7_1vpu_biounit"))
{
return;
}
// Disable biomts until loading problem is resolved
if (biomt)
{
return;
}
// Load atom set from pdb file
var atomSet = PdbLoader.LoadAtomSet(pdbName);
// If the set is empty return
if (atomSet.Count == 0)
{
return;
}
var atomSpheres = AtomHelper.GetAtomSpheres(atomSet);
var centerPosition = AtomHelper.ComputeBounds(atomSpheres).center;
var biomtTransforms = biomt ? PdbLoader.LoadBiomtTransforms(pdbName) : new List <Matrix4x4>();
var biomtCenter = AtomHelper.GetBiomtCenter(biomtTransforms);
var containsACarbonOnly = AtomHelper.ContainsACarbonOnly(atomSet);
// Center atoms
AtomHelper.OffsetSpheres(ref atomSpheres, centerPosition);
// Compute bounds
var bounds = AtomHelper.ComputeBounds(atomSpheres);
// Get ingredient color
// TODO: Move color palette code into dedicated function
var cid = ColorPaletteGenerator.GetRandomUniqFromSample(current_color, usedColors[current_color]);
usedColors[current_color].Add(cid);
var sample = ColorPaletteGenerator.colorSamples[cid];
var c = ColorPaletteGenerator.lab2rgb(sample) / 255.0f;
var color = new Color(c[0], c[1], c[2]);
// Define cluster decimation levels
var clusterLevels = (containsACarbonOnly)
? new List <float>()
{
0.85f, 0.25f, 0.1f
}
: new List <float>()
{
0.10f, 0.05f, 0.01f
};
// Add ingredient type
//SceneManager.Instance.AddIngredient(name, bounds, atomSpheres, color);
SceneManager.Instance.AddIngredient(name, bounds, atomSpheres, color, clusterLevels);
int instanceCount = 0;
for (int k = 0; k < ingredientDictionary["results"].Count; k++)
{
var p = ingredientDictionary["results"][k][0];
var r = ingredientDictionary["results"][k][1];
var position = new Vector3(-p[0].AsFloat, p[1].AsFloat, p[2].AsFloat);
var rotation = new Quaternion(r[0].AsFloat, r[1].AsFloat, r[2].AsFloat, r[3].AsFloat);
var mat = Helper.quaternion_matrix(rotation);
var euler = Helper.euler_from_matrix(mat);
rotation = Helper.MayaRotationToUnity(euler);
if (!biomt)
{
// Find centered position
if (!center)
{
position += Helper.QuaternionTransform(rotation, centerPosition);
}
SceneManager.Instance.AddIngredientInstance(name, position, rotation);
instanceCount++;
}
else
{
foreach (var transform in biomtTransforms)
{
var biomtOffset = Helper.RotationMatrixToQuaternion(transform) * centerPosition;
var biomtInstanceRot = rotation * Helper.RotationMatrixToQuaternion(transform);
var biomtInstancePos = rotation * (new Vector3(transform.m03, transform.m13, transform.m23) + biomtOffset) + position - biomtCenter;
SceneManager.Instance.AddIngredientInstance(name, biomtInstancePos, biomtInstanceRot);
instanceCount++;
}
}
}
Debug.Log("*****");
Debug.Log("Added ingredient: " + name);
if (containsACarbonOnly)
{
Debug.Log("Alpha-carbons only");
}
Debug.Log("Pdb name: " + pdbName + " *** " + "Num atoms: " + atomSpheres.Count + " *** " + "Num instances: " + instanceCount + " *** " + "Total atom count: " + atomSpheres.Count * instanceCount);
}
public static void AddProteinIngredient(JSONNode ingredientDictionary, params string[] pathElements)
{
var name = ingredientDictionary["name"];
var path = MyUtility.GetUrlPath(pathElements.ToList(), name);
var biomt = (bool)ingredientDictionary["source"]["biomt"].AsBool;
var center = (bool)ingredientDictionary["source"]["transform"]["center"].AsBool;
var pdbName = ingredientDictionary["source"]["pdb"].Value.Replace(".pdb", "");
List <Vector4> atomSpheres;
List <Matrix4x4> biomtTransforms = new List <Matrix4x4>();
Vector3 biomtCenter = Vector3.zero;
bool containsACarbonOnly = false;
bool oneLOD = false;
if ((pdbName == "") || (pdbName == "null") || (pdbName == "None") || pdbName.StartsWith("EMDB"))
{
return;
////check for sphere file//information in the file. if not in file is it on disk ? on repo ?
////possibly read the actuall recipe definition ?
////check if bin exist
//var filePath = PdbLoader.DefaultPdbDirectory + ingredientDictionary["name"] + ".bin";
//if (File.Exists(filePath)){
// atomSpheres = new List<Vector4>();
// var points = MyUtility.ReadBytesAsFloats(filePath);
// for (var i = 0; i < points.Length; i += 4) {
// var currentAtom = new Vector4 (points [i], points [i + 1], points [i + 2], points [i + 3]);
// atomSpheres.Add (currentAtom);
// }
// containsACarbonOnly = true;
// oneLOD = true;
//}
//else if (ingredientDictionary ["radii"] != null) {
// atomSpheres = MyUtility.gatherSphereTree(ingredientDictionary)[0];
// Debug.Log ("nbprim "+atomSpheres.Count.ToString());//one sphere
// oneLOD = true;
//} else {
// float radius = 30.0f;
// if (name.Contains("dLDL"))
// radius = 108.08f;//or use the mesh? or make sphere from the mesh ?
// if (name.Contains("iLDL"))
// radius = 105.41f;//or use the mesh? or make sphere from the mesh ?
// atomSpheres = new List<Vector4>();
// atomSpheres.Add (new Vector4(0,0,0,radius));
// //No LOD since only one sphere
// oneLOD = true;
//}
}
else
{
//if (pdbName.StartsWith("EMDB")) return;
//if (pdbName.Contains("1PI7_1vpu_biounit")) return;//??
// Load atom set from pdb file
var atomSet = PdbLoader.LoadAtomSet(pdbName);
// If the set is empty return
if (atomSet.Count == 0)
{
return;
}
atomSpheres = AtomHelper.GetAtomSpheres(atomSet);
containsACarbonOnly = AtomHelper.ContainsCarbonAlphaOnly(atomSet);
}
var centerPosition = AtomHelper.ComputeBounds(atomSpheres).center;
// Center atoms
AtomHelper.OffsetSpheres(ref atomSpheres, centerPosition);
// Compute bounds
var bounds = AtomHelper.ComputeBounds(atomSpheres);
biomtTransforms = biomt ? PdbLoader.LoadBiomtTransforms(pdbName) : new List <Matrix4x4>();
biomtCenter = AtomHelper.GetBiomtCenter(biomtTransforms, centerPosition);
//if (!pdbName.Contains("1TWT_1TWV")) return;
// Disable biomts until loading problem is resolved
//if (!biomt) return;
// Get ingredient color
// TODO: Move color palette code into dedicated function
var cid = ColorPaletteGenerator.GetRandomUniqFromSample(current_color, usedColors[current_color]);
usedColors[current_color].Add(cid);
var sample = ColorPaletteGenerator.colorSamples[cid];
var c = ColorPaletteGenerator.lab2rgb(sample) / 255.0f;
var color = new Color(c[0], c[1], c[2]);
// Define cluster decimation levels
var clusterLevels = (containsACarbonOnly)
? new List <float>()
{
0.85f, 0.25f, 0.1f
}
: new List <float>()
{
0.15f, 0.10f, 0.05f
};
if (oneLOD)
{
clusterLevels = new List <float> ()
{
1, 1, 1
}
}
;
// Add ingredient type
//SceneManager.Instance.AddIngredient(name, bounds, atomSpheres, color);
SceneManager.Get.AddProteinIngredient(path, bounds, atomSpheres, color, clusterLevels, oneLOD);
int instanceCount = 0;
for (int k = 0; k < ingredientDictionary["results"].Count; k++)
{
var p = ingredientDictionary["results"][k][0];
var r = ingredientDictionary["results"][k][1];
var position = new Vector3(-p[0].AsFloat, p[1].AsFloat, p[2].AsFloat);
var rotation = new Quaternion(r[0].AsFloat, r[1].AsFloat, r[2].AsFloat, r[3].AsFloat);
var mat = MyUtility.quaternion_matrix(rotation);
var euler = MyUtility.euler_from_matrix(mat);
rotation = MyUtility.MayaRotationToUnity(euler);
if (!biomt)
{
// Find centered position
if (!center)
{
position += MyUtility.QuaternionTransform(rotation, centerPosition);
}
SceneManager.Get.AddProteinInstance(path, position, rotation);
instanceCount++;
}
else
{
foreach (var transform in biomtTransforms)
{
var biomteuler = MyUtility.euler_from_matrix(transform);
var rotBiomt = MyUtility.MayaRotationToUnity(biomteuler);
var offset = MyUtility.QuaternionTransform(rotBiomt, centerPosition); //Helper.RotationMatrixToQuaternion(matBiomt), GetCenter());
var posBiomt = new Vector3(-transform.m03, transform.m13, transform.m23) + offset - biomtCenter;
var biomtOffset = MyUtility.RotationMatrixToQuaternion(transform) * centerPosition;
var biomtInstanceRot = rotation * rotBiomt; //Helper.RotationMatrixToQuaternion(transform);
var biomtInstancePos = rotation * posBiomt + position;
SceneManager.Get.AddProteinInstance(path, biomtInstancePos, biomtInstanceRot);
instanceCount++;
}
}
}
SceneManager.Get.AddIngredientProperties(atomSpheres.Count, instanceCount);
Debug.Log("*****");
Debug.Log("Added ingredient: " + path);
//if (isCarbonAlphaOnly) Debug.Log("Alpha-carbons only");
//Debug.Log("Pdb name: " + pdbName + " *** " + "Num atoms: " + atomSet.Count + " *** " + "Num instances: " + instanceCount + " *** " + "Total atom count: " + atomSet.Count * instanceCount);
}
