//*** Membrane Ingredients ****//
public void AddMembrane(string filePath, Vector3 position, Quaternion rotation)
{
var groupName = "membrane";
var groupPath = "root.envelope." + groupName;
var nameInner = "inner_membrane";
var nameOuter = "outer_membrane";
var pathInner = groupPath + "." + nameInner;
var pathOuter = groupPath + "." + nameOuter;
RemoveElementFromHierarchy("membrane");
RemoveIngredientGroupFromName("membrane");
RemoveIngredientGroupFromName("membrane");
_ingredientNames.Clear();
LipidIngredientNames.Clear();
RemoveIngredientGroup(groupPath);
RemoveElementFromHierarchy(groupPath);
CPUBuffers.Get.LipidAtomPositions.Clear();
CPUBuffers.Get.LipidInstanceInfos.Clear();
CPUBuffers.Get.LipidInstanceInfos2.Clear();
CPUBuffers.Get.LipidInstancePositions.Clear();
//*****//
AddIngredientToHierarchy(pathInner);
AddIngredientToHierarchy(pathOuter);
LipidIngredientNames.Add(pathInner);
LipidIngredientNames.Add(pathOuter);
var ingredientIdInner = AllIngredientNames.IndexOf(pathInner);
var ingredientIdOuter = AllIngredientNames.IndexOf(pathOuter);
var envelopeSurfaceGroup = GetIngredientGroup("root.envelope.surface");
var envelopeMembraneGroup = new IngredientGroup();
envelopeMembraneGroup.Ingredients = new List <Ingredient>();
envelopeMembraneGroup.compartment_id = envelopeSurfaceGroup.compartment_id;
envelopeMembraneGroup.unique_id = IngredientGroups.Count;
envelopeMembraneGroup._groupType = -1;
envelopeMembraneGroup.name = groupName;
envelopeMembraneGroup.path = groupPath;
envelopeMembraneGroup.NumIngredients = 2;
var innerMembraneIngredient = new Ingredient();
innerMembraneIngredient.nbMol = 1;
innerMembraneIngredient._nbChains = 1;
innerMembraneIngredient._ingredientGroupId = envelopeMembraneGroup.unique_id;
innerMembraneIngredient._ingredientId = ingredientIdInner;
innerMembraneIngredient.name = nameInner;
innerMembraneIngredient.path = pathInner;
var outerMembraneIngredient = new Ingredient();
outerMembraneIngredient.nbMol = 1;
outerMembraneIngredient.nbChains = 1;
outerMembraneIngredient.ingredient_group_id = envelopeMembraneGroup.unique_id;
outerMembraneIngredient._ingredientId = ingredientIdOuter;
outerMembraneIngredient.name = nameOuter;
outerMembraneIngredient.path = pathOuter;
envelopeMembraneGroup.Ingredients.Add(innerMembraneIngredient);
envelopeMembraneGroup.Ingredients.Add(outerMembraneIngredient);
IngredientGroups.Add(envelopeMembraneGroup);
ColorManager.Get.InitColors();
//int a = 0;
var currentLipidAtoms = new List <Vector4>();
var membraneData = MyUtility.ReadBytesAsFloats(filePath);
var step = 5;
var dataIndex = 0;
var lipidAtomStart = 0;
var previousLipidId = -1;
while (true)
{
var flushCurrentBatch = false;
var breakAfterFlushing = false;
if (dataIndex >= membraneData.Count())
{
flushCurrentBatch = true;
breakAfterFlushing = true;
}
else
{
var lipidId = (int)membraneData[dataIndex + 4];
if (previousLipidId < 0)
{
previousLipidId = lipidId;
}
if (lipidId != previousLipidId)
{
flushCurrentBatch = true;
previousLipidId = lipidId;
}
}
if (flushCurrentBatch)
{
var bounds = AtomHelper.ComputeBounds(currentLipidAtoms);
var center = new Vector4(bounds.center.x, bounds.center.y, bounds.center.z, 0);
for (var j = 0; j < currentLipidAtoms.Count; j++)
{
currentLipidAtoms[j] -= center;
}
var innerMembrane = Vector3.Magnitude(bounds.center) < 727;
Vector4 batchPosition = position + bounds.center;
batchPosition.w = Vector3.Magnitude(bounds.extents);
CPUBuffers.Get.LipidInstancePositions.Add(batchPosition);
CPUBuffers.Get.LipidInstanceInfos.Add(new Vector4(innerMembrane ? ingredientIdInner : ingredientIdOuter, lipidAtomStart, currentLipidAtoms.Count));
CPUBuffers.Get.LipidInstanceInfos2.Add(new Vector4((int)InstanceState.Normal, 0, 0));
lipidAtomStart += currentLipidAtoms.Count;
CPUBuffers.Get.LipidAtomPositions.AddRange(currentLipidAtoms);
currentLipidAtoms.Clear();
if (breakAfterFlushing)
{
break;
}
}
var currentAtom = new Vector4(membraneData[dataIndex], membraneData[dataIndex + 1], membraneData[dataIndex + 2], membraneData[dataIndex + 3]);
currentLipidAtoms.Add(currentAtom);
dataIndex += step;
}
}
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 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);
}
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);
}
//*** Membrane Ingredients ****//
public void AddMembrane(string filePath, Vector3 position, Quaternion rotation)
{
var pathInner = "root.membrane.inner_membrane";
var pathOuter = "root.membrane.outer_membrane";
AddIngredientToHierarchy(pathInner);
AddIngredientToHierarchy(pathOuter);
LipidIngredientNames.Clear();
LipidIngredientNames.Add(pathInner);
LipidIngredientNames.Add(pathOuter);
LipidAtomPositions.Clear();
LipidInstanceInfos.Clear();
LipidInstancePositions.Clear();
var currentLipidAtoms = new List <Vector4>();
var membraneData = MyUtility.ReadBytesAsFloats(filePath);
var ingredientIdInner = AllIngredientNames.IndexOf(pathInner);
var ingredientIdOuter = AllIngredientNames.IndexOf(pathOuter);
var step = 5;
var dataIndex = 0;
var lipidAtomStart = 0;
var previousLipidId = -1;
while (true)
{
var flushCurrentBatch = false;
var breakAfterFlushing = false;
if (dataIndex >= membraneData.Count())
{
flushCurrentBatch = true;
breakAfterFlushing = true;
}
else
{
var lipidId = (int)membraneData[dataIndex + 4];
if (previousLipidId < 0)
{
previousLipidId = lipidId;
}
if (lipidId != previousLipidId)
{
flushCurrentBatch = true;
previousLipidId = lipidId;
}
}
if (flushCurrentBatch)
{
var bounds = AtomHelper.ComputeBounds(currentLipidAtoms);
var center = new Vector4(bounds.center.x, bounds.center.y, bounds.center.z, 0);
for (var j = 0; j < currentLipidAtoms.Count; j++)
{
currentLipidAtoms[j] -= center;
}
var innerMembrane = Vector3.Magnitude(bounds.center) < 727;
Vector4 batchPosition = position + bounds.center;
batchPosition.w = Vector3.Magnitude(bounds.extents);
LipidInstancePositions.Add(batchPosition);
LipidInstanceInfos.Add(new Vector4(innerMembrane ? ingredientIdInner : ingredientIdOuter, lipidAtomStart, currentLipidAtoms.Count));
lipidAtomStart += currentLipidAtoms.Count;
LipidAtomPositions.AddRange(currentLipidAtoms);
currentLipidAtoms.Clear();
if (breakAfterFlushing)
{
break;
}
}
var currentAtom = new Vector4(membraneData[dataIndex], membraneData[dataIndex + 1], membraneData[dataIndex + 2], AtomHelper.AtomRadii[(int)membraneData[dataIndex + 3]]);
currentLipidAtoms.Add(currentAtom);
dataIndex += step;
}
int a = 0;
}