public static List <Vector4> LoadAtomSpheresBiomt(string fileName)
{
var path = GetPdbFile(fileName, DefaultPdbDirectory);
var atomData = ReadAtomData(path);
var atomSpheres = AtomHelper.GetAtomSpheres(atomData);
var biomtTransforms = ReadBiomtData(path);
atomSpheres = AtomHelper.BuildBiomt(atomSpheres, biomtTransforms);
return(atomSpheres);
}
public static List <List <Vector4> > ComputeLodProxiesBiomt(List <Vector4> atomSpheres, List <Matrix4x4> biomtTransforms, List <float> decimationFactors)
{
var clusterLevelsBiomt = new List <List <Vector4> >();
var clusterLevels = ComputeLodProxies(atomSpheres, decimationFactors);
foreach (var level in clusterLevels)
{
var biomtSpheres = AtomHelper.BuildBiomt(level, biomtTransforms);
//AtomHelper.CenterSpheres(ref biomtSpheres);
clusterLevelsBiomt.Add(biomtSpheres);
}
return(clusterLevelsBiomt);
}
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");
}