public static List<Atom> GetAtoms(Ingredient ingredient)
{
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 static void AddProteinIngredient(ref Ingredient ingredient)
{
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");
}
