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);
}