/// <summary>Atom模式选取</summary>
public void SetData(AtomDisplayer atomDisplayer)
{
AtomInAminoacid atomInAminoacid = atomDisplayer.AtomInAminoacid;
AminoacidInProtein aminoacidInProtein = atomDisplayer.AminoacidInProtein;
Chain chain = aminoacidInProtein.Chain;
Protein protein = chain.Protein;
SetProteinData(protein);
SetChainData(chain);
SetAminoacidData(aminoacidInProtein);
SetAtomData(aminoacidInProtein, atomInAminoacid);
}
public void SetBoardInfo(AtomDisplayer atomDisplayer)
{
if (atomDisplayer == null)
{
proteinInfoText.text = "";
chaininInfoText.text = "";
aminoacidInfoText.text = "";
atomInfoText.text = "";
return;
}
AtomInAminoacid atomInAminoacid = atomDisplayer.AtomInAminoacid;
AminoacidInProtein aminoacidInProtein = atomDisplayer.AminoacidInProtein;
Chain chain = aminoacidInProtein.Chain;
Protein protein = chain.Protein;
proteinInfoText.text = string.Format("-Protein-\nID: {0}\nClassification: {1}\nPublishDate: {2}",
protein.ID, protein.Classification, protein.PublishDate);
chaininInfoText.text = string.Format("-Chain-\nID: {0}\nOXT: {1}",
chain.ID, chain.OXT != null);
aminoacidInfoText.text = string.Format("-Aminoacid-\nSeq: {0}\nType: {1}\nIsStandard: {2}",
aminoacidInProtein.ResidueSeq, aminoacidInProtein.Aminoacid.Type.ToString(), aminoacidInProtein.Aminoacid.IsStandard);
atomInfoText.text = string.Format("-Atom-\nName: {0}\nSerial: {1}\nPosition: {2}",
atomInAminoacid.Name, aminoacidInProtein.AtomInAminoacidSerial[atomInAminoacid], aminoacidInProtein.AtomInAminoacidPos[atomInAminoacid].ToString("F3"));
}
public ShowInfoInBoardCommand(AtomDisplayer atomDisplayer)
{
this.AtomDisplayer = atomDisplayer;
}
public void SetBoardInfo(AtomDisplayer atomDisplayer)
{
polymerInfoDisplayer.SetData(atomDisplayer);
}
/// <summary>根据DisplayMode创建整个蛋白质模型 </summary>
public void CreateProtein(Protein protein, DisplayMode displayMode)
{
Vector3 initPos = Vector3.zero;
//若之前已创建Protein 则继承原来的位置 否则在摄像机的前2米初始化
if (proteinDisplayerGo != null)
{
initPos = proteinDisplayerGo.transform.position;
}
else
{
Camera mainCamera = Camera.main;
initPos = mainCamera.transform.position + oriOffsetToMainCamera.z * mainCamera.transform.forward
+ oriOffsetToMainCamera.y * mainCamera.transform.up + oriOffsetToMainCamera.x * mainCamera.transform.right;
}
proteinDisplayerGo = Instantiate(proteinTemplatePrefeb, Displayer3DRoot.transform, true);
proteinDisplayerGo.name = protein.ID;
proteinDisplayerGo.GetComponent <ProteinDisplayer>().Protein = protein;
foreach (var chainKvp in protein.Chains)
{
Chain chain = chainKvp.Value;
GameObject chainDisplayerGo = new GameObject(chain.ID, typeof(ChainDisplayer));
chainDisplayerGo.GetComponent <ChainDisplayer>().Chain = chain;
chainDisplayerGo.transform.SetParent(proteinDisplayerGo.transform);
//创建每个原子模型
foreach (var aminoacidKvp in chain.SeqAminoacids)
{
AminoacidInProtein aminoacidInProtein = aminoacidKvp.Value;
//GameObject aminoacidDisplayerGo = new GameObject(aminoacidInProtein.ResidueSeq.ToString(), typeof(AminoacidDisplayer));
GameObject aminoacidDisplayerGo = Instantiate <GameObject>(residueTemplatePrefeb, chainDisplayerGo.transform);
aminoacidDisplayerGo.name = aminoacidInProtein.ResidueSeq.ToString();
AminoacidDisplayer aminoacidDisplayer = aminoacidDisplayerGo.GetComponent <AminoacidDisplayer>();
aminoacidDisplayer.AminoacidInProtein = aminoacidInProtein;
//棍状模型不显示原子球
if (displayMode != DisplayMode.Sticks)
{
foreach (var atomKvp in aminoacidInProtein.AtomInAminoacidSerial)
{
AtomInAminoacid atomInAminoacid = atomKvp.Key;
GameObject atomDisplayerGoPrefeb = GetAtomPrefeb(atomInAminoacid.Aminoacid.Type);
switch (displayMode)
{
case DisplayMode.Spacefill: atomDisplayerGoPrefeb.transform.localScale = new Vector3(AtomFillSize, AtomFillSize, AtomFillSize); break;
case DisplayMode.BallStick: atomDisplayerGoPrefeb.transform.localScale = new Vector3(AtomBallStickSize, AtomBallStickSize, AtomBallStickSize); break;
default: throw new System.Exception(string.Format("Unhandled displayMode: {0}", displayMode));
}
GameObject atomDisplayerGo = Instantiate(atomDisplayerGoPrefeb, aminoacidDisplayerGo.transform, false);
atomDisplayerGo.name = atomInAminoacid.Name;
atomDisplayerGo.transform.localPosition = (aminoacidInProtein.AtomInAminoacidPos[atomInAminoacid] - protein.CenterPos) * BallStickPosScale;
AtomDisplayer atomDisplayer = atomDisplayerGo.GetComponent <AtomDisplayer>();
atomDisplayer.AtomInAminoacid = atomInAminoacid;
atomDisplayer.AminoacidInProtein = aminoacidInProtein;
}
}
//创建每个键的模型
if (displayMode == DisplayMode.BallStick || displayMode == DisplayMode.Sticks)
{
AminoacidInProtein lastAminoacidInProtein = null;
//若在该链存在上一序列号的残基 则构造一个该残基的N连通上一残基的C形成的肽键
if (aminoacidInProtein.Chain.SeqAminoacids.TryGetValue(aminoacidInProtein.ResidueSeq - 1, out lastAminoacidInProtein))
{
//两个Bond 两个颜色
string name1 = string.Format("{0}-{1}-Peptidebond", lastAminoacidInProtein.ResidueSeq, aminoacidInProtein.ResidueSeq);
string name2 = string.Format("{0}-{1}-Peptidebond", aminoacidInProtein.ResidueSeq, lastAminoacidInProtein.ResidueSeq);
Vector3 pos1 = (lastAminoacidInProtein.AtomInAminoacidPos[lastAminoacidInProtein.Aminoacid["C"]] - protein.CenterPos) * BallStickPosScale;
Vector3 pos3 = (aminoacidInProtein.AtomInAminoacidPos[aminoacidInProtein.Aminoacid["N"]] - protein.CenterPos) * BallStickPosScale;
Vector3 pos2 = (pos1 + pos3) / 2;
BondType bondType = BondType.Single;
Transform parent = aminoacidDisplayerGo.transform;
AminoacidType aminoacidType1 = lastAminoacidInProtein.Aminoacid.Type;
AminoacidType aminoacidType2 = aminoacidInProtein.Aminoacid.Type;
GenerateBondGameObject(name1, pos1, pos2, bondType, parent, aminoacidType1, displayMode);
GenerateBondGameObject(name2, pos2, pos3, bondType, parent, aminoacidType2, displayMode);
}
//氨基酸内的化学键(从本地Aminoacid数据中获取的连接关系)
foreach (var connection in aminoacidInProtein.Aminoacid.Connections)
{
string name = string.Format("{0}-{1}-bond", connection.Key.Key.Name, connection.Key.Value.Name);
Vector3 pos1 = Vector3.zero; Vector3 pos2 = Vector3.zero;
//若读取的pdb文件中的某残基中没有连接关系中的某个原子 说明源pdb文件出现数据遗漏
try {
pos1 = (aminoacidInProtein.AtomInAminoacidPos[connection.Key.Key] - protein.CenterPos) * BallStickPosScale;
pos2 = (aminoacidInProtein.AtomInAminoacidPos[connection.Key.Value] - protein.CenterPos) * BallStickPosScale;
}
catch (KeyNotFoundException ex) {
//Debug.LogWarning(string.Format("The aminoacidInProtein: {0} is not complete, the atom in connection: {1}-{2} is losed", aminoacidInProtein, connection.Key.Key.Name, connection.Key.Value.Name));
continue;
}
BondType bondType = connection.Value;
Transform parent = aminoacidDisplayerGo.transform;
AminoacidType aminoacidType = aminoacidInProtein.Aminoacid.Type;
GenerateBondGameObject(name, pos1, pos2, bondType, parent, aminoacidType, displayMode);
}
}
//若合并Mesh 在Residue的mesh合并渲染 所有子物体不渲染
if (conbineMesh)
{
MeshFilter residueMeshFilter = aminoacidDisplayerGo.AddComponent <MeshFilter>();
MeshRenderer residueMeshRenderer = aminoacidDisplayerGo.AddComponent <MeshRenderer>();
residueMeshFilter.sharedMesh = aminoacidDisplayerGo.transform.CombineChildsMesh();
residueMeshRenderer.sharedMaterial = GetMaterial(aminoacidInProtein.Aminoacid.Type);
MeshRenderer[] childMeshRenderers = aminoacidDisplayerGo.GetComponentsInChildren <MeshRenderer>();
foreach (var renderer in childMeshRenderers)
{
renderer.enabled = false;
}
residueMeshRenderer.enabled = true;
aminoacidDisplayer.Normal = GetMaterial(aminoacidInProtein.Aminoacid.Type);
aminoacidDisplayer.HighLight = GetHighlightMaterial(aminoacidInProtein.Aminoacid.Type);
}
}
}
proteinDisplayerGo.transform.localScale = new Vector3(0.2f, 0.2f, 0.2f); //缩放0.2倍
proteinDisplayerGo.transform.position = initPos;
}
public void ShowProtein(Protein protein)
{
GameObject proteinDisplayerGo = new GameObject(protein.ID, typeof(ProteinDisplayer));
proteinDisplayerGo.GetComponent <ProteinDisplayer>().Protein = protein;
Displayer3DRoot.transform.localPosition = Vector3.zero;
Displayer3DRoot.transform.localRotation = Quaternion.identity;
Displayer3DRoot.transform.localScale = new Vector3(1, 1, 1);
proteinDisplayerGo.transform.SetParent(Displayer3DRoot.transform);
foreach (var chainKvp in protein.Chains)
{
Chain chain = chainKvp.Value;
GameObject chainDisplayerGo = new GameObject(chain.ID, typeof(ChainDisplayer));
chainDisplayerGo.GetComponent <ChainDisplayer>().Chain = chain;
chainDisplayerGo.transform.SetParent(proteinDisplayerGo.transform);
//创建每个原子模型
foreach (var aminoacidKvp in chain.SeqAminoacids)
{
AminoacidInProtein aminoacidInProtein = aminoacidKvp.Value;
GameObject aminoacidDisplayerGo = new GameObject(aminoacidInProtein.ResidueSeq.ToString(), typeof(AminoacidDisplayer));
aminoacidDisplayerGo.GetComponent <AminoacidDisplayer>().AminoacidInProtein = aminoacidInProtein;
aminoacidDisplayerGo.transform.SetParent(chainDisplayerGo.transform);
foreach (var atomKvp in aminoacidInProtein.AtomInAminoacidSerial)
{
AtomInAminoacid atomInAminoacid = atomKvp.Key;
GameObject atomDisplayerGoPrefeb = GetAtomPrefeb(atomInAminoacid.Aminoacid.Type);
switch (displayMode)
{
case DisplayMode.Spacefill: atomDisplayerGoPrefeb.transform.localScale = new Vector3(AtomFillSize, AtomFillSize, AtomFillSize); break;
case DisplayMode.BallStick: atomDisplayerGoPrefeb.transform.localScale = new Vector3(AtomBallStickSize, AtomBallStickSize, AtomBallStickSize); break;
case DisplayMode.Stick: atomDisplayerGoPrefeb.transform.localScale = new Vector3(AtomStickSize, AtomStickSize, AtomStickSize); break;
default: throw new System.Exception(string.Format("Unhandled displayMode: {0}", displayMode));
}
GameObject atomDisplayerGo = Instantiate(atomDisplayerGoPrefeb, aminoacidDisplayerGo.transform, false);
atomDisplayerGo.name = atomInAminoacid.Name;
atomDisplayerGo.transform.localPosition = (aminoacidInProtein.AtomInAminoacidPos[atomInAminoacid] - protein.CenterPos) * BallStickPosScale;
AtomDisplayer atomDisplayer = atomDisplayerGo.GetComponent <AtomDisplayer>();
atomDisplayer.AtomInAminoacid = atomInAminoacid;
atomDisplayer.AminoacidInProtein = aminoacidInProtein;
}
//创建每个键的模型
if (displayMode == DisplayMode.BallStick || displayMode == DisplayMode.Stick)
{
AminoacidInProtein lastAminoacidInProtein = null;
//若在该链存在上一序列号的残基 则构造一个该残基的N连通上一残基的C形成的肽键
if (aminoacidInProtein.Chain.SeqAminoacids.TryGetValue(aminoacidInProtein.ResidueSeq - 1, out lastAminoacidInProtein))
{
//两个Bond 两个颜色
string name1 = string.Format("{0}-{1}-Peptidebond", lastAminoacidInProtein.ResidueSeq, aminoacidInProtein.ResidueSeq);
string name2 = string.Format("{0}-{1}-Peptidebond", aminoacidInProtein.ResidueSeq, lastAminoacidInProtein.ResidueSeq);
Vector3 pos1 = (lastAminoacidInProtein.AtomInAminoacidPos[lastAminoacidInProtein.Aminoacid["C"]] - protein.CenterPos) * BallStickPosScale;
Vector3 pos3 = (aminoacidInProtein.AtomInAminoacidPos[aminoacidInProtein.Aminoacid["N"]] - protein.CenterPos) * BallStickPosScale;
Vector3 pos2 = (pos1 + pos3) / 2;
BondType bondType = BondType.Single;
Transform parent = aminoacidDisplayerGo.transform;
AminoacidType aminoacidType1 = lastAminoacidInProtein.Aminoacid.Type;
AminoacidType aminoacidType2 = aminoacidInProtein.Aminoacid.Type;
GenerateBondGameObject(name1, pos1, pos2, bondType, parent, aminoacidType1);
GenerateBondGameObject(name2, pos2, pos3, bondType, parent, aminoacidType2);
}
//氨基酸内的化学键(从本地Aminoacid数据中获取的连接关系)
foreach (var connection in aminoacidInProtein.Aminoacid.Connections)
{
string name = string.Format("{0}-{1}-bond", connection.Key.Key.Name, connection.Key.Value.Name);
Vector3 pos1 = Vector3.zero; Vector3 pos2 = Vector3.zero;
//若读取的pdb文件中的某残基中没有连接关系中的某个原子 说明源pdb文件出现数据遗漏
try
{
pos1 = (aminoacidInProtein.AtomInAminoacidPos[connection.Key.Key] - protein.CenterPos) * BallStickPosScale;
pos2 = (aminoacidInProtein.AtomInAminoacidPos[connection.Key.Value] - protein.CenterPos) * BallStickPosScale;
}
catch (KeyNotFoundException)
{
//Debug.LogWarning(string.Format("The aminoacidInProtein: {0} is not complete, the atom in connection: {1}-{2} is losed", aminoacidInProtein, connection.Key.Key.Name, connection.Key.Value.Name));
continue;
}
BondType bondType = connection.Value;
Transform parent = aminoacidDisplayerGo.transform;
AminoacidType aminoacidType = aminoacidInProtein.Aminoacid.Type;
GenerateBondGameObject(name, pos1, pos2, bondType, parent, aminoacidType);
}
}
}
}
}
//public void OnBallStickToggleChanged(bool value)
//{
// ProteinDisplayModel model = GetModel<ProteinDisplayModel>();
// ProteinDisplayView view = GetView<ProteinDisplayView>();
// Protein protein = model.DisplayedProteinData;
// view.displayMode = value ? DisplayMode.BallStick : DisplayMode.Spacefill;
// DestroyProtein();
// view.ShowProtein(protein);
//}
public void ShowInfoInBoard(AtomDisplayer atomDisplayer)
{
ProteinDisplayView view = GetView <ProteinDisplayView>();
view.SetBoardInfo(atomDisplayer);
}