/// <summary>
/// 公有构造函数
/// </summary>
/// <param name="type">氨基酸类型</param>
/// <param name="isStandard">是否是标准残基</param>
/// <param name="atoms">构成氨基酸得原子</param>
/// <param name="connection">原子间的连接关系</param>
internal Aminoacid(AminoacidType type, string chinese, bool isStandard, IList <string> atomNames, IDictionary <KeyValuePair <string, string>, BondType> connection)
{
this.Type = type;
this.Chinese = chinese;
List <AtomInAminoacid> atoms = new List <AtomInAminoacid>();
foreach (string name in atomNames)
{
AtomInAminoacid atomInAminoacid = new AtomInAminoacid(name)
{
Aminoacid = this,
};
atoms.Add(atomInAminoacid);
}
//Atoms = new ReadOnlyCollection<AtomInAminoacid>(atoms);
atomDic = new Dictionary <string, AtomInAminoacid>();
foreach (var child in atoms)
{
atomDic.Add(child.Name, child);
}
Dictionary <KeyValuePair <AtomInAminoacid, AtomInAminoacid>, BondType> connectDic = new Dictionary <KeyValuePair <AtomInAminoacid, AtomInAminoacid>, BondType>();
foreach (var child in connection)
{
// this是38行的索引器的调用，即输入原子名字string(含后缀的)，返回对应的原子实例
connectDic.Add(new KeyValuePair <AtomInAminoacid, AtomInAminoacid>(this[child.Key.Key], this[child.Key.Value]), child.Value);
}
Connections = new ReadOnlyDictionary <KeyValuePair <AtomInAminoacid, AtomInAminoacid>, BondType>(connectDic);
}
public static Aminoacid Generate(AminoacidType type)
{
Aminoacid aminoacid = null;
if (!Aminoacids.TryGetValue(type, out aminoacid))
{
throw new ArgumentException("Unhandled AminoacidType:" + type.ToString());
}
return(Aminoacids[type]);
}
/// <summary>根据残基类型获取原子预制体</summary>
private GameObject GetAtomPrefeb(AminoacidType aminoacidType)
{
GameObject prefeb = null;
if (!AtomPrefebsDic.TryGetValue(aminoacidType, out prefeb))
{
prefeb = Resources.Load <GameObject>(string.Format("{0}/{1}", AtomSpherePrefebPath, aminoacidType.ToString()));
AtomPrefebsDic.Add(aminoacidType, prefeb);
}
return(AtomPrefebsDic[aminoacidType]);
}
/// <summary>从本地加载氨基酸数据 </summary>
public static async Task LoadDataAsync()
{
if (loaded)
{
throw new PolymerModelException("PolymerModel has been loaded");
}
string aminoacidData = await IOUtil.ReadInStreamingAssetsAsync(string.Empty, "Aminoacid.csv");
AminoacidDt = CSVHelper.ReadCSVStr(aminoacidData);
string connectionData = await IOUtil.ReadInStreamingAssetsAsync(string.Empty, "Connection.csv");
ConnectionDt = CSVHelper.ReadCSVStr(connectionData);
//将Connection数据表转化为字典，有助于后续的数据查找
Dictionary <string, List <DataRow> > connectionDic = new Dictionary <string, List <DataRow> >();
foreach (DataRow connectionDataRow in ConnectionDt.Rows)
{
string type = connectionDataRow["Type"].ToString();
if (!connectionDic.ContainsKey(type))
{
connectionDic.Add(type, new List <DataRow>());
}
connectionDic[type].Add(connectionDataRow);
}
//遍历氨基酸数据表 + connectionDic 一起构建氨基酸数据结构
foreach (DataRow aminoacidDataRow in AminoacidDt.Rows)
{
string type = aminoacidDataRow["Type"].ToString();
AminoacidType aminoacidType = (AminoacidType)Enum.Parse(typeof(AminoacidType), type);
string chinese = aminoacidDataRow["Chinese"].ToString();
bool isStandard = aminoacidDataRow["IsStandard"].ToString() == "1";
string[] atomNames = aminoacidDataRow["Atoms"].ToString().Trim('[', ']').Split(' ');
Dictionary <KeyValuePair <string, string>, BondType> connection = new Dictionary <KeyValuePair <string, string>, BondType>();
if (connectionDic.ContainsKey(type))
{
//若该残基包含键
foreach (DataRow connectionDataRow in connectionDic[type])
{
string firstAtom = connectionDataRow["First"].ToString();
string secondAtom = connectionDataRow["Second"].ToString();
BondType bondType = (BondType)Enum.Parse(typeof(BondType), connectionDataRow["BondType"].ToString());
connection.Add(new KeyValuePair <string, string>(firstAtom, secondAtom), bondType);
}
}
Aminoacid aminoacid = new Aminoacid(aminoacidType, chinese, isStandard, atomNames, connection);
Aminoacid.Aminoacids.Add(aminoacid.Type, aminoacid);
}
loaded = true;
}
private Material GetHighlightMaterial(AminoacidType aminoacidType)
{
return(GetAtomPrefeb(aminoacidType).GetComponent <AtomDisplayer>().highLight);
}
/// <summary>根据残基类型获取材质</summary>
private Material GetMaterial(AminoacidType aminoacidType)
{
return(GetAtomPrefeb(aminoacidType).GetComponent <AtomDisplayer>().normal);
}
//这里的position是真正坐标而不是pdb文件中读取的坐标
/// <summary>创建键</summary>
private GameObject GenerateBondGameObject(string name, Vector3 pos1, Vector3 pos2, BondType bondType, Transform parent, AminoacidType aminoacidType, DisplayMode displayMode)
{
GameObject bondGo = null;
Material material = GetMaterial(aminoacidType);
Material hightLightMaterial = GetHighlightMaterial(aminoacidType);
float bondLength = (pos1 - pos2).magnitude; //键长
Vector3 bondDirection = (pos1 - pos2).normalized; //键方向
//Sticks模式只创建单键
if (bondType == BondType.Single || displayMode == DisplayMode.Sticks)
{
bondGo = Instantiate(SingleBondPrefeb, parent, false);
}
else if (bondType == BondType.Double)
{
bondGo = Instantiate(DoubleBondPrefeb, parent, false);
}
else
{
throw new System.Exception("Unhandled bondType :" + bondType);
}
BondDisplayer bondDisplayer = bondGo.GetComponent <BondDisplayer>();
bondDisplayer.BondType = bondType;
bondDisplayer.normal = material;
bondDisplayer.highLight = hightLightMaterial;
bondGo.name = name;
foreach (Transform child in bondGo.transform)
{
child.GetComponent <Renderer>().material = material;
}
bondGo.transform.localPosition = (pos1 + pos2) / 2;
bondGo.transform.localScale = new Vector3(0.01f, 0.01f, bondLength / 2);
Vector3 targetPos = Vector3.Cross(bondDirection, Vector3.up) + (pos1 + pos2) / 2;
bondGo.transform.LookAt(pos1);
return(bondGo);
}
/// <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);
}
}
}
}
}
private Material GetMaterial(AminoacidType aminoacidType)
{
return(GetAtomPrefeb(aminoacidType).GetComponent <Renderer>().sharedMaterial);
}
