public override object VisitChain([NotNull] smilesParser.ChainContext context)
{
foreach (IParseTree tree in context.children)
{
if (typeof(smilesParser.ChainContext).IsAssignableFrom(tree.GetType()))
{
VisitChain((smilesParser.ChainContext)tree);
}
else if (typeof(smilesParser.Branched_atomContext).IsAssignableFrom(tree.GetType()))
{
VisitBranched_atom((smilesParser.Branched_atomContext)tree);
}
else if (typeof(smilesParser.BondContext).IsAssignableFrom(tree.GetType()))
{
nextBond = (BondType)VisitBond((smilesParser.BondContext)tree);
}
else if (typeof(smilesParser.DotContext).IsAssignableFrom(tree.GetType()))
{
nextBond = (BondType)VisitDot((smilesParser.DotContext)tree);
}
else
{
nextBond = BondType.Any;
}
}
return(null);
}
public Bond(Node thisNode, Node thatNode, BondType t, Orientation o)
{
Node1 = thisNode;
Node2 = thatNode;
Type = t;
Orientation = o;
}
public Bond AddBond(Atom atom, BondType type, BondStereo stereo, BondTopology topology, BondReactingCenterStatus rcStatus)
{
Bond b = new Bond(this, atom, type, BondStereo.NotStereoOrUseXYZ, BondTopology.Either, BondReactingCenterStatus.notACenter);
this.BondedAtoms.Add(b);
return(b);
}
public void Align(uint[] instanceIds, ChainType chainType, Vex.Point target, List <Bond> addedBonds, List <Bond> previousBonds)
{
BondAttachment bt = chainType.GetAttachment();
BondType bondType = chainType.IsAligned() ? BondType.Anchor : BondType.Spring;
Bond b;
Bond prev = null;
for (int i = 0; i < instanceIds.Length - 1; i++)
{
uint id = instanceIds[i];
if (chainType.IsDistributed())
{
if (i > 0)
{
RemoveCollidingBond(id, bt, previousBonds, BondType.Anchor);
}
if (i < instanceIds.Length - 1)
{
BondAttachment btOpp = chainType.GetOppositeAttachment();
RemoveCollidingBond(id, btOpp, previousBonds, BondType.Anchor);
}
}
else
{
RemoveCollidingBond(id, bt, previousBonds, BondType.Anchor);
}
b = new Bond(id, bt, bondType);
b.ChainType = chainType;
b.TargetLocation = target;
AddBond(b);
addedBonds.Add(b);
b.Previous = prev;
if (prev != null)
{
prev.Next = b;
}
prev = b;
}
int lastIndex = instanceIds.Length - 1;
uint lastId = instanceIds[lastIndex];
RemoveCollidingBond(lastId, bt, previousBonds, BondType.Anchor);
b = new Bond(lastId, bt, bondType);
b.ChainType = chainType;
b.TargetLocation = target;
AddBond(b);
addedBonds.Add(b);
b.Previous = prev;
prev.Next = b;
}
public BondLine(PointF p0, PointF p1, BondType bondType, BondAttachment attachment)
{
this.bondType = bondType;
this.attachment = attachment;
this.p0 = p0;
this.p1 = p1;
offset = Point.Empty;
GetOffset(p0, p1);
}
public Bond(Atom parent, Atom connectedAtom, BondType type, BondStereo stereo, BondTopology topology, BondReactingCenterStatus rcStatus)
{
ParentAtom = parent;
ConnectedAtom = connectedAtom;
BondType = type;
DrawType = type;
Stereo = stereo;
Topology = topology;
ReactingCenter = rcStatus;
BondLength = 0; // parent.CovalentRadius + connectedAtom.CovalentRadius;
}
/// <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;
}
public Bond(float x1 = 0, float y1 = 0, float x2 = 0, float y2 = 0, float thickness = 1.5f, SKColor?colour = null, BondType typeOfBond = BondType.Single, BondStyle subtype = BondStyle.Plain, int anchorID1 = -1, int anchorID2 = -1)
{
DiagramID = Program.DForm.CurrentDiagram.NextFreeID();
X1 = x1;
Y1 = y1;
X2 = x2;
Y2 = y2;
Thickness = thickness;
Colour = (colour == null) ? DefaultColour : colour.Value;
TypeOfBond = typeOfBond;
BondSubtype = subtype;
AnchorID1 = anchorID1;
AnchorID2 = anchorID2;
}
private static HandleIcon GetHandleIcon(BondType bt, TransformKind tk)
{
HandleIcon result;
switch (bt)
{
case BondType.Handle:
result = (tk == Enums.TransformKind.Scale) ? HandleIcon.Handle : HandleIcon.Rotate;
break;
case BondType.Join:
result = HandleIcon.Join;
break;
case BondType.Anchor:
result = HandleIcon.Anchor;
break;
case BondType.Lock:
result = HandleIcon.Lock;
break;
case BondType.Pin:
result = HandleIcon.Pin;
break;
case BondType.Spring:
result = HandleIcon.Spring;
break;
default:
result = HandleIcon.Handle;
break;
}
return(result);
}
public void GetBondTypesFromXML()
{
string path = "Assets/Resources/Data/Bonds.xml";
bondTypesDict = new Dictionary <string, BondType> ();
XDocument bondsX = FileIO.ReadXML(path);
XElement atomsX = bondsX.Element("elements");
string atomElement;
string otherElement;
string a0El;
string a1El;
foreach (XElement atomEl in atomsX.Elements("atom"))
{
atomElement = atomEl.Attribute("element").Value;
foreach (XElement otherEl in atomEl.Elements("other"))
{
otherElement = otherEl.Attribute("element").Value;
BondType bondType = new BondType();
XElement singleEl = otherEl.Element("single");
if (singleEl != null)
{
bondType.singleThresh = float.Parse(singleEl.Value);
}
XElement aromaticEl = otherEl.Element("aromatic");
if (aromaticEl != null)
{
bondType.aromaticThresh = float.Parse(aromaticEl.Value);
}
XElement doubleEl = otherEl.Element("double");
if (doubleEl != null)
{
bondType.doubleThresh = float.Parse(doubleEl.Value);
}
XElement tripleEl = otherEl.Element("triple");
if (tripleEl != null)
{
bondType.tripleThresh = float.Parse(tripleEl.Value);
}
a0El = string.Compare(atomElement, otherElement) > 0 ? atomElement : otherElement;
a1El = string.Compare(atomElement, otherElement) > 0 ? otherElement : atomElement;
string key = string.Format("{0}-{1}", a0El, a1El);
if (bondTypesDict.ContainsKey(key))
{
Debug.LogErrorFormat("Duplicate exists in XML file: {0} ({1})", path, key);
}
else
{
bondTypesDict.Add(key, bondType);
}
}
}
}
public Bond(BondType type)
{
Id = Guid.NewGuid();
Type = type;
isPriceAvailable = false;
}
public static void DoBond(BondType bondType, Reactor reactor, bool forRed)
{
foreach (PotentialBond potentialBond in GetPotentialBonds(reactor, bondType))
{
Molecule molecule1 = reactor.moleculeList.getMoleculeAtCoords(potentialBond.coords);
Molecule molecule2 = reactor.moleculeList.getMoleculeAtCoords(potentialBond.getCoordsOfOtherBonder());
if (molecule1 != null && molecule2 != null)
{
MoleculeDefinition resultMolecule = molecule1.GetTransformedDefinition(Vector2i.NULL);
if (bondType == BondType.Plus)
{
if (molecule1 != molecule2)
{
resultMolecule.CopyAtomsAndBonds(molecule2.GetTransformedDefinition(Vector2i.NULL));
}
BondCount numBonds = (BondCount)1;
// Math.Min(atom.bondCount(potentialBond).Value + 1, 3)
// aka increase bonds by 1 but not more than 3
if (resultMolecule.GetBondCount(potentialBond).HasValue)
{
numBonds = (BondCount)Math.Min((int)(resultMolecule.GetBondCount(potentialBond).Value + 1), 3);
}
if (resultMolecule.SetBondCountWithMaxBondsCheck(potentialBond, numBonds))
{
reactor.moleculeList.Remove(molecule1);
if (molecule1 != molecule2)
{
reactor.moleculeList.Remove(molecule2);
}
reactor.moleculeList.Add(new Molecule(resultMolecule, reactor));
reactor.AddBondEffect((potentialBond.coords + potentialBond.getCoordsOfOtherBonder()) * 0.5f, BondEffectStyle.Plus, forRed);
}
else
{
reactor.AddBondEffect((potentialBond.coords + potentialBond.getCoordsOfOtherBonder()) * 0.5f, BondEffectStyle.MaxBonds, forRed);
// The next line is the only change in this method, and should fix the telekinesis bug.
// If both waldos hold the same molecule and we allow execution to continue to the next foreach,
// the following would happen:
// 1. The pull vectors of the molecule are cleared.
// 2. The red waldo adds itself to the molecule's pull vectors in GrabDrop().
// 3. The pull vectors of the molecule are cleared _again_, removing the red waldo.
// 4. The blue waldo adds itself to the molecule's pull vectors in GrabDrop().
// The end result is that the game thinks only blue is holding the molecule, triggering the telekinesis bug.
// It's safe to skip this foreach since hitting max bonds means no molecule was changed and the current pull vectors are still OK.
continue;
}
}
// bondType != BondType.Plus
else if (molecule1 == molecule2 && resultMolecule.GetBondCount(potentialBond).HasValue)
{
reactor.moleculeList.Remove(molecule1);
int newBondCount = (int)(resultMolecule.GetBondCount(potentialBond).Value - 1);
if (newBondCount < 1)
{
foreach (MoleculeDefinition newMolecule in MoleculeDefinition.BreakBond(resultMolecule, potentialBond))
{
reactor.moleculeList.Add(new Molecule(newMolecule, reactor));
}
}
else
{
resultMolecule.SetBondCount(potentialBond, new BondCount?((BondCount)newBondCount));
reactor.moleculeList.Add(new Molecule(resultMolecule, reactor));
}
reactor.AddBondEffect((potentialBond.coords + potentialBond.getCoordsOfOtherBonder()) * 0.5f, BondEffectStyle.Minus, forRed);
}
else
{
continue;
}
foreach (Waldo waldo in reactor.waldos.Values)
{
if (waldo.molecule != null)
{
waldo.molecule.WaldoPullVectors.Clear();
waldo.molecule = null;
waldo.GrabDrop();
}
}
}
}
if (isBonderFeatureCache == null)
{
isBonderFeatureCache = new Func <ReactorMember, bool>(IsBonderFeature);
}
foreach (BonderFeature bonderFeature in reactor.GetMembers().Where(isBonderFeatureCache).Cast <BonderFeature>())
{
bonderFeature.Activate(forRed);
}
}
public static LinkedList <PotentialBond> GetPotentialBonds(Reactor reactor, BondType bondType)
{
return(null);
}
public BondInstruction(Reactor reactor, BondType bondType)
{
}
/// <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;
}
//static Molecule ReadMoleFile(string filename)
//{
// using (var reader = new System.IO.StreamReader(filename))
// {
// string s = reader.ReadToEnd();
// if (s.Contains("V2000")) return MoleFileReader.ParseMoleFile2(s);
// if (s.Contains("V3000")) throw new Exception("Version 3000 Mol file is currently not supported.");
// throw new Exception("Mol file type not recognized. It is does not contain a version number.");
// }
//}
static Molecule ParseMoleFile2(string moleFile)
{
Molecule molecule = new Molecule();
//atoms.Clear();
//cycles.Clear();
//fusedRings.Clear();
int numAtoms = 0;
int numBonds = 0;
// This information is contained in the header (first 3 lines) of the mol file. It is currently not being used, but code has been created for
// future use.
string name = string.Empty;
string program = string.Empty;
string user = string.Empty;
//// used to test Line 2 reading below.
//string MM = string.Empty;
//string DD = string.Empty;
//string YY = string.Empty;
//string HH = string.Empty;
//string mm = string.Empty;
int MM = 1;
int DD = 1;
int YY = 0;
int HH = 0;
int mm = 0;
string dimensionalCodes = string.Empty;
//// used to test Line 2 reading below.
//string scalingFactor1 = string.Empty;
int scalingFactor1 = 0;
//// used to test Line 2 reading below.
//string scalingFactor2 = string.Empty;
double scalingFactor2 = 0;
// used to test Line 2 reading below.
string energy = string.Empty;
string registryNumber = string.Empty;
string comments = string.Empty;
string[] lines = moleFile.Split('\n');
// Line 1 contains the compound name. It can not be longer than 80 characters, and is allowed to be empty.
// The length of the line is not relevant in how this is read, so it is not checked.
name = lines[0];
//// used to test Line 2 reading below.
//lines[1] = "IIPPPPPPPPMMDDYYHHmmddSSssssssssssEEEEEEEEEEEERRRRRR";
// Line 2 is optional. Skip this if it is not there.
if (lines[1] != string.Empty)
{
// Line format: IIPPPPPPPPMMDDYYHHmmddSSssssssssssEEEEEEEEEEEERRRRRR
// A2<--A8--><---A10-->A2I2<--F10.5-><---F12.5--><-I6->
//User's first and last initials (l), program name (P), date/time (M/D/Y,H:m),
//dimensional codes (d), scaling factors (S, s), energy (E) if modeling program input,
//internal registry number (R) if input through MDL form.
if (lines[1].Length > 2)
{
user = lines[1].Substring(0, 2); // II
}
if (lines[1].Length > 10)
{
program = lines[1].Substring(2, 8); // PPPPPPPP
}
if (lines[1].Length > 20)
{
//// used to test Line 2 reading below.
//MM = lines[1].Substring(10, 2); // MMDDYYHHmm
//DD = lines[1].Substring(12, 2); // MMDDYYHHmm
//YY = lines[1].Substring(14, 2); // MMDDYYHHmm
//HH = lines[1].Substring(16, 2); // MMDDYYHHmm
//mm = lines[1].Substring(18, 2); // MMDDYYHHmm
MM = Convert.ToInt32(lines[1].Substring(10, 2)); // MMDDYYHHmm
DD = Convert.ToInt32(lines[1].Substring(12, 2)); // MMDDYYHHmm
YY = Convert.ToInt32(lines[1].Substring(14, 2)); // MMDDYYHHmm
HH = Convert.ToInt32(lines[1].Substring(16, 2)); // MMDDYYHHmm
mm = Convert.ToInt32(lines[1].Substring(18, 2)); // MMDDYYHHmm
}
if (lines[1].Length > 22)
{
dimensionalCodes = lines[1].Substring(20, 2); // dd
}
//// used to test Line 2 reading below.
// if (lines[1].Length > 24) scalingFactor1 = lines[1].Substring(22, 2); //SS
if (lines[1].Length > 24)
{
scalingFactor1 = Convert.ToInt32(lines[1].Substring(22, 2)); //SS
}
//// used to test Line 2 reading below.
// if (lines[1].Length > 34) scalingFactor2 = lines[1].Substring(24, 10); //ss
if (lines[1].Length > 34)
{
scalingFactor2 = Convert.ToDouble(lines[1].Substring(24, 10)); //ss
}
if (lines[1].Length > 46)
{
energy = lines[1].Substring(34, 12); //EEEEEEEEEEEE
}
if (lines[1].Length == 52)
{
registryNumber = lines[1].Substring(46, 6); //RRRRRR
}
}
comments = lines[2];
// Counts Line
// aaabbblllfffcccsssxxxrrrpppiiimmmvvvvvv
numAtoms = Convert.ToInt32(lines[3].Substring(0, 3));
numBonds = Convert.ToInt32(lines[3].Substring(3, 3));
int atomLists = Convert.ToInt32(lines[3].Substring(6, 3));
//int fObsolete = Convert.ToInt32(lines[3].Substring(9, 3));
bool chiral = false;
if (Convert.ToInt32(lines[3].Substring(12, 3)) == 1)
{
chiral = true;
}
int sText = Convert.ToInt32(lines[3].Substring(15, 3));
//int xObsolete = Convert.ToInt32(lines[3].Substring(18, 3));
//int rObsolete = Convert.ToInt32(lines[3].Substring(21, 3));
//int pObsolete = Convert.ToInt32(lines[3].Substring(24, 3));
//int iObsolete = Convert.ToInt32(lines[3].Substring(27, 3));
int properties = Convert.ToInt32(lines[3].Substring(30, 3));
string version = lines[3].Substring(33, 6);
for (int i = 0; i < numAtoms; i++)
{
Atom a = new ChemInfo.Atom(lines[4 + i].Substring(31, 3).Trim());
molecule.AddAtom(a);
// xxxxx.xxxxyyyyy.yyyyzzzzz.zzzz aaaddcccssshhhbbbvvvHHHrrriiimmmnnneee
//a.x = Convert.ToDouble(lines[4 + i].Substring(0, 10));
//a.y = Convert.ToDouble(lines[4 + i].Substring(10, 10));
//a.z = Convert.ToDouble(lines[4 + i].Substring(20, 10));
string text = lines[4 + i].Substring(34, 2);
a.MassDiff = Convert.ToInt32(lines[4 + i].Substring(34, 2));
a.Charge = Convert.ToInt32(lines[4 + i].Substring(36, 3));
a.StereoParity = Convert.ToInt32(lines[4 + i].Substring(39, 3));
a.HydrogenCount = Convert.ToInt32(lines[4 + i].Substring(42, 3));
a.StereoCareBox = Convert.ToInt32(lines[4 + i].Substring(45, 3));
//a.Valence = Convert.ToInt32(lines[4 + i].Substring(48, 3));
// string H0 = lines[4 + i].Substring(51, 3);
// a.HO = Convert.ToInt32(lines[4 + i].Substring(51, 3));
a.RNotUsed = lines[4 + i].Substring(54, 3);
a.INotUsed = lines[4 + i].Substring(57, 3);
a.AtomMapping = Convert.ToInt32(lines[4 + i].Substring(60, 3));
a.InversionRetension = Convert.ToInt32(lines[4 + i].Substring(63, 3));
a.ExactChange = Convert.ToInt32(lines[4 + i].Substring(66, 3));
}
for (int i = 0; i < numBonds; i++)
{
//Bond b = new Bond();
// 111222tttsssxxxrrrccc
string line = lines[4 + numAtoms + i];
int firstAtom = Convert.ToInt32(lines[4 + numAtoms + i].Substring(0, 3));
int secondAtom = Convert.ToInt32(lines[4 + numAtoms + i].Substring(3, 3));
BondType bondType = (BondType)Convert.ToInt32(lines[4 + numAtoms + i].Substring(6, 3));
BondStereo bondStereo = (BondStereo)Convert.ToInt32(lines[4 + numAtoms + i].Substring(9, 3));
string xNotUsed = lines[4 + numAtoms + i].Substring(12, 3);
BondTopology bondTopology = (BondTopology)Convert.ToInt32(lines[4 + numAtoms + i].Substring(15, 3));
int rc = Convert.ToInt32(lines[4 + numAtoms + i].Substring(18, 3));
BondReactingCenterStatus reactingCenter = BondReactingCenterStatus.Unmarked;
if (rc == 13)
{
reactingCenter = BondReactingCenterStatus.bondMadeOrBroken | BondReactingCenterStatus.bondOrderChanges | BondReactingCenterStatus.aCenter;
}
else if (rc == 12)
{
reactingCenter = BondReactingCenterStatus.bondMadeOrBroken | BondReactingCenterStatus.bondOrderChanges;
}
else if (rc == 9)
{
reactingCenter = BondReactingCenterStatus.bondOrderChanges | BondReactingCenterStatus.aCenter;
}
else if (rc == 5)
{
reactingCenter = BondReactingCenterStatus.bondMadeOrBroken | BondReactingCenterStatus.aCenter;
}
else
{
reactingCenter = (BondReactingCenterStatus)rc;
}
molecule.AddBond(molecule.Atoms[firstAtom - 1], molecule.Atoms[secondAtom - 1], bondType, bondStereo, bondTopology, reactingCenter);
}
molecule.FindRings();
return(molecule);
}
public Bond(uint sourceInstanceId, BondAttachment sourceAttachment, BondType bondType)
{
this.sourceInstanceId = sourceInstanceId;
this.sourceAttachment = sourceAttachment;
this.bondType = bondType;
}
private bool RemoveCollidingBond(uint instanceId, BondAttachment attachment, List <Bond> previousBonds, BondType newBondType)
{
bool result = true;
if (!attachment.IsGuide() && bonds.ContainsKey(instanceId))
{
Bond cb = null;
foreach (Bond b in bonds[instanceId])
{
cb = b.GetCollidingBond(attachment);
if (cb != null)
{
break;
}
}
if (cb != null)
{
bool oldIsFlow = cb.ChainType != ChainType.None;
bool newIsLock = newBondType == BondType.Lock;
// locks can't break flow bonds
if (oldIsFlow && newIsLock)
{
result = false;
}
else
{
RemoveBond(cb);
previousBonds.Add(cb);
}
}
}
return(result);
}
//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);
}
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 Bond(uint sourceInstanceId, BondAttachment sourceAttachment, BondType bondType)
{
this.sourceInstanceId = sourceInstanceId;
this.sourceAttachment = sourceAttachment;
this.bondType = bondType;
}
public Bond(Node thisNode, Node thatNode, BondType t)
{
Node1 = thisNode;
Node2 = thatNode;
Type = t;
}
//public override object VisitBracket_atom(smilesParser.Bracket_atomContext context)
//{
// string symbol = string.Empty;
// Chirality ch = Chirality.UNSPECIFIED;
// int isotope = 0;
// int hCount = 0;
// int charge = 0;
// int atomClass = 0;
// foreach (IParseTree tree in context.children)
// {
// if (typeof(smilesParser.SymbolContext).IsAssignableFrom(tree.GetType()))
// {
// symbol = (string)VisitSymbol((smilesParser.SymbolContext)tree);
// }
// if (typeof(smilesParser.ChiralContext).IsAssignableFrom(tree.GetType()))
// {
// ch = (Chirality)VisitChiral((smilesParser.ChiralContext)tree);
// }
// if (typeof(smilesParser.IsotopeContext).IsAssignableFrom(tree.GetType()))
// {
// isotope = (int)VisitIsotope((smilesParser.IsotopeContext)tree);
// }
// if (typeof(smilesParser.HcountContext).IsAssignableFrom(tree.GetType()))
// {
// hCount = (int)VisitHcount((smilesParser.HcountContext)tree);
// }
// if (typeof(smilesParser.ChargeContext).IsAssignableFrom(tree.GetType()))
// {
// charge = (int)VisitCharge((smilesParser.ChargeContext)tree);
// }
// if (typeof(smilesParser.AtomclassContext).IsAssignableFrom(tree.GetType()))
// {
// atomClass = (int)VisitAtomclass((smilesParser.AtomclassContext)tree);
// }
// }
// return new Atom(symbol, AtomType.NONE, isotope, ch, hCount, charge, atomClass);
//}
public override object VisitBranch([NotNull] smilesParser.BranchContext context)
{
if (context.ChildCount == 3)
{
if (typeof(smilesParser.ChainContext).IsAssignableFrom(context.GetChild(1).GetType()))
{
return(VisitChain((smilesParser.ChainContext)context.GetChild(1)));
}
return(VisitBranch((smilesParser.BranchContext)context.GetChild(1)));
}
if (typeof(smilesParser.BondContext).IsAssignableFrom(context.GetChild(1).GetType()))
{
if (context.GetChild(1).GetText() == "\\")
{
if (string.IsNullOrEmpty(cisTrans))
{
cisTrans = "/";
}
else
{
if (context.GetText() == cisTrans)
{
if (((doubleBonds.Count - 1) % 2) == 0)
{
foreach (Bond b in doubleBonds)
{
b.Stereo = BondStereo.cis;
}
}
}
else
{
if (((doubleBonds.Count - 1) % 2) == 0)
{
foreach (Bond b in doubleBonds)
{
b.Stereo = BondStereo.trans;
}
}
}
cisTrans = string.Empty;
doubleBonds.Clear();
}
}
else if (context.GetChild(1).GetText() == "/")
{
if (string.IsNullOrEmpty(cisTrans))
{
cisTrans = "\\";
}
else
{
if (context.GetText() == cisTrans)
{
if (((doubleBonds.Count - 1) % 2) == 0)
{
foreach (Bond b in doubleBonds)
{
b.Stereo = BondStereo.cis;
}
}
}
else
{
if (((doubleBonds.Count - 1) % 2) == 0)
{
foreach (Bond b in doubleBonds)
{
b.Stereo = BondStereo.trans;
}
}
}
cisTrans = string.Empty;
doubleBonds.Clear();
}
}
else
{
nextBond = (BondType)VisitBond((smilesParser.BondContext)context.GetChild(1));
}
return(VisitChain((smilesParser.ChainContext)context.GetChild(2)));
}
nextBond = (BondType)VisitDot((smilesParser.DotContext)context.GetChild(1));
return(VisitChain((smilesParser.ChainContext)context.GetChild(2)));
}
public override object VisitBranched_atom([NotNull] smilesParser.Branched_atomContext context)
{
foreach (IParseTree tree in context.children)
{
if (typeof(smilesParser.AtomContext).IsAssignableFrom(tree.GetType()))
{
Atom current = (Atom)VisitAtom((smilesParser.AtomContext)tree);
if (current.Element != ELEMENTS.H)
{
retVal.AddAtom(current);
if (addExplicitHToNext)
{
current.ExplicitHydrogens++;
addExplicitHToNext = false;
}
if (last != null)
{
if (last.AtomType == AtomType.AROMATIC && current.AtomType == AtomType.AROMATIC)
{
nextBond = BondType.Aromatic;
}
}
Bond b = retVal.AddBond(last, current, nextBond, BondStereo.NotStereoOrUseXYZ, BondTopology.Either, BondReactingCenterStatus.Unmarked);
if (!string.IsNullOrEmpty(cisTrans) && nextBond == BondType.Double)
{
doubleBonds.Add(b);
}
nextBond = BondType.Single;
last = current;
}
else
{
if (last != null)
{
last.ExplicitHydrogens++;
}
else
{
addExplicitHToNext = true;
}
}
}
else if (typeof(smilesParser.RingbondContext).IsAssignableFrom(tree.GetType()))
{
int ring = (int)VisitRingbond((smilesParser.RingbondContext)tree);
if (ringAtoms.ContainsKey(ring))
{
BondType nextType = (BondType)ringbonds[ring];
if (nextType != BondType.Single && (nextBond == BondType.Single || nextBond == nextType))
{
nextBond = nextType;
}
Bond b = retVal.AddBond(last, (Atom)ringAtoms[ring], nextBond, BondStereo.NotStereoOrUseXYZ, BondTopology.Either, BondReactingCenterStatus.Unmarked);
if (!string.IsNullOrEmpty(cisTrans) && nextBond == BondType.Double)
{
doubleBonds.Add(b);
}
nextBond = BondType.Single;
ringAtoms.Remove(ring);
ringbonds.Remove(ring);
}
else
{
ringAtoms.Add(ring, last);
ringbonds.Add(ring, nextBond);
nextBond = BondType.Single;
}
}
else if (typeof(smilesParser.BranchContext).IsAssignableFrom(tree.GetType()))
{
Atom temp = last;
VisitBranch((smilesParser.BranchContext)tree);
last = temp;
}
else if (typeof(smilesParser.BondContext).IsAssignableFrom(tree.GetType()))
{
nextBond = (BondType)VisitBond((smilesParser.BondContext)context.GetChild(1));
}
else
{
throw new System.InvalidOperationException("uhoh");
}
}
return(null);
}
} // End of Awake().
public void Update()
{
Vector3 vectorAtoB = nodeB.transform.position - nodeA.transform.position;
dirAtoB = vectorAtoB.normalized;
float bondLength = vectorAtoB.magnitude;
// The following billboards the bond graphic with the camera.
Quaternion bondDirection = Quaternion.LookRotation(nodeB.transform.position - nodeA.transform.position);
bondBillboard.rotation = bondDirection;
bondBillboard.position = nodeA.transform.position + (vectorAtoB * 0.5f);
bondBillboard.rotation *= Quaternion.AngleAxis(90, Vector3.up);
Vector3 camRelativePos = bondBillboard.InverseTransformPoint(Camera.main.transform.position);
float arcBillboardAngle = Mathf.Atan2(camRelativePos.z, camRelativePos.y) * Mathf.Rad2Deg;
bondBillboard.rotation *= Quaternion.AngleAxis(arcBillboardAngle + 90, Vector3.right);
Vector3 bondBillboardScale = new Vector3(bondLength * signalLink, bondWidth, 1f);
bondBillboard.localScale = bondBillboardScale;
// DEBUG - attraction is a constant.
float attraction = 12.0f;
nodeA.rigidbody.AddForce(vectorAtoB.normalized * attraction);
nodeB.rigidbody.AddForce(-vectorAtoB.normalized * attraction);
// Determine calorie transfer.
float calorieTransferStrength = attraction * 0.03f;
float calorieTransfer = (nodeB.calories - nodeA.calories) * calorieTransferStrength;
nodeA.caloriesDelta += calorieTransfer;
nodeB.caloriesDelta += -calorieTransfer;
// Different effects based on bond type.
if ((nodeA.nodeType == NodeType.sense) && (nodeB.nodeType == NodeType.control) ||
(nodeB.nodeType == NodeType.sense) && (nodeA.nodeType == NodeType.control))
{
// Signal Bond
// Sense -> Control
bondType = BondType.signal;
bondBillboard.renderer.material = GameManager.graphics.signalBondMat;
if (nodeA.nodeType == NodeType.sense)
{
signalLink = 1;
if (nodeA.signal > nodeB.synapse)
{
nodeB.synapse = nodeA.signal;
}
}
else
{
signalLink = -1;
if (nodeB.signal > nodeA.synapse)
{
nodeA.synapse = nodeB.signal;
}
}
}
else
if ((nodeA.nodeType == NodeType.control) && (nodeB.nodeType == NodeType.muscle) ||
(nodeB.nodeType == NodeType.control) && (nodeA.nodeType == NodeType.muscle))
{
// Synapse bond
// Control -> Muscle
bondType = BondType.synapse;
bondBillboard.renderer.material = GameManager.graphics.synapseBondMat;
if (nodeA.nodeType == NodeType.control)
{
signalLink = 1;
if (nodeA.synapse > nodeB.thrust)
{
nodeB.thrust = nodeA.synapse;
}
nodeB.thrust = Mathf.Clamp(nodeB.thrust, 0.1f, Mathf.Infinity);
nodeB.rigidbody.AddForce(-vectorAtoB * 10f * nodeB.thrust);
}
else
{
signalLink = -1;
if (nodeB.synapse > nodeA.thrust)
{
nodeA.thrust = nodeB.synapse;
}
nodeA.thrust = Mathf.Clamp(nodeA.thrust, 0.1f, Mathf.Infinity);
nodeA.rigidbody.AddForce(vectorAtoB * 10f * nodeA.thrust);
}
}
else
if ((nodeA.nodeType == NodeType.control) && (nodeB.nodeType == NodeType.control))
{
// Synapse propogation bond
// Control <-> Control
bondType = BondType.synapsePropogate;
bondBillboard.renderer.material = GameManager.graphics.synapsePropBondMat;
if (nodeA.synapse > nodeB.synapse)
{
nodeB.synapse = nodeA.synapse;
}
else
{
nodeA.synapse = nodeB.synapse;
}
}
else
if ((nodeA.nodeType == NodeType.muscle) && (nodeB.nodeType == NodeType.muscle))
{
// Muscle propogation bond
// Muscle <-> Muscle
bondType = BondType.thrustPropogate;
bondBillboard.renderer.material = GameManager.graphics.thrustPropBondMat;
if (nodeA.thrust > nodeB.thrust)
{
nodeB.thrust = nodeA.thrust;
}
else
{
nodeA.thrust = nodeB.thrust;
}
}
else
{
// Not a functional bond.
bondBillboard.renderer.material = GameManager.graphics.uselessBondMat;
bondType = BondType.useless;
}
} // End of Update().
