/// <summary>
/// Matrices to generate PISA Assembly given an assemblySeqID
/// </summary>
/// <param name="pdbId"></param>
/// <returns></returns>
public Dictionary <string, List <SymOpMatrix> > GetPisaBuMatrices(string pdbId, string assemblySeqId, DataTable buMatrixTable)
{
DataRow[] buMatrixRows = buMatrixTable.Select(string.Format("PdbID = '{0}' AND AssemblySeqID = '{1}'",
pdbId, assemblySeqId));
Dictionary <string, List <SymOpMatrix> > assemblyMatricesHash = new Dictionary <string, List <SymOpMatrix> >();
string asymChain = "";
string matrixString = "";
SymOpMatrix symOpMatrix = null;
foreach (DataRow dRow in buMatrixRows)
{
asymChain = dRow["AsymChain"].ToString().Trim();
matrixString = dRow["Matrix"].ToString().Trim();
symOpMatrix = GetCoordSymOpMatrix(matrixString);
symOpMatrix.symmetryString = dRow["SymmetryString"].ToString().TrimEnd();
symOpMatrix.symmetryOpNum = dRow["SymOpSeqID"].ToString().TrimEnd();
if (assemblyMatricesHash.ContainsKey(asymChain))
{
assemblyMatricesHash[asymChain].Add(symOpMatrix);
}
else
{
List <SymOpMatrix> matrixList = new List <SymOpMatrix> ();
matrixList.Add(symOpMatrix);
assemblyMatricesHash.Add(asymChain, matrixList);
}
}
return(assemblyMatricesHash);
}
/// <summary>
/// convert a symmetry operator to a full symmetry string
/// 1_656 to 1+X,Y,1+Z based on the symmetry matrices
/// </summary>
/// <param name="symOpMatrices"></param>
/// <param name="symOpString"></param>
/// <returns></returns>
public string ConvertSymOpStringToFull(SymOpMatrix[] symOpMatrices, string symOpString)
{
SymOpMatrix fullSymOpMatrix = GetSymmetryMatrixFromSymmetryString(symOpMatrices, symOpString);
string fullSymString = fullSymOpMatrix.ToFullSymString();
return(FormatFullSymString(fullSymString));
}
/// <summary>
///
/// </summary>
/// <param name="asuTable"></param>
/// <returns></returns>
private Dictionary <string, Dictionary <string, List <SymOpMatrix> > > GetEntryAsuComponentInfoHash(DataTable asuTable)
{
Dictionary <string, Dictionary <string, List <SymOpMatrix> > > asuInfoHash = new Dictionary <string, Dictionary <string, List <SymOpMatrix> > > ();
Dictionary <string, List <SymOpMatrix> > chainMatrixHash = new Dictionary <string, List <SymOpMatrix> > ();
string buId = "1";
string asymChain = "";
SymOpMatrix symOpMatrix = null;
foreach (DataRow asuRow in asuTable.Rows)
{
asymChain = asuRow["AsymID"].ToString().TrimEnd();
symOpMatrix = GetOrigCoordSymOpMatrix();
symOpMatrix.symmetryString = "1_555";
symOpMatrix.symmetryOpNum = "1";
if (chainMatrixHash.ContainsKey(asymChain))
{
chainMatrixHash[asymChain].Add(symOpMatrix);
}
else
{
List <SymOpMatrix> matrixList = new List <SymOpMatrix> ();
matrixList.Add(symOpMatrix);
chainMatrixHash.Add(asymChain, matrixList);
}
}
asuInfoHash.Add(buId, chainMatrixHash);
return(asuInfoHash);
}
/// <summary>
/// apply cartesian symmetry operators on cartesian coordinates
/// directly to provide transformed cartesian coordinate
/// </summary>
/// <param name="symOpMatrix"></param>
/// <param name="fractTransMatrix"></param>
/// <param name="cartnInverseMatrix"></param>
/// <returns></returns>
public AtomInfo TransformAtom(SymOpMatrix symOpMatrix)
{
AtomInfo transformedAtom = (AtomInfo)this.Clone();;
transformedAtom.xyz = symOpMatrix * this.xyz;
return(transformedAtom);
}
/// <summary>
/// Matrices to generate PISA Assembly given an assemblySeqID
/// </summary>
/// <param name="pdbId"></param>
/// <returns></returns>
public Dictionary <string, List <SymOpMatrix> > GetPisaBuMatrices(string pdbId, string assemblySeqId)
{
string queryString = string.Format("Select * From PisaBuMatrix " +
" Where PdbID = '{0}' AND AssemblySeqID = {1};", pdbId, assemblySeqId);
DataTable pisaBusTable = ProtCidSettings.pdbfamQuery.Query(queryString);
Dictionary <string, List <SymOpMatrix> > assemblyMatricesHash = new Dictionary <string, List <SymOpMatrix> > ();
string asymChain = "";
string matrixString = "";
SymOpMatrix symOpMatrix = null;
foreach (DataRow dRow in pisaBusTable.Rows)
{
asymChain = dRow["AsymChain"].ToString().Trim();
matrixString = dRow["Matrix"].ToString().Trim();
symOpMatrix = GetCoordSymOpMatrix(matrixString);
symOpMatrix.symmetryString = dRow["SymmetryString"].ToString().TrimEnd();
symOpMatrix.symmetryOpNum = dRow["SymOpSeqId"].ToString().TrimEnd();
if (assemblyMatricesHash.ContainsKey(asymChain))
{
assemblyMatricesHash[asymChain].Add(symOpMatrix);
}
else
{
List <SymOpMatrix> matrixList = new List <SymOpMatrix> ();
matrixList.Add(symOpMatrix);
assemblyMatricesHash.Add(asymChain, matrixList);
}
}
return(assemblyMatricesHash);
}
/// <summary>
/// get symmetry matrix for a specific symmetry operation string
/// may need translation
/// linear search
/// </summary>
/// <param name="symOpMatrices"></param>
/// <param name="symOpString"></param>
/// <returns></returns>
public SymOpMatrix GetSymmetryMatrixFromSymmetryString(SymOpMatrix[] symOpMatrices, string symOpString)
{
int index1 = symOpString.IndexOf("_");
int index2 = symOpString.LastIndexOf("_");
string symOpNum = "";
string symString = "";
if (index1 == index2)
{
symOpNum = symOpString.Substring(0, index1);
symString = symOpString.Substring(index1 + 1, symOpString.Length - index1 - 1);
}
else
{
symOpNum = symOpString.Substring(index1 + 1, index2 - index1 - 1);
symString = symOpString.Substring(index2 + 1, symOpString.Length - index2 - 1);
}
SymOpMatrix convertedSymOpMatrix = null;
foreach (SymOpMatrix symOpMatrix in symOpMatrices)
{
if (symOpMatrix.symmetryOpNum == symOpNum)
{
convertedSymOpMatrix = (SymOpMatrix)symOpMatrix.Clone();
break;
}
}
if (convertedSymOpMatrix != null)
{
if (symString.Length == 3)
{
for (int i = 0; i < 3; i++)
{
if (symString[i] == '5')
{
continue;
}
convertedSymOpMatrix.Add(i, 3, convertedSymOpMatrix.Value(i, 3) + (double)(Convert.ToInt32(symString[i].ToString()) - 5));
}
}
/* should deal with a symmetry string with translate vectors > 5
* format of this type of symmetry string: 1_+10-1+6
* translate vector (+5, -6, +1)
*/
else if (symString.Length > 3)
{
string[] vectStrings = SeparateSymmetryString(symString);
convertedSymOpMatrix.Add(0, 3, convertedSymOpMatrix.Value(0, 3) +
(double)(Convert.ToInt32(vectStrings[0]) - 5));
convertedSymOpMatrix.Add(1, 3, convertedSymOpMatrix.Value(1, 3) +
(double)(Convert.ToInt32(vectStrings[1]) - 5));
convertedSymOpMatrix.Add(2, 3, convertedSymOpMatrix.Value(2, 3) +
(double)(Convert.ToInt32(vectStrings[2]) - 5));
}
}
return(convertedSymOpMatrix);
}
/// <summary>
/// build a PDB biological unit
/// by applying the symmetry operations provided in XML
/// </summary>
/// <param name="chainAtomsList">chains in XML</param>
/// <param name="buGenStructList">symmetry operations</param>
/// <param name="buSymmetryMatrixList">symmetry matrix</param>
/// <returns>biological units with corresponding chains</returns>
/// </summary>
private Dictionary <string, AtomInfo[]> BuildFullPdbBuByPdbSymOps(string pdbId, string biolUnitId, EntryCrystal thisEntryCrystal)
{
Dictionary <string, AtomInfo[]> buHash = null;
ChainAtoms[] chainAtomsList = thisEntryCrystal.atomCat.ChainAtomList;
BuGenStruct[] buGenStructList = thisEntryCrystal.buGenCat.BuGenStructList;
List <string> symOpStrList = new List <string> ();
List <string> fullSymOpStrList = new List <string> ();
List <SymOpMatrix> symOpMatrixList = new List <SymOpMatrix> ();
for (int asymCount = 0; asymCount < buGenStructList.Length; asymCount++)
{
if (biolUnitId != buGenStructList[asymCount].biolUnitId)
{
continue;
}
string asymId = buGenStructList[asymCount].asymId;
foreach (ChainAtoms chain in chainAtomsList)
{
if (chain.AsymChain == asymId)
{
SymOpMatrix symOpMatrix =
thisEntryCrystal.buGenCat.FindSymOpMatrix(buGenStructList[asymCount].symOperId);
if (symOpMatrix == null)
{
fullSymOpStrList.Add(buGenStructList[asymCount].symmetryMatrix);
symOpStrList.Add(asymId + "_" + buGenStructList[asymCount].symmetryString);
}
else
{
if (symOpMatrix.symmetryString == "" || symOpMatrix.symmetryString == "-")
{
// put the symmetry operator id if the symmetry string is empty
symOpStrList.Add(asymId + "_" + buGenStructList[asymCount].symOperId);
}
else
{
symOpStrList.Add(asymId + "_" + symOpMatrix.symmetryString);
}
symOpMatrixList.Add(symOpMatrix);
}
}
}
}
string[] symOpStrings = symOpStrList.ToArray();
if (symOpMatrixList.Count > 0)
{
buHash = BuildPdbBu(thisEntryCrystal, symOpStrings, symOpMatrixList.ToArray());
}
else if (fullSymOpStrList.Count > 0)
{
buHash = BuildPdbBu(thisEntryCrystal, symOpStrings, fullSymOpStrList.ToArray());
}
return(buHash);
}
/// <summary>
///
/// </summary>
/// <param name="fullSymOpString">X-1,Y,Z+1</param>
/// <param name="spaceGroup"></param>
/// <returns>e.g. 1_456</returns>
public string ConvertFullSymOpStringToShort(string fullSymOpString, string spaceGroup)
{
SymOpMatrix symOpMatrix = new SymOpMatrix();
symOpMatrix.fullSymmetryString = fullSymOpString;
SetSymOpMatrix(fullSymOpString, ref symOpMatrix);
string symString = ConvertMatrixToSymString(symOpMatrix, 1);
return(symString);
}
/// <summary>
/// are these two symmetry operator matrices same
/// </summary>
/// <param name="symOp1"></param>
/// <param name="symOp2"></param>
/// <returns></returns>
private bool AreSymOpMatricesSame(SymOpMatrix symOp1, SymOpMatrix symOp2)
{
int compResult = string.Compare(symOp1.fullSymmetryString, symOp2.fullSymmetryString, true);
if (compResult == 0)
{
return(true);
}
return(false);
}
/// <summary>
/// transform a protein chain by applying a specific symmetry operation
/// either from PDB xml or from a user-defined
/// </summary>
/// <param name="chainCoordList"></param>
/// <param name="symMatrix"></param>
/// <returns></returns>
public AtomInfo[] TransformChainBySpecificSymOp(AtomInfo[] chainAtomList, SymOpMatrix symMatrix)
{
AtomInfo[] transformedAtomList = new AtomInfo [chainAtomList.Length];
for (int atomI = 0; atomI < chainAtomList.Length; atomI++)
{
AtomInfo thisAtomInfo = chainAtomList[atomI].TransformAtom(symMatrix, cartn2fractMatrix, fract2cartnMatrix);
transformedAtomList[atomI] = thisAtomInfo;
}
return(transformedAtomList);
}
public new Object Clone()
{
SymOpMatrix newMatrix = new SymOpMatrix();
newMatrix.MatrixElements = ((Matrix)(base.Clone())).MatrixElements;
newMatrix.symmetryOpNum = this.symmetryOpNum;
newMatrix.symmetryString = this.symmetryString;
newMatrix.fullSymmetryString = this.fullSymmetryString;
return(newMatrix);
}
/// <summary>
/// transform a protein chain by applying a specific symmetry operation
/// either from PDB xml or from a user-defined
/// </summary>
/// <param name="chainCoordList"></param>
/// <param name="symMatrix"></param>
/// <returns></returns>
private AtomInfo[] TransformChainByCartesianSymOp(AtomInfo[] chainAtomList, SymOpMatrix symMatrix)
{
AtomInfo[] transformedAtomList = new AtomInfo[chainAtomList.Length];
for (int atomI = 0; atomI < chainAtomList.Length; atomI++)
{
AtomInfo thisAtomInfo = chainAtomList[atomI].TransformAtom(symMatrix);
transformedAtomList[atomI] = thisAtomInfo;
}
return(transformedAtomList);
}
/// <summary>
/// build crystal from the xml serialization object and full symmetry operators
/// </summary>
/// <param name="thisEntryCrystal"></param>
/// <param name="symOpStrings"></param>
/// <param name="fullSymOpStrings"></param>
/// <returns></returns>
public Dictionary <string, AtomInfo[]> BuildPdbBu(EntryCrystal thisEntryCrystal, string[] symOpStrings, string[] fullSymOpStrings)
{
SymOperator symOp = new SymOperator();
CrystalInfo crystal1 = thisEntryCrystal.crystal1;
Dictionary <string, AtomInfo[]> crystalChainsHash = new Dictionary <string, AtomInfo[]>();
base.cartn2fractMatrix = thisEntryCrystal.scaleCat.ScaleMatrix;
base.fract2cartnMatrix = cartn2fractMatrix.Inverse();
AtomInfo[] transformedAtoms = null;
SymOpMatrix symOpMatrix = null;
//ChainAtoms[] chainAtomsList = thisEntryCrystal.atomCat.ChainAtomList;
ChainAtoms[] chainAtomsList = thisEntryCrystal.atomCat.ChainAtomList;
for (int i = 0; i < symOpStrings.Length; i++)
{
if (crystalChainsHash.ContainsKey(symOpStrings[i]))
{
continue;
}
string chainId = symOpStrings[i].Substring(0, symOpStrings[i].IndexOf("_"));
string symOpString = symOpStrings[i].Substring(symOpStrings[i].IndexOf("_") + 1,
symOpStrings[i].Length - symOpStrings[i].IndexOf("_") - 1);
int asymCount = 0;
for (asymCount = 0; asymCount < chainAtomsList.Length; asymCount++)
{
string asymChain = chainAtomsList[asymCount].AsymChain;
if (asymChain == chainId)
{
break;
}
}
if (symOpString == origSymOpString)
{
crystalChainsHash.Add(symOpStrings[i], chainAtomsList[asymCount].CartnAtoms);
continue;
}
// get the symmetry operator matrix
if (IsFullSymOpStringAMatrix(fullSymOpStrings[i]))
{
symOpMatrix = GetSymMatrixFromMatrixString(fullSymOpStrings[i]);
transformedAtoms = TransformChainByCartesianSymOp
(chainAtomsList[asymCount].CartnAtoms, symOpMatrix);
}
else
{
symOpMatrix = symOp.GetSymMatrix(fullSymOpStrings[i], symOpStrings[i]);
transformedAtoms = TransformChainBySpecificSymOp(chainAtomsList[asymCount].CartnAtoms, symOpMatrix);
}
crystalChainsHash.Add(symOpStrings[i], transformedAtoms);
}
return(crystalChainsHash);
}
/// <summary>
///
/// </summary>
/// <param name="matrixList"></param>
/// <param name="symMatrix"></param>
/// <returns></returns>
private bool IsSymMatrixExist(List <SymOpMatrix> matrixList, SymOpMatrix symMatrix)
{
foreach (SymOpMatrix symOpMatrix in matrixList)
{
if (symOpMatrix.symmetryString == symMatrix.symmetryString)
{
return(true);
}
}
return(false);
}
/// <summary>
/// a. change a cartesian coordinate to fractional coordinate
/// b. transform the fractional coordinate
/// c. compute the cartesian coordinate
/// for the transformed fractional coordinate
/// </summary>
/// <param name="symOpMatrix"></param>
/// <param name="fractTransMatrix"></param>
/// <param name="cartnInverseMatrix"></param>
/// <returns></returns>
public AtomInfo TransformAtom(SymOpMatrix symOpMatrix, Matrix fractTransMatrix, Matrix cartnInverseMatrix)
{
AtomInfo transformedAtom = (AtomInfo)this.Clone();;
if (this.fractCoord == null)
{
this.fractCoord = fractTransMatrix * this.xyz;
}
transformedAtom.fractCoord = symOpMatrix * this.fractCoord;
transformedAtom.xyz = cartnInverseMatrix * (symOpMatrix * this.fractCoord);
return(transformedAtom);
}
/// <summary>
/// get the symmetry matrix from full symmetry string
/// </summary>
/// <param name="fullSymOpString"></param>
/// <returns></returns>
public SymOpMatrix GetSymMatrix(string fullSymOpString, string symOpString)
{
SymOpMatrix symOpMatrix = new SymOpMatrix();
symOpMatrix.fullSymmetryString = fullSymOpString;
symOpMatrix.symmetryOpNum = symOpString.Substring
(symOpString.IndexOf("_") + 1, symOpString.LastIndexOf("_") - symOpString.IndexOf("_") - 1);
symOpMatrix.symmetryString = symOpString;
//SetSymOpMatrix (fullSymOpString, symOpString.Substring (symOpString.Length - 3, 3), ref symOpMatrix);
SetSymOpMatrix(fullSymOpString, ref symOpMatrix);
return(symOpMatrix);
}
/// <summary>
/// transform a protein chain by applying a specific symmetry operation
/// either from PDB xml or from a user-defined
/// </summary>
/// <param name="chainCoordList"></param>
/// <param name="symMatrix"></param>
/// <returns></returns>
private AtomInfo[] TransformChainBySymOpAndTrans(AtomInfo[] chainAtomList, SymOpMatrix symMatrix, double[] transVector)
{
AtomInfo[] transformedAtomList = new AtomInfo [chainAtomList.Length];
for (int atomI = 0; atomI < chainAtomList.Length; atomI++)
{
AtomInfo thisAtomInfo = chainAtomList[atomI].TransformAtom(symMatrix, cartn2fractMatrix, fract2cartnMatrix);
thisAtomInfo.xyz.X += transVector[0];
thisAtomInfo.xyz.Y += transVector[1];
thisAtomInfo.xyz.Z += transVector[2];
transformedAtomList[atomI] = thisAtomInfo;
}
return(transformedAtomList);
}
/// <summary>
/// get matrix from a symmetry operation string
/// </summary>
/// <param name="symOpStr"></param>
/// <param name="symOpMatrix"></param>
public void SetSymOpMatrix(string fullSymOpStr, /*string symOpString,*/ ref SymOpMatrix symOpMatrix)
{
double[] indexValues = new double [3];
string [] symOpRows = fullSymOpStr.ToUpper().Split(',');
for (int dimNo = 0; dimNo < 3; dimNo++)
{
string symOpRow = symOpRows[dimNo];
symOpMatrix.Add(dimNo, 0, GetDimIndex(symOpRow, "X"));
symOpMatrix.Add(dimNo, 1, GetDimIndex(symOpRow, "Y"));
symOpMatrix.Add(dimNo, 2, GetDimIndex(symOpRow, "Z"));
//int transVector = Convert.ToInt32 (symOpString[dimNo].ToString ()) - 5;
//symOpMatrix.Add (dimNo, 3, GetVectorValue(symOpRow) - transVector);
symOpMatrix.Add(dimNo, 3, GetVectorValue(symOpRow));
}
}
/// <summary>
/// calculate and transfer all chains based on the input symmetry strings
/// </summary>
/// <param name="thisEntryCrystal"></param>
/// <param name="symmetryStrings">digits: 2_565</param>
/// <returns></returns>
public Dictionary <string, AtomInfo[]> BuildCrystalWithAllChains(EntryCrystal thisEntryCrystal, string[] symmetryStrings)
{
SymOperator symOp = new SymOperator();
crystal1 = thisEntryCrystal.crystal1;
if (AppSettings.symOps == null)
{
AppSettings.LoadSymOps();
}
if (crystal1.spaceGroup == "-")
{
crystal1.spaceGroup = "P 1";
}
SymOpMatrix[] sgSymOpMatrices = AppSettings.symOps.FindSpaceGroup(crystal1.spaceGroup);
Dictionary <string, AtomInfo[]> crystalChainsHash = new Dictionary <string, AtomInfo[]>();
cartn2fractMatrix = thisEntryCrystal.scaleCat.ScaleMatrix;
fract2cartnMatrix = cartn2fractMatrix.Inverse();
ChainAtoms[] chainAtomsList = thisEntryCrystal.atomCat.ChainAtomList;
string symOpString = "";
for (int i = 0; i < symmetryStrings.Length; i++)
{
for (int asymCount = 0; asymCount < chainAtomsList.Length; asymCount++)
{
string asymChain = chainAtomsList[asymCount].AsymChain;
symOpString = asymChain + "_" + symmetryStrings[i];
if (crystalChainsHash.ContainsKey(symOpString))
{
continue;
}
if (symmetryStrings[i] == origSymOpString)
{
crystalChainsHash.Add(symOpString, chainAtomsList[asymCount].CartnAtoms);
continue;
}
SymOpMatrix symOpMatrix = symOp.GetSymmetryMatrixFromSymmetryString(sgSymOpMatrices, symmetryStrings[i]);
AtomInfo[] transformedAtoms = TransformChainBySpecificSymOp(chainAtomsList[asymCount].CartnAtoms, symOpMatrix);
crystalChainsHash.Add(symOpString, transformedAtoms);
}
}
return(crystalChainsHash);
}
/// <summary>
/// transform one chain
/// </summary>
/// <param name="chain"></param>
/// <param name="symMatrix"></param>
/// <returns></returns>
public AtomInfo[] BuildOneChain(ChainAtoms chain, SymOpMatrix symMatrix)
{
if (symMatrix.symmetryString == "1_555")
{
return chain.CartnAtoms;
}
AtomInfo[] transformedAtoms = new AtomInfo[chain.CartnAtoms.Length];
int i = 0;
foreach (AtomInfo atom in chain.CartnAtoms)
{
AtomInfo transformedAtom = atom.TransformAtom(symMatrix);
transformedAtoms[i] = transformedAtom;
i++;
}
return transformedAtoms;
}
/// <summary>
///
/// </summary>
/// <param name="pdbId"></param>
/// <param name="assemblyComponentHash"></param>
public void GetPisaBuLigandsMatrices(string pdbId, ref Dictionary <string, Dictionary <string, List <SymOpMatrix> > > assemblyComponentHash)
{
string queryString = string.Format("Select * From PisaBuLigand WHere PdbID = '{0}';", pdbId);
DataTable ligandTable = ProtCidSettings.pdbfamQuery.Query(queryString);
string assemblySeqId = "";
string asymChain = "";
string matrixString = "";
SymOpMatrix symOpMatrix = null;
foreach (DataRow dRow in ligandTable.Rows)
{
assemblySeqId = dRow["AssemblySeqID"].ToString();
asymChain = dRow["AsymChain"].ToString().Trim();
matrixString = dRow["Matrix"].ToString().Trim();
symOpMatrix = GetCoordSymOpMatrix(matrixString);
symOpMatrix.symmetryString = dRow["SymmetryString"].ToString().TrimEnd();
if (assemblyComponentHash.ContainsKey(assemblySeqId))
{
Dictionary <string, List <SymOpMatrix> > chainMatrixHash = assemblyComponentHash[assemblySeqId];
if (chainMatrixHash.ContainsKey(asymChain))
{
if (!IsSymMatrixExist(chainMatrixHash[asymChain], symOpMatrix))
{
chainMatrixHash[asymChain].Add(symOpMatrix);
}
}
else
{
List <SymOpMatrix> matrixList = new List <SymOpMatrix> ();
matrixList.Add(symOpMatrix);
chainMatrixHash.Add(asymChain, matrixList);
}
}
else
{
Dictionary <string, List <SymOpMatrix> > chainMatrixHash = new Dictionary <string, List <SymOpMatrix> > ();
List <SymOpMatrix> matrixList = new List <SymOpMatrix> ();
matrixList.Add(symOpMatrix);
chainMatrixHash.Add(asymChain, matrixList);
assemblyComponentHash.Add(assemblySeqId, chainMatrixHash);
}
}
}
/// <summary>
///
/// </summary>
/// <param name="buGenTable"></param>
/// <returns></returns>
private Dictionary <string, Dictionary <string, List <SymOpMatrix> > > GetEntryBuComponentInfoHash(DataTable buGenTable)
{
Dictionary <string, Dictionary <string, List <SymOpMatrix> > > pdbBuComponentInfoHash = new Dictionary <string, Dictionary <string, List <SymOpMatrix> > >();
string buId = "";
string asymChain = "";
string matrixString = "";
SymOpMatrix symOpMatrix = null;
foreach (DataRow buGenRow in buGenTable.Rows)
{
buId = buGenRow["BiolUnitID"].ToString().TrimEnd();
asymChain = buGenRow["AsymID"].ToString().Trim();
matrixString = buGenRow["SymmetryMatrix"].ToString().Trim();
symOpMatrix = GetCoordSymOpMatrix(matrixString);
symOpMatrix.symmetryString = buGenRow["SymmetryString"].ToString().TrimEnd();
symOpMatrix.symmetryOpNum = buGenRow["SymOpNum"].ToString().TrimEnd();
if (pdbBuComponentInfoHash.ContainsKey(buId))
{
Dictionary <string, List <SymOpMatrix> > chainMatrixHash = pdbBuComponentInfoHash[buId];
if (chainMatrixHash.ContainsKey(asymChain))
{
chainMatrixHash[asymChain].Add(symOpMatrix);
}
else
{
List <SymOpMatrix> matrixList = new List <SymOpMatrix> ();
matrixList.Add(symOpMatrix);
chainMatrixHash.Add(asymChain, matrixList);
}
}
else
{
Dictionary <string, List <SymOpMatrix> > chainMatrixHash = new Dictionary <string, List <SymOpMatrix> >();
List <SymOpMatrix> matrixList = new List <SymOpMatrix> ();
matrixList.Add(symOpMatrix);
chainMatrixHash.Add(asymChain, matrixList);
pdbBuComponentInfoHash.Add(buId, chainMatrixHash);
}
}
return(pdbBuComponentInfoHash);
}
/// <summary>
/// the symmetry matrix from matrix string
/// s00, s01, s02, v0, s10, s11, s12, v1, s20, s21, s22, v2
/// </summary>
/// <param name="matrixString"></param>
/// <returns></returns>
private SymOpMatrix GetSymMatrixFromMatrixString(string matrixString)
{
string[] fields = matrixString.Split(',');
SymOpMatrix symOpMatrix = new SymOpMatrix();
int numOfCol = 4;
int colNum = -1;
int rowNum = -1;
for (int i = 0; i < fields.Length; i++)
{
colNum++;
if (i % numOfCol == 0)
{
rowNum++;
colNum = 0;
}
symOpMatrix.Add(rowNum, colNum, Convert.ToDouble(fields[i]));
}
return(symOpMatrix);
}
/// <summary>
///
/// </summary>
/// <param name="atoms"></param>
/// <param name="spaceGroup"></param>
/// <param name="symOpString"></param>
/// <returns></returns>
public AtomInfo[] TransformChainBySpecificSymOp(AtomInfo[] atoms, string spaceGroup, string symOpString)
{
if (symOpString == origSymOpString)
{
return(atoms);
}
if (AppSettings.symOps == null)
{
AppSettings.LoadSymOps();
}
SymOperator symOp = new SymOperator();
SymOpMatrix[] sgSymOpMatrices = AppSettings.symOps.FindSpaceGroup(spaceGroup);
SymOpMatrix symOpMatrix = symOp.GetSymmetryMatrixFromSymmetryString(sgSymOpMatrices, symOpString);
AtomInfo[] transformedAtoms = TransformChainBySpecificSymOp(atoms, symOpMatrix);
return(transformedAtoms);
}
/// <summary>
/// the symmetry operator string
/// </summary>
/// <param name="infoNode"></param>
/// <returns></returns>
public SymOpMatrix GetOrigCoordSymOpMatrix()
{
SymOpMatrix symOpMatrix = new SymOpMatrix();
List<double> itemList = new List<double> ();
itemList.Add(1.0);
itemList.Add(0.0);
itemList.Add(0.0);
itemList.Add(0.0);
symOpMatrix.Add(0, itemList.ToArray ());
itemList.Clear();
itemList.Add(0.0);
itemList.Add(1.0);
itemList.Add(0.0);
itemList.Add(0.0);
symOpMatrix.Add(1, itemList.ToArray ());
itemList.Clear();
itemList.Add(0.0);
itemList.Add(0.0);
itemList.Add(1.0);
itemList.Add(0.0);
symOpMatrix.Add(2, itemList.ToArray ());
return symOpMatrix;
}
/// <summary>
/// the symmetry operator string
/// </summary>
/// <param name="infoNode"></param>
/// <returns></returns>
public SymOpMatrix GetCoordSymOpMatrix(string matrixString)
{
string[] fields = matrixString.Split(',');
SymOpMatrix symOpMatrix = new SymOpMatrix();
List<double> itemList = new List<double> ();
itemList.Add(Convert.ToDouble(fields[0]));
itemList.Add(Convert.ToDouble(fields[1]));
itemList.Add(Convert.ToDouble(fields[2]));
itemList.Add(Convert.ToDouble(fields[3]));
symOpMatrix.Add(0, itemList.ToArray ());
itemList.Clear();
itemList.Add(Convert.ToDouble(fields[4]));
itemList.Add(Convert.ToDouble(fields[5]));
itemList.Add(Convert.ToDouble(fields[6]));
itemList.Add(Convert.ToDouble(fields[7]));
symOpMatrix.Add(1, itemList.ToArray ());
itemList.Clear();
itemList.Add(Convert.ToDouble(fields[8]));
itemList.Add(Convert.ToDouble(fields[9]));
itemList.Add(Convert.ToDouble(fields[10]));
itemList.Add(Convert.ToDouble(fields[11]));
symOpMatrix.Add(2, itemList.ToArray ());
return symOpMatrix;
}
public void Add(SymOpMatrix symOpMatrix)
{
symmetryOpList.Add(symOpMatrix);
}
/// <summary>
/// build a PDB biological unit
/// by applying the symmetry operations provided in XML
/// </summary>
/// <param name="chainAtomsList">chains in XML</param>
/// <param name="buGenStructList">symmetry operations</param>
/// <param name="buSymmetryMatrixList">symmetry matrix</param>
/// <returns>biological units with corresponding chains</returns>
/// </summary>
private Dictionary <string, AtomInfo[]> BuildPdbBuByPdbSymOps(string pdbId, string biolUnitId, EntryCrystal thisEntryCrystal)
{
ChainAtoms[] chainAtomsList = thisEntryCrystal.atomCat.ChainAtomList;
BuGenStruct[] buGenStructList = thisEntryCrystal.buGenCat.BuGenStructList;
List <string> symOpStrList = new List <string> ();
List <string> fullSymOpStrList = new List <string> ();
List <SymOpMatrix> symOpMatrixList = new List <SymOpMatrix> ();
for (int asymCount = 0; asymCount < buGenStructList.Length; asymCount++)
{
if (biolUnitId != buGenStructList[asymCount].biolUnitId)
{
continue;
}
string asymId = buGenStructList[asymCount].asymId;
foreach (ChainAtoms chain in chainAtomsList)
{
if (chain.AsymChain == asymId)
{
// at this step, only consider polypeptide chains
if (chain.PolymerType == "polypeptide")
{
SymOpMatrix symOpMatrix =
thisEntryCrystal.buGenCat.FindSymOpMatrix(buGenStructList[asymCount].symOperId);
if (symOpMatrix == null)
{
fullSymOpStrList.Add(buGenStructList[asymCount].symmetryMatrix);
symOpStrList.Add(asymId + "_" + buGenStructList[asymCount].symmetryString);
}
else
{
if (symOpMatrix.symmetryString == "")
{
// put the symmetry operator id if the symmetry string is empty
symOpStrList.Add(asymId + "_" + buGenStructList[asymCount].symOperId);
}
else
{
symOpStrList.Add(asymId + "_" + symOpMatrix.symmetryString);
}
symOpMatrixList.Add(symOpMatrix);
}
break;
}
}
}
}
Dictionary <string, AtomInfo[]> buHash = null;
string[] symOpStrings = new string[symOpStrList.Count];
symOpStrList.CopyTo(symOpStrings);
if (symOpMatrixList.Count > 0)
{
SymOpMatrix[] symOpMatrices = new SymOpMatrix[symOpMatrixList.Count];
symOpMatrixList.CopyTo(symOpMatrices);
buHash = BuildPdbBu(thisEntryCrystal, symOpStrings, symOpMatrices);
}
else if (fullSymOpStrList.Count > 0)
{
string[] fullSymmetryStrings = new string[fullSymOpStrList.Count];
fullSymOpStrList.CopyTo(fullSymmetryStrings);
buHash = BuildPdbBu(thisEntryCrystal, symOpStrings, fullSymmetryStrings);
}
return(buHash);
}
/// <summary>
/// build crystal from the xml serialization object and full symmetry operators
/// </summary>
/// <param name="thisEntryCrystal"></param>
/// <param name="symOpStrings"></param>
/// <param name="fullSymOpStrings"></param>
/// <returns></returns>
public Dictionary <string, AtomInfo[]> BuildCrystal(EntryCrystal thisEntryCrystal, string[] symOpStrings, string[] fullSymOpStrings)
{
SymOperator symOp = new SymOperator();
crystal1 = thisEntryCrystal.crystal1;
Dictionary <string, AtomInfo[]> crystalChainsHash = new Dictionary <string, AtomInfo[]>();
cartn2fractMatrix = thisEntryCrystal.scaleCat.ScaleMatrix;
fract2cartnMatrix = cartn2fractMatrix.Inverse();
//ChainAtoms[] chainAtomsList = thisEntryCrystal.atomCat.ChainAtomList;
ChainAtoms[] chainAtomsList = new ChainAtoms [thisEntryCrystal.atomCat.ChainAtomList.Length];
switch (atomType)
{
case "CA":
chainAtomsList = thisEntryCrystal.atomCat.CalphaAtomList();
// clear the whole atom list,free memory
thisEntryCrystal.atomCat.ChainAtomList = null;
break;
case "CB":
chainAtomsList = thisEntryCrystal.atomCat.CbetaAtomList();
// clear the whole atom list, free memory
thisEntryCrystal.atomCat.ChainAtomList = null;
break;
case "CA_CB":
chainAtomsList = thisEntryCrystal.atomCat.CalphaCbetaAtomList();
// clear the whole atom list, free memory
thisEntryCrystal.atomCat.ChainAtomList = null;
break;
case "ALL":
chainAtomsList = thisEntryCrystal.atomCat.ChainAtomList;
break;
default:
break;
}
for (int i = 0; i < symOpStrings.Length; i++)
{
if (crystalChainsHash.ContainsKey(symOpStrings[i]))
{
continue;
}
string chainId = symOpStrings[i].Substring(0, symOpStrings[i].IndexOf("_"));
string symOpString = symOpStrings[i].Substring(symOpStrings[i].IndexOf("_") + 1,
symOpStrings[i].Length - symOpStrings[i].IndexOf("_") - 1);
int asymCount = 0;
for (asymCount = 0; asymCount < chainAtomsList.Length; asymCount++)
{
string asymChain = chainAtomsList[asymCount].AsymChain;
if (asymChain == chainId)
{
break;
}
}
if (symOpString == origSymOpString)
{
crystalChainsHash.Add(symOpStrings[i], chainAtomsList[asymCount].CartnAtoms);
continue;
}
SymOpMatrix symOpMatrix = symOp.GetSymMatrix(fullSymOpStrings[i], symOpStrings[i]);
AtomInfo[] transformedAtoms = TransformChainBySpecificSymOp(chainAtomsList[asymCount].CartnAtoms, symOpMatrix);
crystalChainsHash.Add(symOpStrings[i], transformedAtoms);
}
return(crystalChainsHash);
}
/// <summary>
/// build base unit cell of a crystal from atom coordinates from XML file,
/// using symmetry operations provided as parameters
/// </summary>
/// <param name="crystalXmlFile">our own crystal XML file</param>
/// <param name="symOpStrings">specified symmetry operators</param>
public Dictionary <string, AtomInfo[]> BuildCrystal(string crystalXmlFile, string[] symOpStrings)
{
SymOperator symOp = new SymOperator();
// read data from crystal xml file
EntryCrystal thisEntryCrystal;
XmlSerializer xmlSerializer = new XmlSerializer(typeof(EntryCrystal));
FileStream xmlFileStream = new FileStream(crystalXmlFile, FileMode.Open);
thisEntryCrystal = (EntryCrystal)xmlSerializer.Deserialize(xmlFileStream);
crystal1 = thisEntryCrystal.crystal1;
xmlFileStream.Close();
Dictionary <string, AtomInfo[]> crystalChainsHash = new Dictionary <string, AtomInfo[]>();
if (AppSettings.symOps == null)
{
AppSettings.LoadSymOps();
}
if (crystal1.spaceGroup == "-" || crystal1.spaceGroup == "")
{
crystal1.spaceGroup = "P 1";
}
SymOpMatrix[] sgSymOpMatrices = AppSettings.symOps.FindSpaceGroup(crystal1.spaceGroup);
if (sgSymOpMatrices == null)
{
throw new Exception("No symmetry operators provided for this entry " + crystalXmlFile);
}
cartn2fractMatrix = thisEntryCrystal.scaleCat.ScaleMatrix;
fract2cartnMatrix = cartn2fractMatrix.Inverse();
// ChainAtoms[] chainAtomsList = thisEntryCrystal.atomCat.ChainAtomList;
ChainAtoms[] chainAtomsList = new ChainAtoms [thisEntryCrystal.atomCat.ChainAtomList.Length];
switch (atomType)
{
case "CA":
chainAtomsList = thisEntryCrystal.atomCat.CalphaAtomList();
// clear the whole atom list,free memory
thisEntryCrystal.atomCat.ChainAtomList = null;
break;
case "CB":
chainAtomsList = thisEntryCrystal.atomCat.CbetaAtomList();
// clear the whole atom list, free memory
thisEntryCrystal.atomCat.ChainAtomList = null;
break;
case "CA_CB":
chainAtomsList = thisEntryCrystal.atomCat.CalphaCbetaAtomList();
// clear the whole atom list, free memory
thisEntryCrystal.atomCat.ChainAtomList = null;
break;
case "ALL":
chainAtomsList = thisEntryCrystal.atomCat.ChainAtomList;
break;
default:
break;
}
// just in case, something is messed up. It should not happen often.
// may hide some bugs
// add on Feb. 20, 2009
bool chainFound = false;
for (int i = 0; i < symOpStrings.Length; i++)
{
string chainId = symOpStrings[i].Substring(0, symOpStrings[i].IndexOf("_"));
string symOpString = symOpStrings[i].Substring(symOpStrings[i].IndexOf("_") + 1,
symOpStrings[i].Length - symOpStrings[i].IndexOf("_") - 1);
int asymCount = 0;
chainFound = false;
for (asymCount = 0; asymCount < chainAtomsList.Length; asymCount++)
{
string asymChain = chainAtomsList[asymCount].AsymChain;
if (asymChain == chainId)
{
chainFound = true;
break;
}
}
if (!chainFound)
{
continue;
}
if (symOpString == origSymOpString)
{
crystalChainsHash.Add(symOpStrings[i], chainAtomsList[asymCount].CartnAtoms);
continue;
}
try
{
SymOpMatrix symOpMatrix = symOp.GetSymmetryMatrixFromSymmetryString(sgSymOpMatrices, symOpString);
AtomInfo[] transformedAtoms = TransformChainBySpecificSymOp(chainAtomsList[asymCount].CartnAtoms, symOpMatrix);
crystalChainsHash.Add(symOpStrings[i], transformedAtoms);
}
catch
{
continue;
}
}
return(crystalChainsHash);
}