/// <summary>
///
/// </summary>
/// <param name="pdbId"></param>
/// <param name="needLigands"></param>
/// <param name="authorOnly"></param>
/// <param name="destPath"></param>
public Dictionary <string, Dictionary <string, AtomInfo[]> > BuildPdbBus(string pdbId, string[] biolUnitIDs, bool needLigands)
{
EntryCrystal thisEntryCrystal = ReadEntryCrystalFromXml(pdbId);
Dictionary <string, Dictionary <string, AtomInfo[]> > buHash = new Dictionary <string, Dictionary <string, AtomInfo[]> > ();
// buHash = buGenerator.BuildPdbBUsFromDb(pdbId, biolUnitIDs, thisEntryCrystal, needLigands);
if (thisEntryCrystal.buGenCat.BuGenStructList.Length == 0) // no bu gen info, use asu
{
if (thisEntryCrystal.buGenCat.BuStatusInfoList.Length > 0 &&
thisEntryCrystal.buGenCat.BuStatusInfoList[0].details == "NMR")
{
Dictionary <string, AtomInfo[]> asuChainHash = new Dictionary <string, AtomInfo[]> ();
foreach (ChainAtoms chain in thisEntryCrystal.atomCat.ChainAtomList)
{
if ((!needLigands) && (chain.PolymerType != "polypeptide"))
{
continue;
}
if (!asuChainHash.ContainsKey(chain.asymChain + "_1_555"))
{
asuChainHash.Add(chain.asymChain + "_1_555", chain.CartnAtoms);
}
}
buHash.Add("1", asuChainHash);
}
else
{
buHash = buGenerator.BuildPdbBUsFromDb(pdbId, biolUnitIDs, thisEntryCrystal, needLigands);
}
}
else
{
Dictionary <string, AtomInfo[]> buChainHash = null;
try
{
foreach (string buId in biolUnitIDs)
{
if (needLigands)
{
buChainHash = BuildFullPdbBuByPdbSymOps(pdbId, buId, thisEntryCrystal);
}
else
{
buChainHash = BuildPdbBuByPdbSymOps(pdbId, buId, thisEntryCrystal);
}
buHash.Add(buId, buChainHash);
}
}
catch (Exception ex)
{
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Generate " + pdbId + " PDB BUs errors: " + ex.Message);
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Generate BUs from DB info.");
buHash = buGenerator.BuildPdbBUsFromDb(pdbId, biolUnitIDs, thisEntryCrystal, needLigands);
}
}
return(buHash);
}
/// <summary>
///
/// </summary>
/// <param name="xmlFile"></param>
/// <param name="chainMatrixHash"></param>
/// <returns></returns>
private Dictionary <string, AtomInfo[]> BuildOnePisaAssembly(EntryCrystal thisEntryCrystal, string pdbId, string assemblySeqId)
{
Dictionary <string, List <SymOpMatrix> > chainMatrixHash = GetPisaBuMatrices(pdbId, assemblySeqId);
Dictionary <string, AtomInfo[]> assemblyHash = BuildOneBuAssembly(thisEntryCrystal, chainMatrixHash, "pisa");
return(assemblyHash);
}
/// <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);
}
public int[] BuildCrystal(EntryCrystal thisEntryCrystal, ref Dictionary <string, AtomInfo[]> crystalChainsHash)
{
if (AppSettings.symOps == null)
{
AppSettings.LoadSymOps();
}
if (crystal1.spaceGroup == "-")
{
crystal1.spaceGroup = "P 1";
}
SymOpMatrix[] symOpMatrices = AppSettings.symOps.FindSpaceGroup(crystal1.spaceGroup);
if (symOpMatrices == null)
{
throw new Exception("No symmetry operators provided for this entry " + thisEntryCrystal.PdbId);
}
cartn2fractMatrix = thisEntryCrystal.scaleCat.ScaleMatrix;
fract2cartnMatrix = cartn2fractMatrix.Inverse();
//ChainAtoms[] chainAtomsList = thisEntryCrystal.atomCat.ChainAtomList;
ChainAtoms[] chainAtomsList = new ChainAtoms [thisEntryCrystal.atomCat.ChainAtomList.Length];
switch (atomType.ToUpper())
{
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;
}
crystalChainsHash = BuildCrystalBySymOps(chainAtomsList, symOpMatrices);
int[] maxSteps = TranslateUnitCell(ref crystalChainsHash);
return(maxSteps);
}
/// <summary>
///
/// </summary>
/// <param name="xmlFile"></param>
/// <param name="chainMatrixHash"></param>
/// <returns></returns>
public Dictionary<string, AtomInfo[]> BuildOneBuAssembly(EntryCrystal thisEntryCrystal, Dictionary<string, List<SymOpMatrix>> chainMatrixHash, string type)
{
Dictionary<string, AtomInfo[]> chainCoordHash = new Dictionary<string,AtomInfo[]> ();
ChainAtoms[] chainAtomsList = thisEntryCrystal.atomCat.ChainAtomList;
ChainAtoms thisChain = null;
foreach (string asymChain in chainMatrixHash.Keys)
{
thisChain = null; // fixed on June 30, 2010
foreach (ChainAtoms chain in chainAtomsList)
{
if (chain.AsymChain == asymChain)
{
thisChain = chain;
break;
}
}
if (thisChain == null)
{
continue;
}
string chainSymOpString = "";
foreach (SymOpMatrix symMatrix in chainMatrixHash[asymChain])
{
if (symMatrix.symmetryString == "-" || symMatrix.symmetryString == "")
{
chainSymOpString = asymChain + "_" + symMatrix.symmetryOpNum + "_-";
}
else
{
chainSymOpString = asymChain + "_" + symMatrix.symmetryString;
if (type == "pisa")
{
if (symMatrix.symmetryOpNum != "" && symMatrix.symmetryOpNum != "0")
{
chainSymOpString += ("(" + symMatrix.symmetryOpNum + ")"); // for those non-NCS operator (same symmetry string)
}
}
}
if (!chainCoordHash.ContainsKey(chainSymOpString))
{
AtomInfo[] atoms = BuildOneChain(thisChain, symMatrix);
chainCoordHash.Add(chainSymOpString, atoms);
}
}
}
return chainCoordHash;
}
/// <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>
///
/// </summary>
/// <param name="pdbXmlFile">a xml file from pdb web site</param>
/// <returns></returns>
public Dictionary <string, Dictionary <string, AtomInfo[]> > BuildPdbBAsAllAtoms(string pdbXmlFile)
{
if (pdbXmlFile.IndexOf(".gz") > -1)
{
string tempDir = "C:\\xml_temp";
if (!Directory.Exists(tempDir))
{
Directory.CreateDirectory(tempDir);
}
pdbXmlFile = ParseHelper.UnZipFile(pdbXmlFile, tempDir);
}
FileParser.XmlAtomParser xmlParser = new CrystalInterfaceLib.FileParser.XmlAtomParser();
EntryCrystal thisEntryCrystal = xmlParser.ParseXmlFile(pdbXmlFile);
Dictionary <string, Dictionary <string, AtomInfo[]> > baChainHash = BuildPdbBAsAllAtoms(thisEntryCrystal);
return(baChainHash);
}
/// <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, SymOpMatrix[] symOpMatrices)
{
AtomInfo[] transformedAtoms = null;
Dictionary <string, AtomInfo[]> crystalChainsHash = new Dictionary <string, AtomInfo[]>();
//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;
}
transformedAtoms = TransformChainByCartesianSymOp(chainAtomsList[asymCount].CartnAtoms, symOpMatrices[i]);
crystalChainsHash.Add(symOpStrings[i], transformedAtoms);
}
return(crystalChainsHash);
}
/// <summary>
/// build PDB biological units
/// 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>
private void GeneratePdbBusByPdbSymOps(string pdbId, EntryCrystal thisEntryCrystal, string destPath)
{
ChainAtoms[] chainAtomsList = thisEntryCrystal.atomCat.ChainAtomList;
BuGenStruct[] buGenStructList = thisEntryCrystal.buGenCat.BuGenStructList;
BuWriter buWriter = new BuWriter();
List <string> buIdList = new List <string> ();
for (int asymCount = 0; asymCount < buGenStructList.Length; asymCount++)
{
string biolUnitId = buGenStructList[asymCount].biolUnitId;
if (!buIdList.Contains(biolUnitId))
{
buIdList.Add(biolUnitId);
}
}
// process biological units
foreach (string buId in buIdList)
{
try
{
Dictionary <string, AtomInfo[]> buChains = BuildPdbBuByPdbSymOps(pdbId, buId.ToString(), thisEntryCrystal);
// writer bu into a PDB formatted file
string fileName = buWriter.WriteBiolUnitFile(pdbId, buId.ToString(), buChains, destPath,
thisEntryCrystal.crystal1, thisEntryCrystal.scaleCat.ScaleMatrix);
// Compress file
ParseHelper.ZipPdbFile(fileName);
}
catch (Exception ex)
{
throw new Exception(string.Format("Cannot generate biological unit file: {0}_{1}: {2}", pdbId, buId.ToString(), ex.Message));
}
}
}
/// <summary>
///
/// </summary>
/// <param name="pdbId"></param>
/// <param name="thisEntryCrystal"></param>
/// <param name="needLigands"></param>
/// <returns></returns>
public Dictionary <string, Dictionary <string, AtomInfo[]> > BuildPdbBUsFromDb(string pdbId, string[] buIDs, EntryCrystal thisEntryCrystal, bool needLigands)
{
Dictionary <string, Dictionary <string, List <SymOpMatrix> > > buComponentInfoHash = GetPdbBuComponentsFromDb(pdbId, buIDs, needLigands);
Dictionary <string, Dictionary <string, AtomInfo[]> > entryBuHash = BuildPdbBUs(pdbId, buComponentInfoHash, thisEntryCrystal, needLigands);
return(entryBuHash);
}
/// <summary>
///
/// </summary>
/// <param name="pdbId"></param>
/// <param name="thisEntryCrystal"></param>
/// <returns></returns>
public Dictionary <string, Dictionary <string, AtomInfo[]> > BuildPdbBAsAllAtoms(EntryCrystal thisEntryCrystal)
{
string pdbId = thisEntryCrystal.PdbId;
Dictionary <string, Dictionary <string, AtomInfo[]> > buHash = null;
if (thisEntryCrystal.buGenCat.BuGenStructList.Length == 0) // no bu gen info, use asu
{
if (thisEntryCrystal.buGenCat.BuStatusInfoList.Length > 0 &&
thisEntryCrystal.buGenCat.BuStatusInfoList[0].details == "NMR")
{
Dictionary <string, AtomInfo[]> asuChainHash = new Dictionary <string, AtomInfo[]> ();
foreach (ChainAtoms chain in thisEntryCrystal.atomCat.ChainAtomList)
{
asuChainHash.Add(chain.asymChain + "_1_555", chain.CartnAtoms);
}
buHash.Add("1", asuChainHash);
}
else
{
buHash = buGenerator.BuildPdbBUsFromDb(pdbId, thisEntryCrystal, true);
}
}
else
{
try
{
buHash = BuildFullPdbBusByPdbSymOps(pdbId, thisEntryCrystal);
}
catch (Exception ex)
{
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Generate " + pdbId + " PDB BUs errors: " + ex.Message);
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Generate BUs from DB info.");
buHash = buGenerator.BuildPdbBUsFromDb(pdbId, thisEntryCrystal, true);
}
}
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 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="thisEntryCrystal"></param>
/// <returns></returns>
private Dictionary <string, Dictionary <string, AtomInfo[]> > GetPisaMonomersFromAsu(EntryCrystal thisEntryCrystal)
{
int assemblySeqId = 1;
string assemblySeqIdString = "";
Dictionary <string, Dictionary <string, AtomInfo[]> > pisaMultimersHash = new Dictionary <string, Dictionary <string, AtomInfo[]> > ();
foreach (ChainAtoms chain in thisEntryCrystal.atomCat.ChainAtomList)
{
/* if (chain.polymerType != "polydeoxyribonucleotide" || chain.polymerType == "polyribonucleotide")
* {
* continue;
* }*/
if (chain.polymerType == "polypeptide")
{
assemblySeqIdString = assemblySeqId.ToString();
if (pisaMultimersHash.ContainsKey(assemblySeqIdString))
{
pisaMultimersHash[assemblySeqIdString].Add(chain.asymChain + "_1_555", chain.CartnAtoms);
}
else
{
Dictionary <string, AtomInfo[]> chainAtomsHash = new Dictionary <string, AtomInfo[]> ();
chainAtomsHash.Add(chain.asymChain + "_1_555", chain.CartnAtoms);
pisaMultimersHash.Add(assemblySeqIdString, chainAtomsHash);
assemblySeqId++;
}
}
else // add ligands into the first monomer
{
if (pisaMultimersHash.ContainsKey("1"))
{
pisaMultimersHash["1"].Add(chain.asymChain + "_1_555", chain.CartnAtoms);
}
else
{
Dictionary <string, AtomInfo[]> chainAtomsHash = new Dictionary <string, AtomInfo[]> ();
chainAtomsHash.Add(chain.asymChain + "_1_555", chain.CartnAtoms);
pisaMultimersHash.Add("1", chainAtomsHash);
}
}
}
return(pisaMultimersHash);
}
/// <summary>
/// build PDB biological units
/// 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>
private Dictionary <string, Dictionary <string, AtomInfo[]> > BuildPdbBusByPdbSymOps(string pdbId, EntryCrystal thisEntryCrystal)
{
ChainAtoms[] chainAtomsList = thisEntryCrystal.atomCat.ChainAtomList;
BuGenStruct[] buGenStructList = thisEntryCrystal.buGenCat.BuGenStructList;
BuWriter buWriter = new BuWriter();
List <string> buIdList = new List <string> ();
for (int asymCount = 0; asymCount < buGenStructList.Length; asymCount++)
{
string biolUnitId = buGenStructList[asymCount].biolUnitId;
if (!buIdList.Contains(biolUnitId))
{
buIdList.Add(biolUnitId);
}
}
// process biological units
Dictionary <string, Dictionary <string, AtomInfo[]> > buHash = new Dictionary <string, Dictionary <string, AtomInfo[]> > ();
foreach (string buId in buIdList)
{
try
{
Dictionary <string, AtomInfo[]> buChains = BuildPdbBuByPdbSymOps(pdbId, buId.ToString(), thisEntryCrystal);
buHash.Add(buId, buChains);
}
catch (Exception ex)
{
throw new Exception(string.Format("Cannot generate biological unit file: {0}_{1}: {2}", pdbId, buId.ToString(), ex.Message));
}
}
return(buHash);
}
/// <summary>
/// build asymmetric unit from NCS
/// </summary>
/// <param name="thisEntryCrystal"></param>
/// <returns></returns>
// public void BuildAsymUnitFromNcs (ref EntryCrystal thisEntryCrystal, string[] origAsymChains, out bool asuChanged)
public void BuildAsymUnitFromNcs(ref EntryCrystal thisEntryCrystal, out bool asuChanged)
{
asuChanged = false;
// chainLetters = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789";
// ChainAtoms[] chainAtomsList = new ChainAtoms [thisEntryCrystal.atomCat.ChainAtomList.Length];
int genNcsNum = 0;
foreach (NcsOperator ncsOp in thisEntryCrystal.ncsCat.NcsOperatorList)
{
if (ncsOp.code == "generate")
{
genNcsNum++;
}
}
if (genNcsNum == 0)
{
return;
}
else if (genNcsNum * thisEntryCrystal.atomCat.ChainAtomList.Length > chainLetters.Length)
/* else if (genNcsNum > chainLetters.Length) */
{
return;
}
List <ChainAtoms> asuChainList = new List <ChainAtoms>();
// RemoveOrigAsuChainNames (thisEntryCrystal.atomCat.ChainAtomList, ref chainLetters);
// int ncsChainCount = 1;
foreach (ChainAtoms chain in thisEntryCrystal.atomCat.ChainAtomList)
{
/* if (chain.PolymerType != "polypeptide")
* {
* continue;
* }*/
asuChainList.Add(chain);
// ncsChainCount = 1;
foreach (NcsOperator ncsOp in thisEntryCrystal.ncsCat.NcsOperatorList)
{
if (ncsOp.code == "given")
{
continue;
}
AtomInfo[] ncsAtoms = ApplyNcsMatrix(chain.CartnAtoms, ncsOp.ncsMatrix);
if (DoesChainExist(ncsAtoms, thisEntryCrystal.atomCat.ChainAtomList))
{
continue;
}
asuChanged = true;
ChainAtoms newChain = new ChainAtoms(chain);
newChain.CartnAtoms = ncsAtoms;
// newChain.AsymChain = chain.AsymChain + chainLetters[ncsChainCount].ToString ();
// newChain.AsymChain =GetAsymChainNameForNcsChain (ref ncsChainCount, chain.AsymChain, origAsymChains);
// name the new chain with original asymmetric chain + a number,
// this should distinguish the original asymmetri chains with these regenerated chains
// newChain.AsymChain = chain.AsymChain + ncsChainCount.ToString();
newChain.AsymChain = chain.AsymChain + ncsOp.ncsId.ToString();
// ncsChainCount ++;
asuChainList.Add(newChain);
}
}
thisEntryCrystal.atomCat.ChainAtomList = asuChainList.ToArray();
}
/// <summary>
/// build PDB biological units
/// by applying the symmetry operations provided in XML
/// </summary>
/// <param name="xmlFile"></param>
/// <returns></returns>
public Dictionary <string, Dictionary <string, AtomInfo[]> > BuildPdbBusFromCoordFile(string pdbId, EntryCrystal thisEntryCrystal, string atomType)
{
// key: biolUnitID, Value: Hashtable (key: )
Dictionary <string, Dictionary <string, AtomInfo[]> > entryBuChainsHash = new Dictionary <string, Dictionary <string, AtomInfo[]> >();
ChainAtoms[] chainAtomsList = thisEntryCrystal.atomCat.ChainAtomList;
BuGenStruct[] buGenStructList = thisEntryCrystal.buGenCat.BuGenStructList;
List <string> buIdList = new List <string> ();
for (int asymCount = 0; asymCount < buGenStructList.Length; asymCount++)
{
string biolUnitId = buGenStructList[asymCount].biolUnitId;
if (!buIdList.Contains(biolUnitId))
{
buIdList.Add(biolUnitId);
}
}
// process biological units
foreach (string buId in buIdList)
{
try
{
Dictionary <string, AtomInfo[]> buChains = BuildPdbBuByPdbSymOps(pdbId, buId.ToString(), thisEntryCrystal);
if (buChains == null || buChains.Count == 0)
{
continue;
}
entryBuChainsHash.Add(buId.ToString(), buChains);
}
catch (Exception ex)
{
string msg = string.Format("Cannot generate biological unit file: {0}_{1}: {2}", pdbId, buId.ToString(), ex.Message);
}
}
return(entryBuChainsHash);
}
/// <summary>
///
/// </summary>
/// <param name="pdbId"></param>
/// <param name="buComponentInfoHash"></param>
/// <param name="thisEntryCrystal"></param>
/// <param name="needLigands"></param>
/// <returns></returns>
private Dictionary <string, Dictionary <string, AtomInfo[]> > BuildPdbBUs(string pdbId, Dictionary <string, Dictionary <string, List <SymOpMatrix> > > buComponentInfoHash, EntryCrystal thisEntryCrystal, bool needLigands)
{
Dictionary <string, Dictionary <string, AtomInfo[]> > entryBuChainAtomsHash = new Dictionary <string, Dictionary <string, AtomInfo[]> > ();
foreach (string buId in buComponentInfoHash.Keys)
{
Dictionary <string, List <SymOpMatrix> > buChainSymMatrixHash = buComponentInfoHash[buId];
Dictionary <string, AtomInfo[]> buChainAtomsHash = BuildOneBuAssembly(thisEntryCrystal, buChainSymMatrixHash, "pdb");
entryBuChainAtomsHash.Add(buId, buChainAtomsHash);
}
return(entryBuChainAtomsHash);
}
/// <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);
}
